transcription initiation site

Summary

Summary: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.

Top Publications

  1. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
  2. pmc Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 322:1845-8. 2008
  3. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
  4. pmc A single-base resolution map of an archaeal transcriptome
    Omri Wurtzel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 20:133-41. 2010
  5. pmc Population genomics of human gene expression
    Barbara E Stranger
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 39:1217-24. 2007
  6. ncbi A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    Zhenhai Zhang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Science 332:977-80. 2011
  7. ncbi Dynamics of replication-independent histone turnover in budding yeast
    Michael F Dion
    Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Science 315:1405-8. 2007
  8. ncbi Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
  9. pmc Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Cell 143:540-51. 2010
  10. pmc Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
    Marco Albrecht
    University of Wurzburg, Biocentre, Department of Microbiology, Am Hubland, D 97074 Wurzburg, Germany
    Nucleic Acids Res 38:868-77. 2010

Detail Information

Publications322 found, 100 shown here

  1. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  2. pmc Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 322:1845-8. 2008
    ..These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription...
  3. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
    ..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
  4. pmc A single-base resolution map of an archaeal transcriptome
    Omri Wurtzel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 20:133-41. 2010
    ..This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation in Bacteria and Archaea...
  5. pmc Population genomics of human gene expression
    Barbara E Stranger
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 39:1217-24. 2007
    ..We also explore several methodologies that improve the current state of analysis of gene expression variation...
  6. ncbi A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    Zhenhai Zhang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Science 332:977-80. 2011
    ..Thus, an active, nonstatistical nucleosome packing mechanism creates chromatin organizing centers at the 5' ends of genes where important regulatory elements reside...
  7. ncbi Dynamics of replication-independent histone turnover in budding yeast
    Michael F Dion
    Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Science 315:1405-8. 2007
    ..In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states...
  8. ncbi Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
    ..Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer...
  9. pmc Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Cell 143:540-51. 2010
    ....
  10. pmc Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
    Marco Albrecht
    University of Wurzburg, Biocentre, Department of Microbiology, Am Hubland, D 97074 Wurzburg, Germany
    Nucleic Acids Res 38:868-77. 2010
    ..trachomatis. The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen...
  11. pmc Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity
    Melanie J Filiatrault
    USDA Agricultural Research Service, Plant Microbe Interactions Research Unit, Cornell University, Plant Science Bldg, Room 334, Ithaca, NY 14853, USA
    J Bacteriol 192:2359-72. 2010
    ..Overall, our approach provides an efficient way to survey global transcriptional activity in bacteria and enables rapid discovery of specific areas in the genome that merit further investigation...
  12. pmc The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
    Carsten Kröger
    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
    Proc Natl Acad Sci U S A 109:E1277-86. 2012
    ..This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model...
  13. pmc The transcription unit architecture of the Escherichia coli genome
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    Nat Biotechnol 27:1043-9. 2009
    ..Furthermore, the transcription unit architecture provides a foundation on which to construct genome-scale transcriptional and translational regulatory networks...
  14. pmc A chromatin landmark and transcription initiation at most promoters in human cells
    Matthew G Guenther
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 130:77-88. 2007
    ..These observations extend to differentiated cells, suggesting that transcription initiation at most genes is a general phenomenon in human cells...
  15. pmc Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli
    Alfredo Mendoza-Vargas
    Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
    PLoS ONE 4:e7526. 2009
    ..coli...
  16. pmc Regulation of gene expression via the core promoter and the basal transcriptional machinery
    Tamar Juven-Gershon
    Section of Molecular Biology, 0347, University of California, San Diego, La Jolla, CA 92093 0347, USA
    Dev Biol 339:225-9. 2010
    ..These findings suggest that the core promoter and basal transcription factors are important yet mostly unexplored components in the regulation of gene expression...
  17. pmc A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    Cizhong Jiang
    Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, 456 North Frear Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 10:R109. 2009
    ..Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/...
  18. pmc The RNA polymerase II core promoter - the gateway to transcription
    Tamar Juven-Gershon
    Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0347, USA
    Curr Opin Cell Biol 20:253-9. 2008
    ..Thus, the core promoter is a sophisticated gateway to transcription that determines which signals will lead to transcription initiation...
  19. pmc Genome-wide analysis of promoter architecture in Drosophila melanogaster
    Roger A Hoskins
    Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 97420, USA
    Genome Res 21:182-92. 2011
    ..Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals...
  20. ncbi Developmental programming of CpG island methylation profiles in the human genome
    Ravid Straussman
    Department of Cellular Biochemistry and Human Genetics, The Hebrew University Hadassah Medical School, Jerusalem, Israel
    Nat Struct Mol Biol 16:564-71. 2009
    ..In short, we show that UMRs are an important aspect of genome structure that have a dynamic role in development...
  21. pmc Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
    Andrey Revyakin
    Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
    Science 314:1139-43. 2006
    ....
  22. pmc Structural and operational complexity of the Geobacter sulfurreducens genome
    Yu Qiu
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    Genome Res 20:1304-11. 2010
    ..The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes...
  23. pmc A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
    Jan Philip Schlüter
    Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany
    BMC Genomics 11:245. 2010
    ..This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations...
  24. pmc G-quadruplexes in promoters throughout the human genome
    Julian L Huppert
    Cambridge University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Nucleic Acids Res 35:406-13. 2007
    ..These observations support the proposal that promoter G-quadruplexes are directly involved in the regulation of gene expression...
  25. pmc Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
    Sergei Nechaev
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Science 327:335-8. 2010
    ..These results indicate that the intrinsic efficiency of early elongation can greatly affect gene expression...
  26. pmc Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
    Piotr J Balwierz
    Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, 4056 CH, Basel, Switzerland
    Genome Biol 10:R79. 2009
    ....
  27. pmc Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Res 21:775-89. 2011
    ..The collected integrative information should provide a useful basis for future biological characterization of TSCs...
  28. pmc G4 motifs correlate with promoter-proximal transcriptional pausing in human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:4975-83. 2011
    ..These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells...
  29. ncbi Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    Y Okazaki
    1 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nature 420:563-73. 2002
    ..The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics...
  30. pmc ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
    Matthew D Young
    Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
    Nucleic Acids Res 39:7415-27. 2011
    ..The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation...
  31. pmc H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
    Chunyuan Jin
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 41:941-5. 2009
    ..Other combinations of variants have different distributions, consistent with distinct roles for histone variants in the modulation of gene expression...
  32. pmc Massive transcriptional start site analysis of human genes in hypoxia cells
    Katsuya Tsuchihara
    Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
    Nucleic Acids Res 37:2249-63. 2009
    ..The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia...
  33. pmc Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry and Department of Physiology, University of California, Los Angeles, CA 90095, USA
    Science 314:1144-7. 2006
    ....
  34. pmc Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    Sushma Shivaswamy
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS Biol 6:e65. 2008
    ..Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes...
  35. pmc Variation in transcription factor binding among humans
    Maya Kasowski
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 328:232-5. 2010
    ..Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences...
  36. pmc ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome
    Gary Hon
    Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 4:e1000201. 2008
    ..The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications...
  37. pmc Divergent transcription from active promoters
    Amy C Seila
    Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 322:1849-51. 2008
    ..These results suggest that divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation...
  38. pmc Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium
    Melanie J Barnett
    Department of Biology, Stanford University, Stanford, California, USA
    J Bacteriol 194:4983-94. 2012
    ..The inferred S. meliloti RpoH promoter consensus sequences share features of Escherichia coli RpoH promoters but lack extended -10 motifs...
  39. pmc DBTSS provides a tissue specific dynamic view of Transcription Start Sites
    Riu Yamashita
    Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Nucleic Acids Res 38:D98-104. 2010
    ..Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/...
  40. ncbi Dynamic regulation of nucleosome positioning in the human genome
    Dustin E Schones
    Laboratory of Molecular Immunology, The National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 132:887-98. 2008
    ..Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome...
  41. pmc Two strategies for gene regulation by promoter nucleosomes
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 18:1084-91. 2008
    ..Analysis of nucleosome positioning in human promoters reproduces the main observations. Our results suggest two distinct strategies for gene regulation by chromatin, which are selectively employed by different genes...
  42. pmc Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Struct Mol Biol 16:847-52. 2009
    ....
  43. pmc Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex
    Jesse Eichner
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    EMBO J 29:706-16. 2010
    ..Consistent with this mechanism, mutations far from the enzyme active site, which alter the binding of either structured TFIIF domains to Pol II, have similar defects in transcription start site usage...
  44. ncbi RNA exosome depletion reveals transcription upstream of active human promoters
    Pascal Preker
    Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, C F Møllers Alle, Building 1130, Aarhus University, Denmark
    Science 322:1851-4. 2008
    ..We propose that PROMPT transcription is a common characteristic of RNA polymerase II (RNAPII) transcribed genes with a possible regulatory potential...
  45. pmc Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs
    Hiroyuki Wakaguri
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
    BMC Genomics 10:312. 2009
    ..To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites...
  46. ncbi Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods
    Hiro Takahashi
    Plant Biology Research Center, Chubu University, Matsumoto cho 1200, Kasugai, Aichi 487 8501, Japan
    J Biosci Bioeng 114:570-5. 2012
    ..sativa. Although these terms were strongly associated in O. sativa, weak associations were identified in other plants. These results will be helpful for elucidating the functional roles of G4 DNA...
  47. pmc The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection
    Nicole C Robb
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    J Mol Biol 425:875-85. 2013
    ..Our study marks the first experimental observation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dynamics within the bubble affect the search for transcription start sites...
  48. ncbi High-throughput verification of transcriptional starting sites by Deep-RACE
    Signe Olivarius
    Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Biotechniques 46:130-2. 2009
    ..In comparison to the sequencing of RACE PCR products, our approach is more precise and more cost-effective even for batches as small as 17...
  49. ncbi ROSE elements occur in disparate rhizobia and are functionally interchangeable between species
    A Nocker
    , , ETH-Zentrum, Schmelzbergstrasse 7, , Switzerland
    Arch Microbiol 176:44-51. 2001
    ..Parasponia) and Rhizobium sp. strain NGR234 integrated into the chromosome of B. japonicum were heat-responsive. The functionality of these heterologous ROSE elements hints at a common regulatory principle conserved in various rhizobia...
  50. pmc Nucleosome organization in the Drosophila genome
    Travis N Mavrich
    Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nature 453:358-62. 2008
    ..At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines...
  51. pmc Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli
    Rahul Raghavan
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 27388, West Haven, CT 06516 7388, USA
    J Bacteriol 193:2871-4. 2011
    ....
  52. pmc Unveiling Mycoplasma hyopneumoniae promoters: sequence definition and genomic distribution
    Shana de Souto Weber
    Centro de Biotecnologia, Programa de Pós Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul UFRGS, Porto Alegre, RS, Brazil
    DNA Res 19:103-15. 2012
    ..This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional...
  53. ncbi Preferential binding of the methyl-CpG binding domain protein 2 at methylated transcriptional start site regions
    Amandine Chatagnon
    Universite de Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon, France
    Epigenetics 6:1295-307. 2011
    ..This hypothesis may represent a functional explanation for the preferential binding of MBD2 at methyl-CpG in TSS regions...
  54. pmc Epigenetic control of the variable expression of a Plasmodium falciparum receptor protein for erythrocyte invasion
    Lubin Jiang
    Laboratory of Malaria Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
    Proc Natl Acad Sci U S A 107:2224-9. 2010
    ..Our data indicate that the failure of Dd2 to express the sialic acid-independent invasion receptor gene RH4 is associated with the epigenetic silencing mark H3K9 trimethylation present throughout the cycle...
  55. pmc Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
    Kasper Thorsen
    Department of Molecular Medicine, Aarhus University Hospital, Skejby, 8200 Aarhus N, Denmark
    BMC Genomics 12:505. 2011
    ..Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage...
  56. ncbi A motif within a complex promoter from the oomycete Phytophthora infestans determines transcription during an intermediate stage of sporulation
    Qijun Xiang
    Department of Plant Pathology and Microbiology, University of California, Riverside, 92521, USA
    Fungal Genet Biol 46:400-9. 2009
    ..Other sequences, such as a CATTTGTT motif, also bound nuclear proteins but did not play an essential role in spore-specific expression...
  57. pmc Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters
    Ionas Erb
    Bioinformatics and Genomics Program, Center for Genomic Regulation and Pompeu Fabra University, Barcelona, Spain
    PLoS ONE 6:e24279. 2011
    ..This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters...
  58. ncbi A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
    I V Kulakovskiy
    Laboratory of bioinformatics and system biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
    Bioinformatics 27:2621-4. 2011
    ..Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code...
  59. pmc Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
    Fatima Valdes-Mora
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:307-21. 2012
    ..Z anti-correlates with promoter H3K27me3 and DNA methylation. We show for the first time, that acetylation of H2A.Z is a key modification associated with gene activity in normal cells and epigenetic gene deregulation in tumorigenesis...
  60. pmc Modeling tissue-specific structural patterns in human and mouse promoters
    Alexis Vandenbon
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
    Nucleic Acids Res 38:17-25. 2010
    ..Together, these results illustrate the validity of our models, but also indicate that the promoter structures for some tissues are easier to model than those of others...
  61. pmc The nucleosome map of the mammalian liver
    Zhaoyu Li
    Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA Institute of Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Nat Struct Mol Biol 18:742-6. 2011
    ....
  62. pmc Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
    Ola Wallerman
    Department of Genetics and Pathology, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
    Nucleic Acids Res 37:7498-508. 2009
    ..An interaction between HNF4a and GABP was seen at TSS, with one-third of the HNF4a positive promoters being bound also by GABP, and this interaction was verified by co-immunoprecipitations...
  63. pmc Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
    Ken Daigoro Yokoyama
    Biology Department, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Nucleic Acids Res 37:e92. 2009
    ..This offers a novel means by which to predict sequence elements with a collective role in gene regulation...
  64. pmc CUX1 and E2F1 regulate coordinated expression of the mitotic complex genes Ect2, MgcRacGAP, and MKLP1 in S phase
    Laetitia Seguin
    INSERM U749, Faculte de Pharmacie Paris XI, 92296 Chatenay Malabry, France
    Mol Cell Biol 29:570-81. 2009
    ....
  65. ncbi Human cis natural antisense transcripts initiated by transposable elements
    Andrew B Conley
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30306, USA
    Trends Genet 24:53-6. 2008
    ..The TE sequences that promote antisense transcription within human genes are relatively ancient, suggesting that selection has acted to conserve their function...
  66. pmc ppdb: a plant promoter database
    Yoshiharu Y Yamamoto
    Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
    Nucleic Acids Res 36:D977-81. 2008
    ..Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence...
  67. pmc Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by two PhyR-type two-component response regulators
    Bénédicte Bastiat
    Laboratoire des Interactions Plantes Microorganismes LIPM, UMR 441 2594 INRA CNRS BP52627, 31326 Castanet Tolosan Cedex, France
    J Bacteriol 192:2255-65. 2010
    ..meliloti adds an unexpected level of complexity, which may allow the regulatory system to integrate multiple stimuli...
  68. pmc T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site
    Beatriz Cámara
    Department of Microbiology and Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 107:2247-52. 2010
    ....
  69. pmc Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to Trichostatin A and 1alpha,25-dihydroxyvitamin D3
    Marjo Malinen
    Department of Biochemistry, University of Kuopio, FIN 70211 Kuopio, Finland
    Nucleic Acids Res 36:121-32. 2008
    ..This suggests that the attenuation of the response to TSA by NCoR1 or that to 1alpha,25(OH)2D3 by HDACs can be overcome by their combined application achieving maximal induction of anti-proliferative target genes...
  70. ncbi Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs
    Bethany A Janowski
    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
    Nat Chem Biol 1:216-22. 2005
    ..Potent inhibition of multiple genes suggests that agRNAs may represent a natural mechanism for controlling transcription, may complement siRNAs and miRNAs that target mRNA, and will be valuable agents for silencing gene expression...
  71. pmc Fine structure of the promoter-sigma region 1.2 interaction
    Shanil P Haugen
    Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 105:3292-7. 2008
    ..2. Our results refine models of RNAP-DNA interactions in the promoter complex that are crucial for regulation of transcription initiation...
  72. pmc Environmental and growth phase regulation of the Streptococcus gordonii arginine deiminase genes
    Yaling Liu
    Department of Oral Biology, University of Florida, P O Box 100424, Gainesville, FL 32610 0424, USA
    Appl Environ Microbiol 74:5023-30. 2008
    ..gordonii was found...
  73. ncbi Nucleosome positioning and nucleosome stacking: two faces of the same coin
    Julien Riposo
    Universite Pierre et Marie Curie, Laboratoire de Physique Theorique de la Matiere Condensee, CNRS UMR 7600, 4, place Jussieu, 75005 Paris, France
    Mol Biosyst 8:1172-8. 2012
    ..We then use a simple toy model to show that attraction between nucleosomes can fasten the formation of the chromatin fiber...
  74. pmc Promoting developmental transcription
    Uwe Ohler
    Institute for Genome Sciences and Policy, Departments of Biostatistics and Bioinformatics and Computer Science, Duke University, Durham, NC 27708, USA
    Development 137:15-26. 2010
    ....
  75. pmc A novel strategy of transcription regulation by intragenic nucleosome ordering
    Cedric Vaillant
    Universite de Lyon, Lyon, France
    Genome Res 20:59-67. 2010
    ....
  76. ncbi pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site
    Pavel Bucek
    Department of Analytical Chemistry, University of Barcelona, Marti i Franques 1 11, 08028 Barcelona, Spain
    Chemistry 15:12663-71. 2009
    ..The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854)...
  77. pmc CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
    Romain Fenouil
    Centre d Immunologie de Marseille Luminy CIML, Aix Marseille University, UM2, Marseille, France
    Genome Res 22:2399-408. 2012
    ..Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals...
  78. pmc Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
    Donghyuk Kim
    Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
    PLoS Genet 8:e1002867. 2012
    ..coli. These results reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization...
  79. pmc Histone H3 trimethylated at lysine 4 is enriched at probable transcription start sites in Trypanosoma brucei
    Jessica R Wright
    Laboratory of Molecular Parasitology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
    Mol Biochem Parasitol 172:141-4. 2010
    ..H3K4me3 largely co-localizes with H4K10ac, but with a skew towards the upstream side of the H4K10ac peak, suggesting that it is a component of specific nucleosomes that play a role in Pol II transcription initiation...
  80. ncbi Towards accurate human promoter recognition: a review of currently used sequence features and classification methods
    Jia Zeng
    Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong
    Brief Bioinform 10:498-508. 2009
    ..The main focus of this review is on feature extraction and model selection for accurate human promoter recognition, with descriptions of what they are, what has been accomplished, and what remains to be done...
  81. ncbi The P1 promoter of the Escherichia coli rpoH gene is utilized by sigma 70 -RNAP or sigma s -RNAP depending on growth phase
    Anna Janaszak
    Department of Molecular Biology, University of Gdansk, Poland
    FEMS Microbiol Lett 291:65-72. 2009
    ....
  82. pmc Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis
    Alias J Smith
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 1489, USA
    Mol Cell Biol 31:1444-58. 2011
    ..In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif...
  83. ncbi Identification of a hydroxyproline transport system in the legume endosymbiont Sinorhizobium meliloti
    Allyson M MacLean
    Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Plant Microbe Interact 22:1116-27. 2009
    ....
  84. pmc Mechanism of start site selection by RNA polymerase II: interplay between TFIIB and Ssl2/XPB helicase subunit of TFIIH
    Shivani Goel
    Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    J Biol Chem 287:557-67. 2012
    ..These results define a novel, functional interaction between TFIIB and Ssl2 that affects start site selection and gene looping...
  85. pmc The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells
    Dong Yi Zhang
    Division of Developmental Biology, Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Nucleic Acids Res 30:3078-85. 2002
    ..We discuss a model in which the TFIIB-RNAPII interaction controls the start site selection process by influencing the conformation of PIC prior to or during PIC assembly, as opposed to PIC stability...
  86. pmc POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization
    Marco A Mendoza-Parra
    Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS INSERM Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, France
    Nucleic Acids Res 40:e30. 2012
    ....
  87. pmc DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 40:D150-4. 2012
    ..DBTSS can be accessed at http://dbtss.hgc.jp...
  88. ncbi Nutrient regime regulates complex transcriptional start site usage within a Pseudoalteromonas chitinase gene cluster
    Marina W Delpin
    School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
    ISME J 3:1053-63. 2009
    ..By bioinformatic review, ChiA, ChiB and ChiC were found to potentially possess additional putative domains...
  89. pmc Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization
    Denys A Khaperskyy
    Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14214 3000, USA
    Mol Cell Biol 28:3757-66. 2008
    ..These results are discussed within a proposed model for the role of yeast TFIIF in modulating conformational changes in the RNAPII active center during initiation and early elongation...
  90. pmc DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks
    T Hughes
    Oklahoma Medical Research Foundation, Oklahoma City, 73104, USA
    Genes Immun 11:554-60. 2010
    ..TSS in the majority of genes with permissive DNA methylation peaks is in DNase I hypersensitive sites, indicating a failure of DNA methylation to induce chromatin inaccessibility in these loci...
  91. ncbi The TRTGn motif stabilizes the transcription initiation open complex
    Martin I Voskuil
    Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, E B Fred Hall, 53706, Madison, WI, USA
    J Mol Biol 322:521-32. 2002
    ....
  92. pmc Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis
    Tsuyoshi Tanaka
    Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan
    Plant Physiol 149:1316-24. 2009
    ..Rice and Arabidopsis might have evolved novel TSSs in an independent manner, which led to diversification of these two species...
  93. pmc Initiation complex structure and promoter proofreading
    Xin Liu
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 333:633-7. 2011
    ..Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control...
  94. pmc Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
    Elizabeth A Rach
    Program in Computational Biology and Bioinformatics, Duke University, Science Drive, Durham, NC 27708, USA
    Genome Biol 10:R73. 2009
    ..mRNA 5' full-length sequencing techniques have enhanced our understanding of mammalian transcription start sites (TSSs), revealing different initiation patterns on a genomic scale...
  95. pmc Heavy involvement of stringent transcription control depending on the adenine or guanine species of the transcription initiation site in glucose and pyruvate metabolism in Bacillus subtilis
    Shigeo Tojo
    Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Japan
    J Bacteriol 192:1573-85. 2010
    ..Such stringent transcription control that affects the transcription initiation rate through reciprocal changes in the GTP and ATP levels likely occurs for numerous genes of B. subtilis...
  96. ncbi Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation
    Jason N Kuehner
    Cellular and Molecular Biology Graduate Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
    Mol Cell 31:201-11. 2008
    ..Mutations in the Rpb1 subunit of Pol II and in TFIIB disrupt IMD2 regulation by altering start site selection. Thus, Pol II initiation can be regulated by the concentration of initiating nucleotide...
  97. pmc QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
    Vinod Kumar Yadav
    G N Ramachandran Knowledge Centre for Genome Informatics and Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, New Delhi 110 007, India
    Nucleic Acids Res 36:D381-5. 2008
    ..e. stem, loop size, etc. 'Pattern Finder' tool can search for motifs in any given sequence. QuadBase is freely available to users from non-profit organization at http://quadbase.igib.res.in/...
  98. pmc Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195 7650, USA
    Nucleic Acids Res 36:1321-33. 2008
    ..These elements could in principle be recognized either as DNA or as RNA, providing structural targets for regulation at the level of transcription or RNA processing...
  99. ncbi Involvement of AGO1 and AGO2 in mammalian transcriptional silencing
    Bethany A Janowski
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9041, USA
    Nat Struct Mol Biol 13:787-92. 2006
    ..Our data indicate key linkages and important mechanistic distinctions between transcriptional and post-transcriptional silencing pathways in mammalian cells...
  100. pmc Differential usage of alternate promoters of the human stress response gene ATF3 in stress response and cancer cells
    Keisuke Miyazaki
    Department of Biochemical Genetics, Medical Research Institute and Laboratory of Genome Structure and Regulation, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, 113 8510, Japan
    Nucleic Acids Res 37:1438-51. 2009
    ....
  101. ncbi High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans
    Graham Coop
    Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA
    Science 319:1395-8. 2008
    ..Notably, however, we found extensive and heritable variation among both males and females in the proportion of crossovers occurring in these hotspots...

Research Grants63

  1. TGF-BETA, CHLORIDE CHANNELS AND MIGRATION OF EOSINOPHILS
    Devendra K Agrawal; Fiscal Year: 2012
    ..In Aim 2, we will analyze the transcription initiation site(s) in the ClC3 promoter and identify transcription factors involved in selective regulation of ClC- 3 ..
  2. Roles of Epstein-Barr virus nuclear antigens 2 and LP in B cell proliferation
    Elliott D Kieff; Fiscal Year: 2013
    ....
  3. Mechanisms of Gene Regulation by EBV EBNA-1 Protein
    Jeffery T Sample; Fiscal Year: 2010
    ....
  4. A Conserved G-rich Region within Human TH Promoter Regulates Its Activity
    Soumitra Basu; Fiscal Year: 2011
    ....
  5. Understanding transcriptional silencing &anti-silencing mechanisms in Shigella
    Helen J Wing; Fiscal Year: 2013
    ....
  6. Mechanisms of transcription initiation in mitochondria
    Dmitry Temiakov; Fiscal Year: 2013
    ..The crystal structure of the core initiation complex that includes mtRNAP, TFAM, TFB2M and promoter DNA will be determined. ..
  7. Runt-dependent regulation of enhancer-promoter interactions
    JOHN PETER GERGEN; Fiscal Year: 2013
    ..The work focuses on understanding the regulation of non-additive interactions between distinct cis-regulatory DNA elements by Runt, the founding member of a protein family with profound roles in human development and disease. ..
  8. Metabolic Signals Regulating GLUT4 Expression in vivo
    Ann Louise Olson; Fiscal Year: 2013
    ..cis-elements regulating the human Glut4 promoter are located within 895 bp immediately 5'of the transcription initiation site. This region contains two major regulatory domains, referred to as Domain I and the MEF2 domain...
  9. Mechanism and Regulation of RNA Polymerase II Elongation
    Craig D Kaplan; Fiscal Year: 2013
    ..These experiments will reveal the nature of elongation defects in vivo, and how alteration of elongation contributes to gene expression. This work will establish new paradigms for the dissection of Pol II elongation factor function. ..
  10. The RNA polymerase II transcription complex
    Stephen Buratowski; Fiscal Year: 2013
    ..This fundamental knowledge is essential for understanding how mutations in transcription factors and histone modifying enzymes lead to diseases such as cancer and developmental defects. ..
  11. Metabolic Signals Regulating GLUT4 Expression in vivo
    ANN OLSON; Fiscal Year: 2009
    ..cis-elements regulating the human Glut4 promoter are located within 895 bp immediately 5'of the transcription initiation site. This region contains two major regulatory domains, referred to as Domain I and the MEF2 domain...
  12. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2013
    ....
  13. Neurotrophin Protection of Hypoxic Ischemic Brain Injury
    Mir Ahamed Hossain; Fiscal Year: 2013
    ..Finally, we will perform the promoter analysis of NP1 gene to identify transcription initiation site and transcription factor(s) involve in the regulation of NP1 induction in brain injury...
  14. Validation and development of specific small molecule inhibitors of HTRA1 for tre
    Shuyuan Yao; Fiscal Year: 2010
    ..Development of specific HTRA1 small molecule inhibitors as described in this SBIR grant application will provide a new therapeutic approach for treating age-related macular degeneration. ..
  15. Molecular Regulation of an Epilepsy Modifier Gene
    BENJAMIN JORGE; Fiscal Year: 2013
    ....
  16. A MACHINE LEARNING APPROACH FOR FINE-SCALE GENOME WIDE DNA METHYLATION ANALYSIS
    John R Edwards; Fiscal Year: 2013
    ..The general framework developed here can be expanded in the future to examine methylation signatures at enhancers and gene bodies, as well as to histone marks or other genomic signals that carry detailed spatial information. ..
  17. Bacterial gene regulation by the NTP substrates of transcription initiation
    Charles L Turnbough; Fiscal Year: 2013
    ..Defining these mechanisms in molecular detail enhances our understanding of the inner workings of bacteria and increases our ability to control bacterial pathogens and to create new tools for biotechnology. ..
  18. Identification of Transcriptional Factor Binding Sites in Human Promoters
    Zhiping Weng; Fiscal Year: 2010
    ..The data generated in this project will be the first systematic functional analysis of TF binding sites at base-pair resolution. ..
  19. Modeling the structure &evolution of regulatory regions in eukaryotic gemomes
    Uwe Ohler; Fiscal Year: 2011
    ..Our research will help to find the exact regulatory regions in DNA, both computationally and experimentally, and to learn the mechanisms that control the expression of genes in model organisms and humans. ..
  20. MECHANISM, ACTIVATION, AND CONTROL OF RRNA TRANSCRIPTION
    Richard L Gourse; Fiscal Year: 2013
    ..coli makes a structure analogous to the eukaryotic nucleolus. We will expand these studies to explore other potential long-range interactions between distant parts of the bacterial chromosome. ..
  21. DNA Methylation in Photoreceptor-Specific Gene Expression and Retinal Disease
    Shannath L Merbs; Fiscal Year: 2010
    ....
  22. Molecular Analysis of Eukaryotic Transcription
    Steven M Hahn; Fiscal Year: 2013
    ....
  23. The Arabidopsis Transcription Factor ORFeome and downstream genomic application
    STEVE A contact KAY; Fiscal Year: 2010
    ..As the knowledge gap is being filled, the study of transcriptional networks in Arabidopsis will ultimately help us understand the biochemical complexity of multicellular organisms and positively impact the biomedical research community. ..
  24. ROLE OF CHROMATIN IN HIV TRANSCRIPTIONAL REGULATION
    ERIC M VERDIN; Fiscal Year: 2010
    ..These experiments have the potential of identifying novel factors mediating HIV transcriptional regulation that could be targeted therapeutically in the future. ..
  25. Structure of the Eukaryote Transcription Apparatus
    Roger D Kornberg; Fiscal Year: 2013
    ..2. Structure determination of pol II - general transcription factor complexes. 3. Structure determination of Mediator and of Mediator - pol II complexes. 4. Development of the HevEM approach. ..
  26. Regulation of the P.aeruginosa Type III Secretion System by the Multifaceted Tran
    Florian David Schubot; Fiscal Year: 2013
    ..Lastly, we will determine the crystal structure of the regulatory domain of ExsA. This will be the first structure reported for this type of domain and may offer intriguing new insights into its functiona role. ..
  27. Biochemical predictions of regulatory elements and XenMINE for Xenopus
    Jin Billy Li; Fiscal Year: 2013
    ..While we will directly interface with multiple efforts, our ole is to utilize biochemistry to 'fill a large gap'in the genomic repertoire of Xenopus to enable accurate mapping of gene models and gene regulatory elements. ..
  28. REGULATION OF BILE ACID SYNTHESIS
    JOHN CHIANG; Fiscal Year: 1999
    ....
  29. DNA Methylation Profiling of Chronic Pain
    Andreas S Beutler; Fiscal Year: 2010
    ..Research outcomes of Aims 1 and 2 will be confirmed in an independent set of animals. If conducted now, the proposed study would be the first to investigate DNA cytosine methylation in pain. ..
  30. Functional analysis of the zebrafish genome through RNA-seq and ribosome profile
    ANTONIO GIRALDEZ; Fiscal Year: 2013
    ..In the future, the results derived from this project will facilitate the functional characterization of the zebrafish genes and will establsh a frame work to understand the structure and the function of vertebrate genes. ..
  31. TYPE III COLLAGEN GENE EXPRESSION IN CARTILAGE
    SHERRILL ADAMS; Fiscal Year: 1993
    ..Furthermore, they will provide more extensive analysis of the structure of the type III collagen gene and its regulation than has heretofore been available...
  32. MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSION
    CAROLE MENDELSON; Fiscal Year: 2007
    ..least four identified DNA response elements which lie within 400 bp[unreadable] upstream of the SP-A transcription initiation site. Mutagenesis of any[unreadable] one of these elements has a marked effect to reduce basal and cAMP[..
  33. TRANSCRIPTIONAL CONTROL IN ENTAMOEBA HISTOLYTICA
    Upinder Singh; Fiscal Year: 2001
    ..at position -30 and MAGMCT between -30 and -14 from the start codon, and ATAGAC+1M within the transcription initiation site. The sequence regions at -30 and +1 differ significantly from consensus TATA and initiator sequences ..
  34. ODC AS A THERAPEUTIC TARGET--GENE FUNCTION ANALYSIS
    Gordon Luk; Fiscal Year: 1992
    ..Structure analysis will include nucleotide sequencing of the ODC gene 5' flanking region, mapping the transcription initiation site, and identifying sequences that interact with DNA-binding proteins...
  35. CARDIAC GROWTH REGULATION
    Kaie Ojamaa; Fiscal Year: 1999
    ..We have identified a cis-acting element at -47 bp from the transcription initiation site, designated hemodynamic response element (HME), that is both necessary and sufficient to confer ..
  36. MOLECULAR BASIS OF NERVE GROWTH FACTOR
    Jeffrey Milbrandt; Fiscal Year: 1993
    ..Elucidating the molecular mechanism by which NGF regulates gene expression will help us understand how NGF influences the survival and differentiation of neural-crest derived cell types...
  37. ROLE OF TESTIS-SPECIFIC HISTONES IN SPERMATOGENESIS
    Chi Bom Chae; Fiscal Year: 1993
    ..be due to the spermatogonia-specific protein which binds to a site between TATAA box and the TH2B transcription initiation site. This will be investigated with partially purified protein in an in vitro transcription system...
  38. Regulation of Mouse Somatostatin Receptor Subtype 5 Gene
    WHITNEY WOODMANSEE; Fiscal Year: 2004
    ..abstract_text> ..
  39. REGULATION OF GLUT1 GENE EXPRESSION BY HYPOXIA
    Faramarz Ismail Beigi; Fiscal Year: 2001
    ....
  40. Mechanism of Transcription Control by Drosophila TAF250
    DAVID WASSARMAN; Fiscal Year: 2006
    ..abstract_text> ..
  41. REGULATION OF GROWTH FACTORS AND EMBRYOGENESIS
    ARNOLD RIZZINO; Fiscal Year: 2005
    ..The last studies are highly significant in their own right, because they will provide novel insights into the mechanisms used by members of two large transcription factor families to stimulate transcription. ..
  42. RIBOSOMAL RNA TRANSCRIPTION FACTOR FUNCTIONAL ANALYSIS
    Marvin Paule; Fiscal Year: 1992
    ..In the long term, the details of the interaction of TIF and polymerase will be evaluated using site-specific point mutagenesis of the TIF gene and cloned RNA polymerase subunit gene(s)...
  43. Human Zinc Transporter Zip 13 and Cellular Zinc Homeostasis
    Joel Walker; Fiscal Year: 2007
    ..Once the transcription initiation site is known, the hZip13 promoter region will be dissected using a luciferase reporter assay where ..
  44. REPLICATION OF VIRULENT AND ONCOGENIC VIRUSES
    ROBERT THACH; Fiscal Year: 1992
    ..Thus many of the answers sought in this study will break entirely new ground. If novel cytotoxicity genes can be identified, then novel antiviral agents may suggest themselves...
  45. GLUCOSE TRANSPORTER EXPRESSION IN TRANSGENIC MICE
    ANN OLSON; Fiscal Year: 1999
    ..Understanding this mechanism will provide useful insight into the mechanisms by which GLUT4 gene expression occurs in vivo. ..
  46. Characterization of the ETEC Virulence Regulator Rns
    GEORGE MUNSON; Fiscal Year: 2009
    ..Studies in this proposal will determine the molecular mechanism of Rns positive autoregulation and the biological significance of Rns-independent, nonproductive RPo complexes near Prns. ..
  47. WILMS TUMOR-1 GENE REGULATION IN KIDNEY DEVELOPMENT
    Vikas Sukhatme; Fiscal Year: 2001
    ..Methods to be used include gel mobility shift assays, DNA footprinting, expression cloning, protein purification, and in situ hybridization. ..
  48. STRUCTURAL BASIS OF C3 FUNCTIONS
    BRIAN TACK; Fiscal Year: 1993
    ..The C3 mRNA in deficient and normal family members will be examined by Northern analysis and the defect at the protein level assessed by sequences analysis of potential transcripts of the defective gene...
  49. REGULATION OF IL 12 IN MUCOSAL IMMUNITY AND IBD
    Scott Plevy; Fiscal Year: 1999
    ..These mechanisms may then be exploited to alter host immunity in infectious and inflammatory disorders, including IBD. ..
  50. A Variant of Ileal Bile Acid Binding Protein in Colon Cancer
    Jeffrey Smith; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  51. REGULATION OF THE MURINE CALCITONIN RECEPTOR GENE
    DEBORAH GALSON; Fiscal Year: 2001
    ..In addition, they will develop ES cell differentiation techniques to generate osteoclasts from E cells for studying the regulation of mCTR gene expression during osteoclast differentiation and development. ..
  52. TRANSCRIPTION OF SMALL RNA GENES IN YEAST
    DAVID BROW; Fiscal Year: 2002
    ..A human homolog of Nrd1 will be sought. These studies will provide fundamental insights into the mechanism of transcription initiation and termination, which are key steps in the control of eukaryotic gene expression. ..
  53. ENDOCRINE PANCREAS--GENE EXPRESSION AND REGULATION
    Doris Stoffers; Fiscal Year: 2000
    ..The transcription initiation site(s) will be identified. Mutational analysis of the mouse IDX-1 regulatory region will be performed...
  54. GENETIC ELEMENTS CONTROLLING MYELOID DIFFERENTIATION
    Edward Agura; Fiscal Year: 1993
    ..These studies may contribute several important aspects to the understanding of normal and disordered eukaryotic gene regulation in myeloid lineages...
  55. Transcriptional Control of AICDA Expression
    Ferenc Livak; Fiscal Year: 2005
    ..abstract_text> ..
  56. REGULATION OF MYELIN BASIC PROTEIN GENE EXPRESSION
    Shohreh Amini; Fiscal Year: 2000
    ..The use of JCV T-antigen in a transgenic mouse model provides an excellent opportunity to decipher the regulatory mechanisms involved in the control of myelin gene expression in normal and disease states. ..
  57. MOLECULAR GENETICS OF LENS CONNEXIN50 (MP70)
    Robert Church; Fiscal Year: 2001
    ..goal, the PI proposes to investigate the following topics: a) to identify the mouse MP70 gene (Gja8) transcription initiation site(s) by performing primer extension assay and S1-nuclease mapping; b) to determine the region(s) ..
  58. Analysis of 5'UTR-Mediated Regulation of p53 Expression
    Philip Lazarus; Fiscal Year: 2006
    ..abstract_text> ..
  59. MOLECULAR STUDY OF CARDIOGENESIS
    Charles Ordahl; Fiscal Year: 2002
    ..Element") contains binding sites for both GATA and MEF-2 and lies 200 nucleotides upstream of the transcription initiation site. The other regulatory domain lies within the proximal promoter region (less than 100 nucleotides ..
  60. NFBP, a novel factor regulating HIV-1 transcription
    Thersa Sweet; Fiscal Year: 2007
    ..The results of these studies should provide critical and novel information on the events involved in control of HIV-1 gene expression in CNS as well as lymphocytic cells. ..
  61. DNA METHYLATION AND SOD2/MNSOD GENE EXPRESSION
    Frederick Domann; Fiscal Year: 2002
    ..A better understanding of the mechanisms of regulation of the expressio of SOD2 during carcinogenesis and differentiation may lead to new strategies for the treatment of diseases in which aberrant SOD2 expression plays a key role. ..
  62. REGULATION OF HIV-1 GENE TRANSCRIPTION IN CNS
    Bassel Sawaya; Fiscal Year: 2004
    ..The outcome from these molecular studies will generate important and unique information, which could be translated into devising and utilizing an effective strategy for the prevention and treatment of HIV-l induced CNS injury in AIDS. ..
  63. PHOSPHODIESTERASES IN PHOTORECEPTOR METABOLISM & DISEASE
    Debora Farber; Fiscal Year: 2003
    ..Overall, these studies are designed to increase our knowledge of the etiology and possibly the pathogenesis of certain hereditary retinal degenerations and open new avenues for future therapeutic modalities. ..