- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Nature 447:799-816. 2007
..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
- 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...
- The transcriptional landscape of the mammalian genome
Science 309:1559-63. 2005
..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
- A single-base resolution map of an archaeal transcriptome
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...
- 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...
- A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
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...
- 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...
- 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...
- 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
- Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
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...
- 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...
- The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
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...
- 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...
- 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...
- Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli
Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
PLoS ONE 4:e7526. 2009
- Regulation of gene expression via the core promoter and the basal transcriptional machinery
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...
- A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
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/...
- The RNA polymerase II core promoter - the gateway to transcription
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...
- 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...
- Developmental programming of CpG island methylation profiles in the human genome
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...
- Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
Science 314:1139-43. 2006
- Structural and operational complexity of the Geobacter sulfurreducens genome
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...
- 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...
- 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...
- Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
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...
- 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
- Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
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...
- G4 motifs correlate with promoter-proximal transcriptional pausing in human genes
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...
- Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
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...
- 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...
- H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
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...
- Massive transcriptional start site analysis of human genes in hypoxia cells
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...
- 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
- Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
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...
- Variation in transcription factor binding among humans
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...
- ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome
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...
- 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...
- 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...
- DBTSS provides a tissue specific dynamic view of Transcription Start Sites
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/...
- 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...
- Two strategies for gene regulation by promoter nucleosomes
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...
- Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
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
- Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex
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...
- RNA exosome depletion reveals transcription upstream of active human promoters
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...
- Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs
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...
- Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods
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...
- 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...
- High-throughput verification of transcriptional starting sites by Deep-RACE
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...
- ROSE elements occur in disparate rhizobia and are functionally interchangeable between species
, , 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...
- 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...
- Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli
Department of Ecology and Evolutionary Biology, Yale University, P O Box 27388, West Haven, CT 06516 7388, USA
J Bacteriol 193:2871-4. 2011
- 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...
- Preferential binding of the methyl-CpG binding domain protein 2 at methylated transcriptional start site regions
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...
- Epigenetic control of the variable expression of a Plasmodium falciparum receptor protein for erythrocyte invasion
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...
- Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
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...
- A motif within a complex promoter from the oomycete Phytophthora infestans determines transcription during an intermediate stage of sporulation
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...
- Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters
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...
- 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...
- Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
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...
- Modeling tissue-specific structural patterns in human and mouse promoters
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...
- The nucleosome map of the mammalian liver
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
- Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
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...
- 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...
- CUX1 and E2F1 regulate coordinated expression of the mitotic complex genes Ect2, MgcRacGAP, and MKLP1 in S phase
INSERM U749, Faculte de Pharmacie Paris XI, 92296 Chatenay Malabry, France
Mol Cell Biol 29:570-81. 2009
- 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...
- 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...
- Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by two PhyR-type two-component response regulators
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...
- T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site
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
- Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to Trichostatin A and 1alpha,25-dihydroxyvitamin D3
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...
- 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...
- 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...
- Environmental and growth phase regulation of the Streptococcus gordonii arginine deiminase genes
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...
- Nucleosome positioning and nucleosome stacking: two faces of the same coin
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...
- Promoting developmental transcription
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
- A novel strategy of transcription regulation by intragenic nucleosome ordering
Universite de Lyon, Lyon, France
Genome Res 20:59-67. 2010
- 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
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)...
- CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
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...
- Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
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...
- 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...
- Towards accurate human promoter recognition: a review of currently used sequence features and classification methods
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...
- The P1 promoter of the Escherichia coli rpoH gene is utilized by sigma 70 -RNAP or sigma s -RNAP depending on growth phase
Department of Molecular Biology, University of Gdansk, Poland
FEMS Microbiol Lett 291:65-72. 2009
- 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...
- 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
- Mechanism of start site selection by RNA polymerase II: interplay between TFIIB and Ssl2/XPB helicase subunit of TFIIH
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...
- 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...
- 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
- DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
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...
- 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...
- 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...
- DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks
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...
- 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
- Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis
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...
- Initiation complex structure and promoter proofreading
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...
- 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...
- 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
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...
- 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...
- 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/...
- Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
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...
- 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...
- Differential usage of alternate promoters of the human stress response gene ATF3 in stress response and cancer cells
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
- High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans
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...