gene expression regulation

Summary

Summary: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action at the level of transcription or translation. These processes include gene activation and genetic induction.

Top Publications

  1. pmc MicroRNAs: target recognition and regulatory functions
    David P Bartel
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 136:215-33. 2009
  2. pmc A new mathematical model for relative quantification in real-time RT-PCR
    M W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 29:e45. 2001
  3. ncbi Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    Benjamin P Lewis
    Cell 120:15-20. 2005
  4. ncbi The functions of animal microRNAs
    Victor Ambros
    Dartmouth Medical School, Department of Genetics, Hanover, New Hampshire 03755, USA E mail
    Nature 431:350-5. 2004
  5. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
  6. doi The widespread regulation of microRNA biogenesis, function and decay
    Jacek Krol
    Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
    Nat Rev Genet 11:597-610. 2010
  7. ncbi Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK 8200 Aarhus N, Denmark
    Cancer Res 64:5245-50. 2004
  8. ncbi MicroRNAs: small RNAs with a big role in gene regulation
    Lin He
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 5:522-31. 2004
  9. pmc Significance analysis of microarrays applied to the ionizing radiation response
    V G Tusher
    Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA
    Proc Natl Acad Sci U S A 98:5116-21. 2001
  10. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003

Detail Information

Publications246 found, 100 shown here

  1. pmc MicroRNAs: target recognition and regulatory functions
    David P Bartel
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 136:215-33. 2009
    ..This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes...
  2. pmc A new mathematical model for relative quantification in real-time RT-PCR
    M W Pfaffl
    Institute of Physiology, FML Weihenstephan, Center of Life and Food Sciences, Technical University of Munich, Germany
    Nucleic Acids Res 29:e45. 2001
    ..High accuracy and reproducibility (<2.5% variation) were reached in LightCycler PCR using the established mathematical model...
  3. ncbi Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    Benjamin P Lewis
    Cell 120:15-20. 2005
    ..Targeting was also detected in open reading frames. In sum, well over one third of human genes appear to be conserved miRNA targets...
  4. ncbi The functions of animal microRNAs
    Victor Ambros
    Dartmouth Medical School, Department of Genetics, Hanover, New Hampshire 03755, USA E mail
    Nature 431:350-5. 2004
    ....
  5. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
    ..elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction...
  6. doi The widespread regulation of microRNA biogenesis, function and decay
    Jacek Krol
    Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
    Nat Rev Genet 11:597-610. 2010
    ..Such regulation has an important role in the context-specific functions of miRNAs...
  7. ncbi Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK 8200 Aarhus N, Denmark
    Cancer Res 64:5245-50. 2004
    ..The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data...
  8. ncbi MicroRNAs: small RNAs with a big role in gene regulation
    Lin He
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 5:522-31. 2004
  9. pmc Significance analysis of microarrays applied to the ionizing radiation response
    V G Tusher
    Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA
    Proc Natl Acad Sci U S A 98:5116-21. 2001
    ..Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation...
  10. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
  11. doi Biogenesis of small RNAs in animals
    V Narry Kim
    School of Biological Sciences and Center for National Creative Research, Seoul National University, Seoul, 151 742, Korea
    Nat Rev Mol Cell Biol 10:126-39. 2009
    ..This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells...
  12. ncbi Signal integration in the endoplasmic reticulum unfolded protein response
    David Ron
    The Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA
    Nat Rev Mol Cell Biol 8:519-29. 2007
    ..The arms of the UPR are integrated to provide a response that remodels the secretory apparatus and aligns cellular physiology to the demands imposed by ER stress...
  13. pmc Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance
    Haiyan Xu
    Millennium Pharmaceuticals, Cambridge, Massachusetts, USA
    J Clin Invest 112:1821-30. 2003
    ..We propose that obesity-related insulin resistance is, at least in part, a chronic inflammatory disease initiated in adipose tissue...
  14. ncbi BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
    Bioinformatics 21:3448-9. 2005
    ....
  15. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
    ..Our data provide new insights into the function of histone methylation and chromatin organization in genome function...
  16. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  17. doi Regulation of mRNA translation and stability by microRNAs
    Marc Robert Fabian
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada
    Annu Rev Biochem 79:351-79. 2010
    ..We also address the issue of cellular localization of miRNA-mediated events and a role for RNA-binding proteins in activation or relief of miRNA repression...
  18. doi Blinded by the Light: The Growing Complexity of p53
    Karen H Vousden
    The Beatson Institute for Cancer Research, Garscube Estate, Glasgow, UK
    Cell 137:413-31. 2009
    ..Control of p53's transcriptional activity is crucial for determining which p53 response is activated, a decision we must understand if we are to exploit efficiently the next generation of drugs that selectively activate or inhibit p53...
  19. pmc Identification of functional elements and regulatory circuits by Drosophila modENCODE
    Sushmita Roy
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 330:1787-97. 2010
    ..Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation...
  20. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression...
  21. ncbi Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    A Fire
    Carnegie Institution of Washington, Department of Embryology, Baltimore, Maryland 21210, USA
    Nature 391:806-11. 1998
    ....
  22. doi Long non-coding RNAs: insights into functions
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nat Rev Genet 10:155-9. 2009
    ..We also consider the medical implications, and the emerging recognition that any transcript, regardless of coding potential, can have an intrinsic function as an RNA...
  23. pmc Understanding mechanisms underlying human gene expression variation with RNA sequencing
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago 60637, USA
    Nature 464:768-72. 2010
    ..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals...
  24. pmc Widespread transcription at neuronal activity-regulated enhancers
    Tae Kyung Kim
    Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 465:182-7. 2010
    ..These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis...
  25. pmc Histone modifications at human enhancers reflect global cell-type-specific gene expression
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 459:108-12. 2009
    ..Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression...
  26. ncbi Translating the histone code
    T Jenuwein
    Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Science 293:1074-80. 2001
    ....
  27. doi Many roads to maturity: microRNA biogenesis pathways and their regulation
    Julia Winter
    Helmholtz University Group Molecular RNA Biology and Cancer, German Cancer Research Center DKFZ and Institute of Pathology, University of Heidelberg, B150 INF 581, D 69120 Heidelberg, Germany
    Nat Cell Biol 11:228-34. 2009
    ..Here we review the recent advances in knowledge of the microRNA biosynthesis pathways and discuss their impact on post-transcriptional microRNA regulation during tumour development...
  28. ncbi Smad-dependent and Smad-independent pathways in TGF-beta family signalling
    Rik Derynck
    Department of Growth and Development, University of California at San Francisco, San Francisco, California 94143 0640, USA
    Nature 425:577-84. 2003
    ..Other signalling pathways further regulate Smad activation and function. In addition, TGF-beta receptors activate Smad-independent pathways that not only regulate Smad signalling, but also allow Smad-independent TGF-beta responses...
  29. pmc Small silencing RNAs: an expanding universe
    Megha Ghildiyal
    Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nat Rev Genet 10:94-108. 2009
    ....
  30. pmc The impact of microRNAs on protein output
    Daehyun Baek
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 455:64-71. 2008
    ..The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output...
  31. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  32. pmc Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    Sung Wook Chi
    Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 460:479-86. 2009
    ..Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions...
  33. pmc MicroRNA genes are transcribed by RNA polymerase II
    Yoontae Lee
    Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, Seoul, Korea
    EMBO J 23:4051-60. 2004
    ..These data indicate that pol II is the main, if not the only, RNA polymerase for miRNA gene transcription. Our study offers a basis for understanding the structure and regulation of miRNA genes...
  34. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  35. ncbi A microRNA component of the p53 tumour suppressor network
    Lin He
    Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 447:1130-4. 2007
    ..The p53 network suppresses tumour formation through the coordinated activation of multiple transcriptional targets, and miR-34 may act in concert with other effectors to inhibit inappropriate cell proliferation...
  36. pmc CTCF: master weaver of the genome
    Jennifer E Phillips
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Cell 137:1194-211. 2009
    ....
  37. ncbi Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA
    Catherine L Jopling
    Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
    Science 309:1577-81. 2005
    ..Therefore, miR-122 is likely to facilitate replication of the viral RNA, suggesting that miR-122 may present a target for antiviral intervention...
  38. ncbi Interleukin-10 and the interleukin-10 receptor
    K W Moore
    Department of Molecular Biology, DNAX Research Institute of Molecular and Cellular Biology Inc, Palo Alto, California 94304, USA
    Annu Rev Immunol 19:683-765. 2001
    ..This review highlights findings that have advanced our understanding of IL-10 and its receptor, as well as its in vivo function in health and disease...
  39. pmc Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 471:480-5. 2011
    ..This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function...
  40. pmc Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
    Ryan D Morin
    Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Genome Res 18:610-21. 2008
    ..Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation...
  41. doi The mechanism of eukaryotic translation initiation and principles of its regulation
    Richard J Jackson
    Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
    Nat Rev Mol Cell Biol 11:113-27. 2010
    ....
  42. pmc Regulation of translation initiation in eukaryotes: mechanisms and biological targets
    Nahum Sonenberg
    Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, H3G 1Y6, Canada
    Cell 136:731-45. 2009
    ....
  43. ncbi Targeted gene expression as a means of altering cell fates and generating dominant phenotypes
    A H Brand
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
    Development 118:401-15. 1993
    ..We have directed expression of an activated form of the Dras2 protein, resulting in dominant eye and wing defects that can be used in screens to identify other members of the Dras2 signal transduction pathway...
  44. pmc Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection
    Robert E Lanford
    Department of Virology and Immunology and Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX 78227, USA
    Science 327:198-201. 2010
    ..The prolonged virological response to SPC3649 treatment without HCV rebound holds promise of a new antiviral therapy with a high barrier to resistance...
  45. pmc miRecords: an integrated resource for microRNA-target interactions
    Feifei Xiao
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    Nucleic Acids Res 37:D105-10. 2009
    ..The miRecords is available at http://miRecords.umn.edu/miRecords...
  46. ncbi Switching from repression to activation: microRNAs can up-regulate translation
    Shobha Vasudevan
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
    Science 318:1931-4. 2007
    ..Thus, activation is a common function of microRNPs on cell cycle arrest. We propose that translation regulation by microRNPs oscillates between repression and activation during the cell cycle...
  47. ncbi The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
    Mitsutoshi Yoneyama
    Department of Tumor Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Nat Immunol 5:730-7. 2004
    ..Subsequent gene activation by these factors induced antiviral functions, including type I interferon production. Thus, RIG-I is key in the detection and subsequent eradication of the replicating viral genomes...
  48. ncbi Requirement for p53 and p21 to sustain G2 arrest after DNA damage
    F Bunz
    The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
    Science 282:1497-501. 1998
    ..Thus, p53 and p21 appear to be essential for maintaining the G2 checkpoint in human cells...
  49. ncbi WAF1, a potential mediator of p53 tumor suppression
    W S El-Deiry
    Oncology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
    Cell 75:817-25. 1993
    ..These studies define a gene whose expression is directly induced by p53 and that could be an important mediator of p53-dependent tumor growth suppression...
  50. ncbi IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines
    Jochen Schmitz
    Schering Plough Biopharma Formerly DNAX Research, Inc, 901 California Avenue, Palo Alto, California 94304, USA
    Immunity 23:479-90. 2005
    ..In vivo, IL-33 induces the expression of IL-4, IL-5, and IL-13 and leads to severe pathological changes in mucosal organs...
  51. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
    ..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
  52. ncbi microRNA functions
    Natascha Bushati
    Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany 69117
    Annu Rev Cell Dev Biol 23:175-205. 2007
    ..In animal cells, miRNAs regulate their targets by translational inhibition and mRNA destabilization. Here, we review recent work in animal models that provide insight into the diverse roles of miRNAs in vivo...
  53. ncbi Nanog safeguards pluripotency and mediates germline development
    Ian Chambers
    MRC Centre Development in Stem Cell Biology, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King s Buildings, West Mains Road, Edinburgh EH9 3JQ, UK
    Nature 450:1230-4. 2007
    ..We surmise that Nanog stabilizes embryonic stem cells in culture by resisting or reversing alternative gene expression states...
  54. ncbi The Wnt signaling pathway in development and disease
    Catriona Y Logan
    Department of Developmental Biology, Beckman Center, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
    Annu Rev Cell Dev Biol 20:781-810. 2004
    ..The next few years are likely to see novel therapeutic reagents aimed at controlling Wnt signaling in order to alleviate these conditions...
  55. doi Conserved role of intragenic DNA methylation in regulating alternative promoters
    Alika K Maunakea
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Nature 466:253-7. 2010
    ..These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies...
  56. ncbi The complex language of chromatin regulation during transcription
    Shelley L Berger
    The Wistar Institute, 3601 Spruce Street, Room 201, Philadelphia, Pennsylvania 19104, USA
    Nature 447:407-12. 2007
    ..Although such modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes...
  57. pmc ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    Adam A Margolin
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
    BMC Bioinformatics 7:S7. 2006
    ..This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods...
  58. ncbi Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  59. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
    ..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
  60. pmc Common regulatory variation impacts gene expression in a cell type-dependent manner
    Antigone S Dimas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
    Science 325:1246-50. 2009
    ..These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity...
  61. 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...
  62. doi Evolution and functions of long noncoding RNAs
    Chris P Ponting
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3QX, UK
    Cell 136:629-41. 2009
    ..Here, we review the evolution of lncRNAs and their roles in transcriptional regulation, epigenetic gene regulation, and disease...
  63. pmc miR2Disease: a manually curated database for microRNA deregulation in human disease
    Qinghua Jiang
    Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China
    Nucleic Acids Res 37:D98-104. 2009
    ..Once approved by the submission review committee, the submitted records will be included in the database. miR2Disease is freely available at http://www.miR2Disease.org...
  64. pmc High-resolution mapping of expression-QTLs yields insight into human gene regulation
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, IL, USA
    PLoS Genet 4:e1000214. 2008
    ..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
  65. doi Genetics of gene expression and its effect on disease
    Valur Emilsson
    deCODE Genetics, 101 Reykjavik, Iceland
    Nature 452:423-8. 2008
    ..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...
  66. ncbi Epigenetic programming by maternal behavior
    Ian C G Weaver
    Douglas Hospital Research Center, 6875 LaSalle Blvd, Montreal, Quebec H4H 1R3, Canada
    Nat Neurosci 7:847-54. 2004
    ..Thus we show that an epigenomic state of a gene can be established through behavioral programming, and it is potentially reversible...
  67. doi Genome-wide evolutionary analysis of eukaryotic DNA methylation
    Assaf Zemach
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Science 328:916-9. 2010
    ..Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes...
  68. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    ..This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks...
  69. pmc The database of experimentally supported targets: a functional update of TarBase
    Giorgos L Papadopoulos
    Institute of Molecular Oncology, Biomedical Sciences Research Center Alexander Fleming, 166 72 Varkiza, Synaptic Ltd, 711 10 Heraklion, Greece
    Nucleic Acids Res 37:D155-8. 2009
    ..Additionally, the database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt. The TarBase5.0 database can be queried or downloaded from http://microrna.gr/tarbase...
  70. pmc An atlas of combinatorial transcriptional regulation in mouse and man
    Timothy Ravasi
    The FANTOM Consortium, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Cell 140:744-52. 2010
    ..The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution...
  71. doi Pre-mRNA processing reaches back to transcription and ahead to translation
    Melissa J Moore
    Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 136:688-700. 2009
    ..The connections of pre-mRNA processing to upstream events in transcription and downstream events, including translation and mRNA decay, are elaborate, extensive, and remarkably interwoven...
  72. pmc An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis
    Matthew P R Berry
    Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Nature 466:973-7. 2010
    ..Our study also provides a broad range of transcriptional biomarkers with potential as diagnostic and prognostic tools to combat the TB epidemic...
  73. pmc TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function
    Liang Zhou
    The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
    Nature 453:236-40. 2008
    ..Therefore, the decision of antigen-stimulated cells to differentiate into either T(H)17 or T(reg) cells depends on the cytokine-regulated balance of RORgammat and Foxp3...
  74. pmc In vitro propagation and transcriptional profiling of human mammary stem/progenitor cells
    Gabriela Dontu
    Department of Internal Medicine, Hematology Oncology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genes Dev 17:1253-70. 2003
    ..The isolation and characterization of these stem cells should help elucidate the molecular pathways that govern normal mammary development and carcinogenesis...
  75. pmc Phenotypic and functional features of human Th17 cells
    Francesco Annunziato
    Center for Research, Transfer and High Education on Chronic, Inflammatory, Degenerative and Neoplastic Disorders DENOThe, University of Florence, Florence 50134, Italy
    J Exp Med 204:1849-61. 2007
    ....
  76. ncbi Stats: transcriptional control and biological impact
    David E Levy
    Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
    Nat Rev Mol Cell Biol 3:651-62. 2002
    ..In addition to several roles in normal cell decisions, dysregulation of STAT function contributes to human disease, making the study of these proteins an important topic of current research...
  77. pmc Histone deacetylases (HDACs): characterization of the classical HDAC family
    Annemieke J M de Ruijter
    Academic Medical Centre, University of Amsterdam, Amsterdam, The, Netherlands
    Biochem J 370:737-49. 2003
    ..This challenging field has generated many fascinating results which will ultimately lead to a better understanding of the mechanism of gene transcription as a whole...
  78. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome...
  79. ncbi Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase
    H P Harding
    Skirball Institute of Biomolecular Medicine, Department of Medicine, NYU School of Medicine, New York 10016, USA
    Nature 397:271-4. 1999
    ..These properties implicate PERK in a signalling pathway that attenuates protein translation in response to ER stress...
  80. pmc The human disease network
    Kwang Il Goh
    Center for Complex Network Research and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA
    Proc Natl Acad Sci U S A 104:8685-90. 2007
    ..A selection-based model explains the observed difference between essential and disease genes and also suggests that diseases caused by somatic mutations should not be peripheral, a prediction we confirm for cancer genes...
  81. ncbi Smad transcription factors
    Joan Massague
    Cancer Biology and Genetics Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Genes Dev 19:2783-810. 2005
    ..Our growing understanding of TGFbeta signaling through the Smad pathway provides general principles for how animal cells translate complex inputs into concrete behavior...
  82. ncbi The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis
    P H Maxwell
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nature 399:271-5. 1999
    ..Thus, constitutive HIF-1 activation may underlie the angiogenic phenotype of VHL-associated tumours. The pVHL/HIF-1 interaction provides a new focus for understanding cellular oxygen sensing...
  83. pmc Differential chromatin marking of introns and expressed exons by H3K36me3
    Paulina Kolasinska-Zwierz
    The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nat Genet 41:376-81. 2009
    ..We propose that H3K36me3 exon marking in chromatin provides a dynamic link between transcription and splicing...
  84. ncbi Interferon-gamma: an overview of signals, mechanisms and functions
    Kate Schroder
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, Australia
    J Leukoc Biol 75:163-89. 2004
    ..In addition, integration of signaling and response with other cytokines and pathogen-associated molecular patterns, such as tumor necrosis factor-alpha, interleukin-4, type I IFNs, and lipopolysaccharide are discussed...
  85. ncbi Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway
    Masahiro Yamamoto
    Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3 1 Yamada oka, Suita Osaka 565 0871, Japan
    Science 301:640-3. 2003
    ..These findings demonstrate that TRIF is essential for TLR3- and TLR4-mediated signaling pathways facilitating mammalian antiviral host defense...
  86. pmc RNA processing and its regulation: global insights into biological networks
    Donny D Licatalosi
    Howard Hughes Medical Institute, Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10021, USA
    Nat Rev Genet 11:75-87. 2010
    ..Together these are providing new insights into molecular cell biology and disease...
  87. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
    ..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
  88. ncbi MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb
    Changchun Xiao
    The CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA
    Cell 131:146-59. 2007
    ....
  89. doi Nucleosome positioning and gene regulation: advances through genomics
    Cizhong Jiang
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 10:161-72. 2009
    ..A detailed picture is starting to emerge of how diverse factors, including underlying DNA sequences and chromatin remodelling complexes, influence nucleosome positioning...
  90. pmc Mechanisms underlying the resistance to diet-induced obesity in germ-free mice
    Fredrik Backhed
    Center for Genome Sciences and Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 104:979-84. 2007
    ..Together, these findings support the notion that the gut microbiota can influence both sides of the energy balance equation, and underscore the importance of considering our metabolome in a supraorganismal context...
  91. doi Transcriptional control of human p53-regulated genes
    Todd Riley
    The Institute for Advanced Study, Princeton, New Jersey, USA
    Nat Rev Mol Cell Biol 9:402-12. 2008
    ..In addition, we present the most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation...
  92. ncbi Bone morphogenetic proteins
    Di Chen
    School of Medicine and Dentistry, Department of Orthopaedics, University of Rochester, Rochester, NY 14642, USA
    Growth Factors 22:233-41. 2004
    ..A significant advancement about the understanding of in vivo functions of BMP ligands, receptors and signaling molecules has been achieved in recent years...
  93. pmc Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
    Mo Chen
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Nat Rev Mol Cell Biol 10:741-54. 2009
    ..Great progress has been made by studying individual transcripts and through genome-wide approaches, which together provide a better picture of the mechanistic regulation of alternative pre-mRNA splicing...
  94. ncbi Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls
    R J Kaufman
    Department of Biological Chemistry and Howard Hughes Medical Institute, The University of Michigan Medical Center, Ann Arbor, Michigan 48109 0650 USA
    Genes Dev 13:1211-33. 1999
  95. doi Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm
    Bernike Kalverda
    Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Cell 140:360-71. 2010
    ..Thus, nucleoporins stimulate developmental and cell-cycle gene expression away from the NPC by interacting with these genes inside the nucleoplasm...
  96. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
    ..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
  97. pmc Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
    Esti Yeger-Lotem
    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nat Genet 41:316-23. 2009
    ..Bridging these data and data from mRNA profiling provided functional explanations for many of these genes and identified previously unknown relations between alpha-synuclein toxicity and basic cellular pathways...
  98. ncbi Requirement for glycogen synthase kinase-3beta in cell survival and NF-kappaB activation
    K P Hoeflich
    Ontario Cancer Institute Princess Margaret Hospital, Toronto, Canada
    Nature 406:86-90. 2000
    ..Thus, GSK-3beta facilitates NF-kappaB function...
  99. pmc Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
    Sami Kilpinen
    Medical Biotechnology, VTT Technical Research Centre and University of Turku, Itäinen Pitkäkatu 4C, Turku, Finland
    Genome Biol 9:R139. 2008
    ..This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available from the GeneSapiens website...
  100. pmc MicroRNA-125b is a novel negative regulator of p53
    Minh T N Le
    Computation and Systems Biology, Singapore Massachusetts Institute of Technology Alliance, Singapore
    Genes Dev 23:862-76. 2009
    ..Together, our study demonstrates that miR-125b is an important negative regulator of p53 and p53-induced apoptosis during development and during the stress response...
  101. pmc MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
    John Tsang
    Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 26:753-67. 2007
    ..Our results strongly suggest that coordinated transcriptional and miRNA-mediated regulation is a recurrent motif to enhance the robustness of gene regulation in mammalian genomes...

Research Grants67

  1. REGULATION OF IRON METABOLISM GENES IN EUKARYOTES
    WILLIAM WALDEN; Fiscal Year: 2001
    ..Successful completion of these studies will provide significant insight towards our understanding of nutrient regulated gene expression. ..
  2. CFTR Biogenesis and Function in Epithelia
    Zsuzsa Bebok; Fiscal Year: 2010
    ..These studies will provide novel information regarding the role of the UPR on gene expression regulation and how mRNA structure may contribute to the pathogenesis of genetic disorders...
  3. CFTR Biogenesis and Function in Epithelia
    Zsuzsanna Bebok; Fiscal Year: 2009
    ..These studies will provide novel information regarding the role of the UPR on gene expression regulation and how mRNA structure may contribute to the pathogenesis of genetic disorders...
  4. Role of MRG15 in Chromatin Changes During Cell Senescence and In Vivo Aging
    Olivia M Pereira Smith; Fiscal Year: 2010
    ..It is becoming increasingly clear that chromatin remodeling is essential for gene expression regulation and organization of DMA structure to allow for repair of DNA damage...
  5. REGULATION OF GENE EXPRESSION BY RETINOID RECEPTORS
    Christopher Glass; Fiscal Year: 2000
    ..Insights derived from these studies are likely to lead to an improved understanding of the mechanisms by which retinoic acid receptors positively and negatively regulate gene expression. ..
  6. microRNA biogenesis and function in spinal muscular atrophy
    Zissimos Mourelatos; Fiscal Year: 2007
    ..miRNAs have the capacity to regulate numerous genes and they may exert profound effects in gene expression regulation. We have identified a novel RNP, termed microRNP (miRNP), that contains miRNAs, the Argonaute2 protein ..
  7. REGULATION OF GLUTAMATE SYNTHESIS IN BACILLUS SUBTILIS
    ABRAHAM SONENSHEIN; Fiscal Year: 2003
    ....
  8. MONOKINE GENE EXPRESSION/REGULATION IN LUNG INJURY
    Steven Kunkel; Fiscal Year: 2007
    ..Our long term goals are to demonstrate the mechanistic contributions of cytokines, TLR, and dendritic cells to the long term problems of severe sepsis and acute lung injury. ..
  9. Interdisciplinary Training in Virology and Gene Therapy
    Ren Sun; Fiscal Year: 2007
    ..The research interests of our faculty encompass viral entry, viral gene expression regulation, replication of viral genome, cell biology during viral infection, viral particle assembly, viral ..
  10. Fas Ligand Gene Transfer Apoptosis Synovial Fibroblasts
    Haidi Zhang; Fiscal Year: 2004
    ..This project simplifies the current problems of gene delivery, gene target and gene expression regulation in human gene therapy...
  11. REGULATION OF HUMAN CLASS II MHC GENES
    JEREMY BOSS; Fiscal Year: 1993
    ..These ideas will be tested. Results from these studies may lead to the development of novel immune therapies, which will allow the control of antigen presentation and the immune response via the manipulation of class II gene expression...
  12. SRCAP Regulation of CREB and GR-mediated Transcription
    John Chrivia; Fiscal Year: 2005
    ..We propose to determine whether this repression of CREB-mediated transcription occurs through formation of a DBX-SRCAP complex. ..
  13. Regulation of mRNA Decay in Yeast by Puf Proteins
    WENDY OLIVAS; Fiscal Year: 2005
    ..The results of these studies will provide insight into how Puf proteins recognize and regulate mRNA in yeast and other eukaryotes, and into the general principles of 3' UTR control of gene expression. ..