Noncoding transcription at enhancers: general principles and functional models.
暂无分享,去创建一个
[1] Monika S. Kowalczyk,et al. Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.
[2] E. Furlong,et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development , 2012, Nature Genetics.
[3] Raymond K. Auerbach,et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.
[4] A. Visel,et al. Large-Scale Discovery of Enhancers from Human Heart Tissue , 2011, Nature Genetics.
[5] Wouter de Laat,et al. A Regulatory Archipelago Controls Hox Genes Transcription in Digits , 2011, Cell.
[6] Michael F. Melgar,et al. Discovery of active enhancers through bidirectional expression of short transcripts , 2011, Genome Biology.
[7] Ananda L Roy,et al. Enhancer-promoter communication and transcriptional regulation of Igh. , 2011, Trends in immunology.
[8] J. Andrau,et al. Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity , 2011, Transcription.
[9] S. Spicuglia,et al. H3K4 tri‐methylation provides an epigenetic signature of active enhancers , 2011, The EMBO journal.
[10] Elinore M Mercer,et al. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. , 2011, Immunity.
[11] Eugene Bolotin,et al. The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. , 2011, Molecular cell.
[12] Zhike Lu,et al. Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.
[13] Jie Wang,et al. Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. , 2011, Developmental biology.
[14] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[15] M. Gut,et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters , 2011, Nature Structural &Molecular Biology.
[16] P. Scacheri,et al. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.
[17] J. Rinn,et al. lincRNAs act in the circuitry controlling pluripotency and differentiation , 2011, Nature.
[18] Paulo P. Amaral,et al. The Reality of Pervasive Transcription , 2011, PLoS biology.
[19] Albert E. Almada,et al. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome , 2011, Proceedings of the National Academy of Sciences.
[20] C. Glass,et al. Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.
[21] Ryan A. Flynn,et al. A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.
[22] M. Groudine,et al. Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.
[23] R. Young,et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.
[24] Sohail Malik,et al. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation , 2010, Nature Reviews Genetics.
[25] T. Derrien,et al. Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.
[26] M. Levine. Transcriptional Enhancers in Animal Development and Evolution , 2010, Current Biology.
[27] A. Visel,et al. ChIP-Seq identification of weakly conserved heart enhancers , 2010, Nature Genetics.
[28] David A. Orlando,et al. Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.
[29] J. Rinn,et al. A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.
[30] G. Natoli. Maintaining cell identity through global control of genomic organization. , 2010, Immunity.
[31] D. Taatjes,et al. The human Mediator complex: a versatile, genome-wide regulator of transcription. , 2010, Trends in biochemical sciences.
[32] J. Ragoussis,et al. A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.
[33] T. Hughes,et al. Most “Dark Matter” Transcripts Are Associated With Known Genes , 2010, PLoS biology.
[34] G. Kreiman,et al. Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.
[35] J. Ragoussis,et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.
[36] A. Rudensky,et al. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate , 2010, Nature.
[37] Alexander Stark,et al. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. , 2009, Current opinion in genetics & development.
[38] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[39] E. Liu,et al. An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.
[40] Leighton J. Core,et al. Divergent transcription: A new feature of active promoters , 2009, Cell cycle.
[41] C. Ponting,et al. Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain , 2009, PLoS genetics.
[42] J. Rinn,et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.
[43] Timothy W. Sikorski,et al. The basal initiation machinery: beyond the general transcription factors. , 2009, Current opinion in cell biology.
[44] Nathaniel D. Heintzman,et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.
[45] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[46] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[47] Dustin E. Schones,et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. , 2009, Cell stem cell.
[48] Gene W. Yeo,et al. Divergent Transcription from Active Promoters , 2008, Science.
[49] Leighton J. Core,et al. Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.
[50] Mikkel H. Schierup,et al. RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters , 2008, Science.
[51] T. Shibata,et al. Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs , 2008, Nature.
[52] C. Bonifer,et al. The LPS-Induced Transcriptional Upregulation of the Chicken Lysozyme Locus Involves CTCF Eviction and Noncoding RNA Transcription , 2008, Molecular cell.
[53] Chris P. Ponting,et al. The functional repertoires of metazoan genomes , 2008, Nature Reviews Genetics.
[54] Michael Q. Zhang,et al. Combinatorial patterns of histone acetylations and methylations in the human genome , 2008, Nature Genetics.
[55] J. Andrau,et al. Genome-wide RNA polymerase II: not genes only! , 2008, Trends in biochemical sciences.
[56] C. Glass,et al. Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription , 2008, Nature.
[57] D. Higgs,et al. Long-range regulation of alpha-globin gene expression. , 2008, Advances in genetics.
[58] F. Grosveld,et al. Beta-globin regulation and long-range interactions. , 2008, Advances in genetics.
[59] M. Krangel,et al. Noncoding transcription controls downstream promoters to regulate T‐cell receptor α recombination , 2007, The EMBO journal.
[60] David Haussler,et al. Human Genome Ultraconserved Elements Are Ultraselected , 2007, Science.
[61] Howard Y. Chang,et al. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.
[62] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[63] P. Stadler,et al. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription , 2007, Science.
[64] F. Grosveld,et al. β-Globin Active Chromatin Hub Formation in Differentiating Erythroid Cells and in p45 NF-E2 Knock-out Mice* , 2007, Journal of Biological Chemistry.
[65] V. Iyer,et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.
[66] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.
[67] C. Hertel,et al. A role for noncoding transcription in activation of the yeast PHO5 gene , 2007, Proceedings of the National Academy of Sciences.
[68] C. Ponting,et al. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. , 2007, Genome research.
[69] Nathaniel D. Heintzman,et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.
[70] Douglas R Higgs,et al. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. , 2007, The EMBO journal.
[71] Bing Li,et al. The Role of Chromatin during Transcription , 2007, Cell.
[72] Daniel Chourrout,et al. Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.
[73] K. Struhl. Transcriptional noise and the fidelity of initiation by RNA polymerase II , 2007, Nature Structural &Molecular Biology.
[74] Ivan Ovcharenko,et al. Predicting tissue-specific enhancers in the human genome. , 2006, Genome research.
[75] F. Grosveld,et al. Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. , 2007, The Journal of biological chemistry.
[76] Christopher L. Warren,et al. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. , 2006, Molecular cell.
[77] B. Steensel,et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.
[78] Alan M. Moses,et al. In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.
[79] Brian S. Clark,et al. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. , 2006, Genes & development.
[80] I. Grummt,et al. Intergenic transcripts regulate the epigenetic state of rRNA genes. , 2006, Molecular cell.
[81] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[82] Shyam Prabhakar,et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. , 2005, Genome research.
[83] A. Dean. On a chromosome far, far away: LCRs and gene expression. , 2006, Trends in genetics : TIG.
[84] Fred Winston,et al. in Saccharomyces cerevisiae , 2005 .
[85] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[86] B. Séraphin,et al. Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.
[87] G. Helt,et al. Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.
[88] R. Paro,et al. Intergenic transcription through a polycomb group response element counteracts silencing. , 2005, Genes & development.
[89] E. Schadt,et al. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. , 2005, Trends in genetics : TIG.
[90] D. Tuan,et al. HS2 Enhancer Function Is Blocked by a Transcriptional Terminator Inserted between the Enhancer and the Promoter*[boxs] , 2004, Journal of Biological Chemistry.
[91] Fred Winston,et al. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene , 2004, Nature.
[92] D. Haussler,et al. Ultraconserved Elements in the Human Genome , 2004, Science.
[93] P. Fraser,et al. Antisense intergenic transcription in V(D)J recombination , 2004, Nature Immunology.
[94] Nikolaus Rajewsky,et al. A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer , 2004, Nature Immunology.
[95] M. Antoniou,et al. Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[96] B. Oostra,et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. , 2003, Human molecular genetics.
[97] Jessica Halow,et al. The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. , 2003, Genes & development.
[98] Jon D. McAuliffe,et al. Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.
[99] W. Reith,et al. Chromatin remodeling and extragenic transcription at the MHC class II locus control region , 2003, Nature Immunology.
[100] R. Paro,et al. Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch , 2002, Molecular and Cellular Biology.
[101] W. Bender,et al. Transcription activates repressed domains in the Drosophila bithorax complex. , 2002, Development.
[102] F. Karch,et al. Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. , 2002, Development.
[103] J. Dekker,et al. Capturing Chromosome Conformation , 2002, Science.
[104] C. Allis,et al. Translating the Histone Code , 2001, Science.
[105] P. Fraser,et al. Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. , 2000, Molecular cell.
[106] P. Cook. The organization of replication and transcription. , 1999, Science.
[107] D. Staynov,et al. Intergenic transcription occurs throughout the human IL-4/IL-13 gene cluster. , 1999, Biochemical and biophysical research communications.
[108] D. Kioussis,et al. Hierarchical interactions of control elements determine CD8alpha gene expression in subsets of thymocytes and peripheral T cells. , 1998, Immunity.
[109] G. Orphanides,et al. A Human RNA Polymerase II Complex Containing Factors That Modify Chromatin Structure , 1998, Molecular and Cellular Biology.
[110] J. T. Kadonaga,et al. Going the distance: a current view of enhancer action. , 1998, Science.
[111] C. Glass,et al. Transcription factor-specific requirements for coactivators and their acetyltransferase functions. , 1998, Science.
[112] E. Davidson,et al. Green Fluorescent Protein in the sea urchin: new experimental approaches to transcriptional regulatory analysis in embryos and larvae. , 1997, Development.
[113] H. Ashe,et al. Intergenic transcription and transinduction of the human beta-globin locus. , 1997, Genes & development.
[114] F. Watrin,et al. Deletion of the mouse T-cell receptor beta gene enhancer blocks alphabeta T-cell development. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[115] R. Young,et al. RNA Polymerase II Holoenzyme Contains SWI/SNF Regulators Involved in Chromatin Remodeling , 1996, Cell.
[116] Michael R. Green,et al. Nuclear protein CBP is a coactivator for the transcription factor CREB , 1994, Nature.
[117] Yang Li,et al. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II , 1994, Cell.
[118] Tom Maniatis,et al. Transcriptional activation: A complex puzzle with few easy pieces , 1994, Cell.
[119] Richard A. Young,et al. An RNA polymerase II holoenzyme responsive to activators , 1994, Nature.
[120] F. Watrin,et al. TCR beta and TCR alpha gene enhancers confer tissue‐ and stage‐specificity on V(D)J recombination events. , 1993, The EMBO journal.
[121] D. Tuan,et al. Transcription of the hypersensitive site HS2 enhancer in erythroid cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[122] F. Grosveld,et al. Definition of the minimal requirements within the human beta‐globin gene and the dominant control region for high level expression. , 1990, The EMBO journal.
[123] M. Atchison,et al. Enhancers: mechanisms of action and cell specificity. , 1988, Annual Review of Cell Biology.
[124] R. Treisman,et al. Simian virus 40 enhancer increases number of RNA polymerase II molecules on linked DNA , 1985, Nature.
[125] Robert Tjian,et al. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins , 1985, Nature.
[126] H. Zentgraf,et al. A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA. , 1984, Journal of molecular biology.
[127] J. Banerji,et al. Expression of a β-globin gene is enhanced by remote SV40 DNA sequences , 1981, Cell.
[128] P. Chambon,et al. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. , 1981, Nucleic acids research.
[129] J. Banerji,et al. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. , 1981, Cell.
[130] Carl Wu. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I , 1980, Nature.
[131] M. Birnstiel,et al. More ribosomal spacer sequences from Xenopus laevis. , 1980, Nucleic acids research.
[132] T. Moss,et al. Sequence organization of the spacer DNA in a ribosomal gene unit of Xenopus laevis , 1979, Cell.
[133] N. Morris. Nucleosome structure in Aspergillus nidulans , 1976, Cell.
[134] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.