Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays

After finishing a human genome reference sequence in 2002, the genomics community has turned to the task of interpreting it. A primary focus is to identify and characterize not only protein-coding genes, but all functional elements in the genome. The effort includes both individual investigators and large-scale projects like the Encyclopedia of DNA Elements (ENCODE) project. As part of the ENCODE project, several groups have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. ChIP-seq experiments have also been used to discover transcription factor binding sites and map histone modifications. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide an overview of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of regulatory elements distributed throughout the genome.

[1]  Myong-Hee Sung,et al.  Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. , 2011, Molecular cell.

[2]  Ryan Dale,et al.  Cell type specificity of chromatin organization mediated by CTCF and cohesin , 2010, Proceedings of the National Academy of Sciences.

[3]  Michael A. Beer,et al.  Discriminative prediction of mammalian enhancers from DNA sequence. , 2011, Genome research.

[4]  Wyeth W. Wasserman,et al.  ConSite: web-based prediction of regulatory elements using cross-species comparison , 2004, Nucleic Acids Res..

[5]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[6]  Joseph K. Pickrell,et al.  DNaseI sensitivity QTLs are a major determinant of human expression variation , 2011, Nature.

[7]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[8]  P. Fraser,et al.  Nuclear organization of the genome and the potential for gene regulation , 2007, Nature.

[9]  P. Park.  ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[10]  S. Elgin,et al.  Heterochromatin and gene regulation in Drosophila. , 1996, Current opinion in genetics & development.

[11]  A. Dean.  On a chromosome far, far away: LCRs and gene expression. , 2006, Trends in genetics : TIG.

[12]  Nathan C. Sheffield,et al.  Predicting cell-type–specific gene expression from regions of open chromatin , 2012, Genome research.

[13]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[14]  R. Altman,et al.  Cooperative transcription factor associations discovered using regulatory variation , 2011, Proceedings of the National Academy of Sciences.

[15]  E. Birney,et al.  High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. , 2011, Genome research.

[16]  H. Weintraub,et al.  Isolation of a subclass of nuclear proteins responsible for conferring a DNase I-sensitive structure on globin chromatin. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[18]  M. Guyer,et al.  Charting a course for genomic medicine from base pairs to bedside , 2011, Nature.

[19]  A. West,et al.  Insulators: many functions, many mechanisms. , 2002, Genes & development.

[20]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[21]  E. Segal,et al.  Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.

[22]  M. Groudine,et al.  Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.

[23]  P. Collas.  The Current State of Chromatin Immunoprecipitation , 2010, Molecular biotechnology.

[24]  Michael P. Snyder,et al.  A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1 , 2011, PLoS genetics.

[25]  Nathaniel D Heintzman,et al.  Finding distal regulatory elements in the human genome. , 2009, Current opinion in genetics & development.

[26]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[27]  Ting Wang,et al.  ENCODE whole-genome data in the UCSC Genome Browser , 2009, Nucleic Acids Res..

[28]  Stephen C. J. Parker,et al.  Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection , 2012, PLoS genetics.

[29]  Dustin E. Schones,et al.  Genome-wide approaches to studying chromatin modifications , 2008, Nature Reviews Genetics.

[30]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[31]  K. Zhao,et al.  3C-based methods to detect long-range chromatin interactions , 2011, Frontiers in Biology.

[32]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[33]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[34]  J. Claverie.  Fewer Genes, More Noncoding RNA , 2005, Science.

[35]  M. Groudine,et al.  Controlling the double helix , 2003, Nature.

[36]  M. Robinson,et al.  Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA , 2012, Genome research.

[37]  R. Flavell,et al.  Interchromosomal associations between alternatively expressed loci , 2005, Nature.

[38]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[39]  B. Pugh,et al.  Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.

[40]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[41]  Michael A. Beer,et al.  Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. , 2008, Genome research.

[42]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[43]  Jacob F. Degner,et al.  Sequence and Chromatin Accessibility Data Accurate Inference of Transcription Factor Binding from Dna Material Supplemental Open Access , 2022 .

[44]  C. Wu,et al.  Tissue-specific exposure of chromatin structure at the 5' terminus of the rat preproinsulin II gene. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[45]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[46]  Richard M Myers,et al.  Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. , 2009, Genome research.

[47]  Raymond K. Auerbach,et al.  Mapping accessible chromatin regions using Sono-Seq , 2009, Proceedings of the National Academy of Sciences.

[48]  Job Dekker,et al.  The three 'C' s of chromosome conformation capture: controls, controls, controls , 2005, Nature Methods.

[49]  Enrique Blanco,et al.  Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing , 2011, Nucleic acids research.

[50]  Karen L. Mohlke,et al.  A map of open chromatin in human pancreatic islets , 2010, Nature Genetics.

[51]  Giacomo Cavalli,et al.  Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation. , 2009, Seminars in cell & developmental biology.

[52]  Robert E. Kingston,et al.  Mechanisms of Polycomb gene silencing: knowns and unknowns , 2009, Nature Reviews Molecular Cell Biology.

[53]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[54]  Robert-Jan Palstra,et al.  HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. , 2012, Genome research.

[55]  Albert J. Vilella,et al.  A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.

[56]  Peter J. Park,et al.  An assessment of histone-modification antibody quality , 2010, Nature Structural &Molecular Biology.

[57]  Carl Wu.  The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I , 1980, Nature.

[58]  Nathan C. Sheffield,et al.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. , 2011, Genome research.

[59]  Michael A. Beer,et al.  Predicting Gene Expression from Sequence , 2004, Cell.

[60]  Chunhui Hou,et al.  CTCF-dependent enhancer-blocking by alternative chromatin loop formation , 2008, Proceedings of the National Academy of Sciences.

[61]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[62]  Manolis Kellis,et al.  Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.

[63]  Michael R. Green,et al.  Transcriptional regulatory elements in the human genome. , 2006, Annual review of genomics and human genetics.

[64]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[65]  Peter A. Jones,et al.  OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes , 2011, Proceedings of the National Academy of Sciences.

[66]  M. Gerstein,et al.  Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line , 2012, PLoS genetics.

[67]  G. Crawford,et al.  DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. , 2010, Cold Spring Harbor protocols.

[68]  M. Gerstein,et al.  Annotating non-coding regions of the genome , 2010, Nature Reviews Genetics.

[69]  Lei Guo,et al.  Predicting Gene Expression from Sequence: A Reexamination , 2007, PLoS Comput. Biol..

[70]  D. S. Gross,et al.  Nuclease hypersensitive sites in chromatin. , 1988, Annual review of biochemistry.

[71]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[72]  Raymond K. Auerbach,et al.  A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.

[73]  H. Tanabe,et al.  Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. , 2009, Developmental cell.

[74]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[75]  E. Birney,et al.  Allele-specific and heritable chromatin signatures in humans. , 2010, Human molecular genetics.

[76]  Jurg Ott,et al.  Distribution and characterization of regulatory elements in the human genome. , 2002, Genome research.

[77]  S. Ohno,et al.  So much "junk" DNA in our genome. , 1972, Brookhaven symposia in biology.