, ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, vol.306, pp.636-640, 2004.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, pp.799-816, 2007. ,
, The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol, vol.9, p.1001046, 2011.
, Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.
The share of human genomic DNA under selection estimated from human-mouse genomic alignments, Cold Spring Harb. Symp. Quant. Biol, vol.68, pp.245-254, 2003. ,
Distribution and intensity of constraint in mammalian genomic sequence, Genome Res, vol.15, pp.901-913, 2005. ,
Local DNA topography correlates with functional noncoding regions of the human genome, Science, vol.324, pp.389-392, 2009. ,
A high-resolution map of human evolutionary constraint using 29 mammals, Nature, vol.478, pp.476-482, 2011. ,
Raising the estimate of functional human sequences, Genome Res, vol.17, pp.1245-1253, 2007. ,
What fraction of the human genome is functional?, Genome Res, vol.21, pp.1769-1776, 2011. ,
Widely distributed noncoding purifying selection in the human genome, Proc. Natl Acad. Sci. USA, vol.104, pp.12410-12415, 2007. ,
ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia, Genome Res, 2012. ,
Measuring reproducibility of highthroughput experiments, Ann. Appl. Stat, vol.5, pp.1752-1779, 2011. ,
GENCODE: The reference human genome annotation for the ENCODE project, Genome Res, 2012. ,
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome, Genome Res, p.111, 2012. ,
Landscape of transcription in human cells, Nature ,
URL : https://hal.archives-ouvertes.fr/hal-01216755
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression, Genome Res, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01205054
The GENCODE pseudogene resource, Genome Biol, vol.13, p.51, 2012. ,
Architecture of the human regulatory network derived from ENCODE data, Nature ,
Subsampling methods for genomic inference, Ann. Appl. Stat, vol.4, pp.1660-1697, 2010. ,
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development, PLoS Genet, vol.7, p.1001290, 2011. ,
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding, Genome Biol, vol.12, p.34, 2011. ,
, ARTICLE RESEARCH
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data, Genome Res, vol.21, pp.447-455, 2011. ,
Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1, Nucleic Acids Res, vol.37, pp.7024-7038, 2009. ,
An expansive human regulatory lexicon encoded in transcription factor footprints, Nature ,
Functional analysis of transcription factor binding sites in human promoters, Genome Biol, vol.13, p.50, 2012. ,
Nuclease hypersensitive sites in chromatin, Annu. Rev. Biochem, vol.57, pp.159-197, 1988. ,
Chromatin remodeling as a guide to transcriptional regulatory networks in mammals, J. Cell. Biochem, vol.88, pp.684-694, 2003. ,
The accessible chromatin landscape of the human genome, Nature ,
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements, Genome Res, p.111, 2012. ,
SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins, Genes Dev, vol.16, pp.919-932, 2002. ,
ZNF274 recruits the histone methyltransferase SETDB1 to the 39 ends of ZNF genes, PLoS ONE, vol.5, p.15082, 2010. ,
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells, Genome Res, vol.21, pp.456-464, 2011. ,
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting, Nature Methods, vol.6, pp.283-289, 2009. ,
Model-based analysis of ChIP-Seq (MACS) ,
, Genome Biol, vol.9, p.137, 2008.
Chromatin modifications and their function, Cell, vol.128, pp.693-705, 2007. ,
The role of chromatin during transcription, Cell, vol.128, pp.707-719, 2007. ,
Predictive chromatin signatures in the mammalian genome, Hum. Mol. Genet, vol.18, pp.195-201, 2009. ,
Charting histone modifications and the functional organization of mammalian genomes, Nature Rev. Genet, vol.12, pp.7-18, 2011. ,
Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, vol.473, pp.43-49, 2011. ,
Discovery and annotation of functional chromatin signatures in the human genome, PLoS Comput. Biol, vol.5, p.1000566, 2009. ,
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells, Nature Biotechnol, vol.27, pp.361-368, 2009. ,
Genome-scale DNA methylation maps of pluripotent and differentiated cells, Nature, vol.454, pp.766-770, 2008. ,
The transcriptional coactivators p300 and CBP are histone acetyltransferases, Cell, vol.87, pp.953-959, 1996. ,
Human DNA methylomes at base resolution show widespread epigenomic differences, Nature, vol.462, pp.315-322, 2009. ,
Gene regulation in the third dimension, Science, vol.319, pp.1793-1794, 2008. ,
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements, Genome Res, vol.16, pp.1299-1309, 2006. ,
My5C: web tools for chromosome conformation capture studies, Nature Methods, vol.6, pp.690-691, 2009. ,
The long-range interaction landscape of gene promoters, Nature ,
An oestrogen-receptor-alpha-bound human chromatin interactome, Nature, vol.462, pp.58-64, 2009. ,
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, vol.148, pp.84-98, 2012. ,
Divergence of transcription factor binding sites across related yeast species, Science, vol.317, pp.815-819, 2007. ,
Tissue-specific transcriptional regulation has diverged significantly between human and mouse, Nature Genet, vol.39, pp.730-732, 2007. ,
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding, Science, vol.328, pp.1036-1040, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01615156
, A map of human genome variation from population-scale sequencing, Nature, vol.467, pp.1061-1073, 2010.
Evolution at two levels in humans and chimpanzees, Science, vol.188, pp.107-116, 1975. ,
Analysis of variation at transcription factor binding sites in Drosophila and humans, Genome Biol, vol.13, p.49, 2012. ,
Mammalian RNA polymerase II core promoters: insights from genome-wide studies, Nature Rev. Genet, vol.8, pp.424-436, 2007. ,
Modeling gene expression using chromatin features in various cellular contexts, Genome Biol, vol.13, p.53, 2012. ,
Reciprocal intronic and exonic histone modification regions in humans, Nature Struct. Mol. Biol, vol.17, pp.1495-1499, 2010. ,
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs, Genome Res, 2012. ,
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, PLoS Genet, vol.4, p.1000138, 2008. ,
Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism, Nucleic Acids Res, vol.16, pp.6677-6690, 1988. ,
Dynamic regulation of nucleosome positioning in the human genome, Cell, vol.132, pp.887-898, 2008. ,
Determinants of nucleosome organization in primary human cells, Nature, vol.474, pp.516-520, 2011. ,
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3, Genome Biol, vol.13, p.52, 2012. ,
Classification of human genomic regions based on experimentallydetermined binding sites of more than 100 transcription-related factors, Genome Biol, vol.13, p.48, 2012. ,
Unsupervised pattern discovery in human chromatin structure through genomic segmentation, Nature Methods, vol.9, pp.473-476, 2012. ,
RNA maps reveal new RNA classes and a possible function for pervasive transcription, Science, vol.316, pp.1484-1488, 2007. ,
Transcription initiation platforms and GTF recruitment at tissuespecific enhancers and promoters, Nature Struct. Mol. Biol, vol.18, pp.956-963, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00609674
GREAT improves functional interpretation of cis-regulatory regions, Nature Biotechnol, vol.28, pp.495-501, 2010. ,
AlleleSeq: analysis of allele-specific expression and binding in a network framework, Mol. Syst. Biol, vol.7, p.522, 2011. ,
Annotation of functional variation in personal genomes using RegulomeDB, Genome Res, 2012. ,
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proc. Natl Acad. Sci. USA, vol.106, pp.9362-9367, 2009. ,
Linking disease associations with regulatory information in the human genome, Genome Res, 2012. ,
Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4, PLoS Genet, vol.3, p.58, 2007. ,
Personal and population genomics of human regulatory variation, Genome Res, 2012. ,
9p21 DNA variants associated with coronary artery disease impair interferon-c signalling response, Nature, vol.470, pp.264-268, 2011. ,
Understanding transcriptional regulation by integrative analysis of transcription factor binding data, Genome Res, p.111, 2012. ,
Complete Khoisan and Bantu genomes from southern Africa, Nature, vol.463, pp.943-947, 2010. ,
, RIKEN Omics Science Center, RIKEN Yokohama Institute, pp.1-7
29 Division of Biology, p.30 ,
, Biological Sciences III, p.31, 2218.
, USA. 32 Department of Biochemistry and Molecular Pharmacology, Genome Technology Branch, vol.5625, p.33, 20892.
, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St CPZN 8400, National Institutes of Health, vol.31, pp.20892-9307, 2152.
, North Carolina 27710, USA. 37 National Human Genome Research Institute, Pediatrics, Division of Medical Genetics, vol.5625, p.38
3380 Central Expressway, p.39 ,
, Departament de
, 40 Department of Genome Sciences, Box 355065, and Department of
, Division of Oncology, Medicine, vol.358081, p.41
, Campus Box, vol.7260, p.120, 1200.
, Mason Farm Road, 3010 Genetic Medicine Building, p.44
, C/Baldiri Reixac, vol.4, p.45
3380 Central Expressway, p.46 ,
, Genopode Building, p.47
, Genome Institute of Singapore, 60 Biopolis Street, p.49, 138672.
, rue Michel-Servet, vol.1, p.50, 1211.
North Carolina 27599-7264, USA. 51 Department of Biostatistics, Gillings School of Global Public Health, p.408 ,
North Carolina 27599-7445, USA. 52 Center for Advanced Computing Research, 94305-4065, USA. 54 DOE Joint Genome Institute, p.55 ,
, One Cyclotron Road, p.56
, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain. 57 School of Life Sciences, p.100084
Institute for Computational Biomedicine, vol.140, p.59 ,
, Missouri 63130, USA. 60 Department of Genetics, p.61, 1301.
, USA. 63 Department of Molecular, Cellular, and Developmental Biology, 451 Health Sciences Drive, vol.95616, p.64
, 65 Biochemistry and Molecular Biology, Biological Chemistry and Molecular Pharmacology, vol.67, 1501.
, 68 Department of Cellular and Structural Biology, Children's Cancer Research Institute-UTHSCSA, Mail code 7784-7703 Floyd Curl Dr, Genetics, p.69
, Im Neuenheimer Feld, vol.230, p.71
, Division of Medical Genetics, vol.357720
, USA (Q.L.); Department of Biostatistics and Bioinformatics and the Institute for, USA (R.F.L.); Department of Cell Biology and Molecular Genetics, vol.90095
,
,
East California Boulevard, 1200. ,
, J.F, vol.169857
, Biomedical Sciences (BMS) Graduate Program, p.513
HSE-1285, USA (S.L.P ,
, ); Department of Machine Learning, NEC Laboratories America, 4 Independence Way, vol.95039
, Paris Cedex, vol.05
, Cancer Research UK
, , vol.6
, Center for Bioinformatics and Computational Biology, vol.3720, p.3115
, Life Surge Building, vol.296