Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo (original) (raw)

• Gross, D.S. & Garrard, W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988).
  Article CAS PubMed Google Scholar
• Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).
  CAS PubMed PubMed Central Google Scholar
• Maurano, M.T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Degner, J.F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390–394 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Palmiter, R.D. & Brinster, R.L. Germ-line transformation of mice. Annu. Rev. Genet. 20, 465–499 (1986).
  Article CAS PubMed PubMed Central Google Scholar
• Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Peterson, K.R. & Stamatoyannopoulos, G. Role of gene order in developmental control of human γ- and β-globin gene expression. Mol. Cell. Biol. 13, 4836–4843 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Thanos, D. & Maniatis, T. Virus induction of human IFN β gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100 (1995).
  Article CAS PubMed Google Scholar
• Archer, T.K., Lefebvre, P., Wolford, R.G. & Hager, G.L. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255, 1573–1576 (1992).
  Article CAS PubMed Google Scholar
• Mendenhall, E.M. et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat. Biotechnol. 31, 1133–1136 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Aalfs, J.D. & Kingston, R.E. What does 'chromatin remodeling' mean? Trends Biochem. Sci. 25, 548–555 (2000).
  Article CAS PubMed Google Scholar
• Ronald, J. et al. Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res. 15, 284–291 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Ni, Y., Hall, A.W., Battenhouse, A. & Iyer, V.R. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet. 13, 46 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Knight, J.C., Keating, B.J., Rockett, K.A. & Kwiatkowski, D.P. In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat. Genet. 33, 469–475 (2003).
  Article CAS PubMed Google Scholar
• McDaniell, R. et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328, 235–239 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Kasowski, M. et al. Variation in transcription factor binding among humans. Science 328, 232–235 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Maurano, M.T., Wang, H., Kutyavin, T. & Stamatoyannopoulos, J.A. Widespread site-dependent buffering of human regulatory polymorphism. PLoS Genet. 8, e1002599 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Kilpinen, H. et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342, 744–747 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Reddy, T.E. et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 22, 860–869 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• McVicker, G. et al. Identification of genetic variants that affect histone modifications in human cells. Science 342, 747–749 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article PubMed PubMed Central Google Scholar
• ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
• Heap, G.A. et al. Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum. Mol. Genet. 19, 122–134 (2010).
  Article CAS PubMed Google Scholar
• Stergachis, A.B. et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342, 1367–1372 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, K. et al. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat. Methods 6, 613–618 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Henikoff, S. & Shilatifard, A. Histone modification: cause or cog? Trends Genet. 27, 389–396 (2011).
  Article CAS PubMed Google Scholar
• Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Spivakov, M. et al. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 13, R49 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Biddie, S.C. et al. Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. Mol. Cell 43, 145–155 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720–1723 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Zhao, Y. & Stormo, G.D. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol. 29, 480–483 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Rohs, R. et al. The role of DNA shape in protein-DNA recognition. Nature 461, 1248–1253 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Meijsing, S.H. et al. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324, 407–410 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327–339 (2013).
  Article CAS PubMed Google Scholar
• Lee, J.-H. et al. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 5, e1000718 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Ding, J. et al. Gene expression in skin and lymphoblastoid cells: refined statistical method reveals extensive overlap in _cis_-eQTL signals. Am. J. Hum. Genet. 87, 779–789 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Price, A.L. et al. Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet. 7, e1001317 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Grundberg, E. et al. Mapping _cis_- and _trans_-regulatory effects across multiple tissues in twins. Nat. Genet. 44, 1084–1089 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Flutre, T., Wen, X., Pritchard, J. & Stephens, M. A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet. 9, e1003486 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Veyrieras, J.-B. et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4, e1000214 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264–268 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• John, S. et al. Genome-scale mapping of DNase I hypersensitivity. Curr. Protoc. Mol. Biol. Chapter 27, Unit 21.27 (2013).
• Wang, H. et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 22, 1680–1688 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
  Article PubMed PubMed Central Google Scholar
• Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919–1920 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  CAS PubMed PubMed Central Google Scholar
• Lazarovici, A. et al. Probing DNA shape and methylation state on a genomic scale with DNase I. Proc. Natl. Acad. Sci. USA 110, 6376–6381 (2013).
  Article PubMed PubMed Central Google Scholar
• 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
• Le Novère, N. MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17, 1226–1227 (2001).
  Article PubMed Google Scholar
• Matys, V. et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108–D110 (2006).
  Article CAS PubMed Google Scholar
• Portales-Casamar, E. et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105–D110 (2010).
  Article CAS PubMed Google Scholar
• Newburger, D.E. & Bulyk, M.L. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 37, D77–D82 (2009).
  Article CAS PubMed Google Scholar
• Grant, C.E., Bailey, T.L. & Noble, W.S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Gupta, S., Stamatoyannopoulos, J.A., Bailey, T.L. & Noble, W.S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Galas, D.J. & Schmitz, A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157–3170 (1978).
  Article CAS PubMed PubMed Central Google Scholar
• Sing, T., Sander, O., Beerenwinkel, N. & Lengauer, T. ROCR: visualizing classifier performance in R. Bioinformatics 21, 3940–3941 (2005).
  Article CAS PubMed Google Scholar
• Cooper, G.M. et al. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 14, 539–548 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310–315 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Gulko, B., Hubisz, M.J., Gronau, I. & Siepel, A. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat. Genet. 47, 276–283 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, D. et al. A method to predict the impact of regulatory variants from DNA sequence. Nat. Genet. 47, 955–961 (2015).
  Article CAS PubMed PubMed Central Google Scholar