Citation: | Zhen-Xing Feng, Qian-Zhong Li, Jian-Jun Meng. Modeling the relationship of diverse genomic signatures to gene expression levels with the regulation of long-range enhancer-promoter interactions. Biophysics Reports, 2019, 5(3): 123-132. doi: 10.1007/s41048-019-0089-z |
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-368
|
Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120-124
|
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304:1321-1325
|
Blackwood EM, Kadonaga JT (1998) Going the distance:a current view of enhancer action. Science 281:60-63
|
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, PlajzerFrick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42:806-810
|
Budden DM, Hurley DG, Crampin EJ (2015) Predictive modelling of gene expression from transcriptional regulatory elements. Brief Bioinform 16:616-628
|
Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039-1043
|
Cheng C, Gerstein M (2012) Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 40:553-568
|
Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M (2011) A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol 12:R15
|
Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal R, Lupien M, Markowitz S, Scacheri PC (2013) Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res 24:1-13
|
de Laat W, Duboule D (2013) Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502:499-506
|
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306-1311
|
Everitt BS (2002) Cambridge dictionary of statistics. J Appl Ecol 36:842-843
|
Fan L, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494:497-501
|
Feng ZX, Li QZ (2017) Recognition of long-range enhancerpromoter interactions by adding genomic signatures of segmented regulatory regions. Genomics 109:341-352
|
Feng ZX, Li QZ, Meng JJ (2018) Recognition of the long range enhancer-promoter interactions by further adding DNA structure properties and transcription factor binding motifs in human cell lines. J Theor Biol 445:136-150
|
Garcı á E, Marcos-Gutiérrez C, del Mar Lorente M, Moreno JC, Vidal M (1999) RYBP, a new repressor protein that interacts with components of the mammalian Polycomb complex, and with the transcription factor YY1. EMBO J 18:3404-3418
|
He B, Chen C, Teng L, Tan K (2014) Global view of enhancerpromoter interactome in human cells. Proc Natl Acad Sci USA 111:2191-2199
|
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, AntosiewiczBourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-typespecific gene expression. Nature 459:108-112
|
Huang NE, Lin CH, Lin YS, Yu WC (2003) Modulation of YY1 activity by SAP30. Biochem Biophys Res Commun 306:267-275
|
Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS (2015) HIPPIEa highthroughput identification pipeline for promoter interacting enhancer elements. Bioinformatics 31:1290-1292
|
Karlic ′ R, Chung HR, Lasserre J, Vlahovicek K, Vingron M (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci USA 107:2926-2931
|
Katsuoka F, Motohashi H, Onodera K, Suwabe N, Engel JD, Yamamoto M (2000) One enhancer mediates mafK transcriptional activation in both hematopoietic and cardiac muscle cells. EMBO J 19:2980-2991
|
Kornberg RD (1999) Eukaryotic transcriptional control. Trends Cell Biol 9:M46
|
Krivega I, Dean A (2012) Enhancer and promoter interactionslong distance calls. Curr Opin Genet Dev 22:79-85
|
Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116-120
|
Lee JS, Galvin KM, See RH, Eckner R, Livingston D, Moran E, Shi Y (1995) Relief of YY1 transcriptional repression by adenovirus E1A is mediated by E1A-associated protein p300. Gene Dev 9:1188-1198
|
Li M, Baumeister P, Roy B, Phan T, Foti D, Luo S, Lee AS (2000) ATF6 as a transcription activator of the endoplasmic reticulum stress element:thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1. Mol Cell Biol 20:5096-5106
|
Li J, Moazed D, Gygi SP (2002) Association of the histone methyltransferase Set2 with RNA polymerase Ⅱ plays a role in transcription elongation. J Biol Chem 277:49383-49388
|
Liu L, Zhao WL, Zhou XB (2016) Modeling co-occupancy of transcription factors using chromatin features. Nucleic Acids Res 5:e49
|
Mcleay RC, Lesluyes T, Cuellar Partida G, Bailey TL (2012) Genome-wide in silico prediction of gene expression. Bioinformatics 28:2789-2796
|
Merkenschlager M, Odom DT (2013) CTCF and cohesinlinking gene regulatory elements with their targets. Cell 152:1285-1297
|
Miele A, Dekker J (2008) Long-range chromosomal interactions and gene regulation. Mol BioSyst 4:1046-1057
|
Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM, Hubner NC, Schulz H (2011) RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS ONE 6:e19470
|
Ouyang Z, Zhou Q, Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci USA 106:21521-21526
|
Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G (2013) Enhancers:five essential questions. Nat Rev Genet 14:288-295
|
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665-1680
|
Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R (2015) A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res 43:8694-8712
|
Sanyal A, Lajoie BR, Jain G, Dekker J (2012) The long-range interaction landscape of gene promoters. Nature 489:109-113
|
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-898
|
Shrivastava A, Saleque S, Kalpana GV, Artandi S, Goff SP, Calame K (1993) Inhibition of transcriptional regulator Yin-Yang-1 by association with c-Myc. Science 262:1889-1892
|
Sims RJ, Mandal SS, Reinberg D (2004) Recent highlights of RNApolymerase-Ⅱ-mediated transcription. Curr Opin Cell Biol 16:263-271
|
Smith E, Shilatifard A (2014) Enhancer biology and enhanceropathies. Nat Struct Mol Biol 21:210-219
|
Song CX, He C (2012) Balance of DNA methylation and demethylation in cancer development. Genome Biol 13:173
|
Stigler MS (1989) Francis Galton's account of the invention of correlation. Stat Sci 4:73-79
|
The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816
|
van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W (2012) Robust 4Cseq data analysis to screen for regulatory DNA interactions. Nat Methods 9:969-972
|
Visel A, Rubin EM, Pennacchio LA (2009a) Genomic views of distant-acting enhancers. Nature 461:199-205
|
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA (2009b) ChIP-seq accurately predicts tissuespecific activity of enhancers. Nature 457:854-858
|
Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120-124
|
Whalen S, Truty RM, Pollard KS (2016) Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet 48:488-496
|
Williamson I, Hill RE, Bickmore WA (2011) Enhancers from developmental genetics to the genetics of common human disease. Dev Cell 21:17-19
|
Williamson I, Berlivet S, Eskeland R, Boyle S, Illingworth RS, Paquette D, Dostie J, Bickmore WA (2014) Spatial genome organizationcontrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev 28:2778-2791
|
Yang WM, Yao YL, Seto E (2001) The FK506-binding protein 25 functionally associates with histone deacetylases and with transcription factor YY1. EMBO J 20:4814-4825
|