Nucleosome organization in the vicinity of transcription factor binding sites in the human genome

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Nie, Yumin ^a   Cheng, Xiangfei ^a   Chen, Jiao ^a   Sun, Xiao ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

Clustering; Nucleosome occupancy; Transcription factor binding site

Indexed keywords

ABF1 PROTEIN; BCL6B PROTEIN; DEOXYRIBONUCLEASE I; HEPATOCYTE NUCLEAR FACTOR 4; REST PROTEIN; RNA POLYMERASE; SERUM RESPONSE FACTOR; TEL 2 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR REL; UNCLASSIFIED DRUG; DNA; NUCLEOSOME; PROTEIN BINDING;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CELL COMPOSITION; CELL LOSS; CELLULAR DISTRIBUTION; CHROMATIN STRUCTURE; DNA BINDING MOTIF; DNA FLANKING REGION; DNA SEQUENCE; GENE EXPRESSION REGULATION; HUMAN; HUMAN GENOME; IN VIVO STUDY; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PROMOTER REGION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; CHEMISTRY; GENETICS; K562 CELL LINE; METABOLISM;

BINDING SITES; DNA; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; K562 CELLS; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84902706391     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-493     Document Type: Article

References (44)

1. Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 2012, 13(4):233-245.
2. van Bakel H. Interactions of transcription factors with chromatin. Subcell Biochem 2011, 52:223-259.
3. Pan Y, Tsai CJ, Ma B, Nussinov R. Mechanisms of transcription factor selectivity. Trends Genet 2010, 26(2):75-83.
4. Iyer VR. Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol 2012, 22(5):250-256.
5. Bai L, Morozov AV. Gene regulation by nucleosome positioning. Trends Genet 2010, 26(11):476-483.
6. Wang X, Bai L, Bryant GO, Ptashne M. Nucleosomes and the accessibility problem. Trends Genet 2011, 27(12):487-492.
7. He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS. Nucleosome dynamics define transcriptional enhancers. Nat Genet 2010, 42(4):343-347.
8. Segal E, Widom J. What controls nucleosome positions?. Trends Genet 2009, 25(8):335-343.
9. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887-898.
10. Hughes AL, Jin Y, Rando OJ, Struhl K. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 2012, 48(1):5-15.
11. Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 2008, 4(7):e1000138.
12. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 2009, 19(1):24-32.
13. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature 2011, 474(7352):516-520.
14. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012, 22(9):1798-1812.
15. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA. DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 2008, 36(Database issue):D88-92.
16. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009, 10(4):252-263.
17. Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR. High nucleosome occupancy is encoded at human regulatory sequences. PLoS One 2010, 5(2):e9129.
18. Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res 2010, 20(4):526-536.
19. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 2011, 21(3):447-455.
20. Struhl K, Segal E. Determinants of nucleosome positioning. Nat Struct Mol Biol 2013, 20(3):267-273.
21. Huebert DJ, Kuan PF, Keles S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012, 32(9):1645-1653.
22. Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2006, 7:29-59.
23. Brogaard K, Xi L, Wang JP, Widom J. A map of nucleosome positions in yeast at base-pair resolution. Nature 2012, 486(7404):496-501.
24. Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012, 8(6):e1002771.
25. Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA. DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes. Mol Cell 2012, 47(2):183-192.
26. The UniProt Consortium Reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Res 2012, 40(Database issue):D71-75. The UniProt Consortium.
27. Burns LG, Peterson CL. The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol Cell Biol 1997, 17(8):4811-4819.
28. Bai L, Charvin G, Siggia ED, Cross FR. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 2010, 18(4):544-555.
29. Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res 2012, 22(9):1735-1747.
30. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007, 39(10):1235-1244.
31. Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, Green MR. ChIPpeakAnno: a bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237.
32. Yanez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res 2012, 22(10):2018-2030.
33. Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011, 25(21):2227-2241.
34. Angelov D, Lenouvel F, Hans F, Muller CW, Bouvet P, Bednar J, Moudrianakis EN, Cadet J, Dimitrov S. The histone octamer is invisible when NF-kappaB binds to the nucleosome. J Biol Chem 2004, 279(41):42374-42382.
35. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842.
36. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137.
37. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25.
38. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, et al. The accessible chromatin landscape of the human genome. Nature 2012, 489(7414):75-82.
39. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858.
40. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24(21):2537-2538.
41. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, et al. Landscape of transcription in human cells. Nature 2012, 489(7414):101-108.
42. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33(Database issue):D501-504.
43. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515.
44. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.