High-throughput functional testing of ENCODE segmentation predictions

Genome Research

Volumn 24, Issue 10, 2014, Pages 1595-1602

  Kwasnieski, Jamie C ^a   Fiore, Christopher ^a   Chaudhari, Hemangi G ^a   Cohen, Barak A ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; GENOMIC DNA; TRANSCRIPTION FACTOR; HISTONE;

ARTICLE; BINDING SITE; CELL TYPE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA BASE COMPOSITION; EMBRYO; EMBRYONIC STEM CELL; ENHANCER REGION; GENE CONTROL; GENETIC SCREENING; HIGH THROUGHPUT SEQUENCING; HISTONE MODIFICATION; HUMAN; HUMAN CELL; HUMAN GENOME; K562 CELL LINE; NUCLEOTIDE SEQUENCE; PREDICTION; PROMOTER REGION; PROTEIN BINDING; PROTEIN EXPRESSION; REPORTER GENE; BIOLOGICAL MODEL; BIOLOGY; GENE EXPRESSION REGULATION; METABOLISM; PROCEDURES; REGULATORY SEQUENCE; SEQUENCE ANALYSIS; STATISTICAL MODEL;

COMPUTATIONAL BIOLOGY; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION; HISTONES; HUMANS; K562 CELLS; LOGISTIC MODELS; MODELS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, RNA;

EID: 84907516453     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.173518.114     Document Type: Article

References (39)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr 19: 716-723.
2. Arvey A, Agius P, Noble WS, Leslie C. 2012. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res 22: 1723-1734.
3. Bailey TL. 2011. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27: 1653-1659.
4. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE,Wang Z,Wei G, Chepelev I, Zhao K. 2007.High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
5. Bishop EP, Rohs R, Parker SC,West SM, Liu P,Mann RS, Honig B, Tullius TD. 2011. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol 6: 1314-1320.
6. Chantalat S, Depaux A,Hery P, Barral S,Thuret JY, Dimitrov S,Gerard M. 2011. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin. Genome Res 21: 1426-1437.
7. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, et al. 2010. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci 107: 21931-21936.
8. The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
9. The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
10. Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
11. Ernst J, Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9: 215-216.
12. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. 2013. Ensembl 2013. Nucleic Acids Res 41: D48-D55.
13. Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. 2012. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res 22: 2290-2301.
14. Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018.
15. Gupta S, Stamatoyannopolous JA, Bailey TL, Noble WS. 2007. Quantifying similarity between motifs. Genome Res 8: R24.
16. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576-589.
17. Hess J, Angel P, Schorpp-Kistner M. 2004. AP-1 subunits: quarrel and harmony among siblings. J Cell Sci 117: 5965-5973.
18. Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9: 473-476.
19. HoffmanMM, Ernst J,Wilder SP, Kundaje A, Harris RS, LibbrechtM,GiardineB, Ellenbogen PM, Bilmes JA, Birney E, et al. 2013. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res 41: 827-841.
20. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, et al. 2013. DNA-binding specificities of human transcription factors. Cell 152: 327-339.
21. Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. 2013. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23: 800-811.
22. Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. 2012. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci 109: 19498-19503.
23. Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM. 2010. Sequence features that drive human promoter function and tissue specificity. Genome Res 20: 890-898.
24. Lee D, Karchin R, Beer MA. 2011. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res 21: 2167-2180.
25. LeProust EM, Peck BJ, Spirin K, McCuen HB, Moore B, Namsaraev E, Caruthers MH. 2010. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 38: 2522-2540.
26. Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E. 2010. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res 20: 1361-1368.
27. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H et al. 2014. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42: D142-D147.
28. Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG Jr, Kinney JB, et al. 2012. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30: 271-277.
29. Muthukrishnan R, Skalnik DG. 2009. Identification of a minimal cis-element and cognate trans-factor(s) required for induction of Rac2 gene expression during K562 cell differentiation. Gene 440: 63-72.
30. Newburger DE, Bulyk ML. 2009. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37: D77-D82.
31. Ney PA, Sorrentino BP, McDonagh KT, Nienhuis AW. 1990. Tandem AP-1-binding sites within the human b-globin dominant control region function as an inducible enhancer in erythroid cells. Genes Dev 4: 993-1006.
32. Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, et al. 2012.Massively parallel functional dissection ofmammalian enhancers in vivo. Nat Biotechnol 30: 265-270.
33. Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. 2009. The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
34. Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, Segal E. 2012. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 30: 521-530.
35. Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. 2013. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 45: 1021-1028.
36. Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403: 41-45.
37. Struhl K, Segal E. 2013. Determinants of nucleosome positioning. Nat Struct Mol Biol 20: 267-273.
38. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, et al. 2012. The accessible chromatin landscape of the human genome. Nature 489: 75-82.
39. White MA, Myers CA, Corbo JC, Cohen BA. 2013. Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc Natl Acad Sci 110: 11952-11957.