Absence of canonical marks of active chromatin in developmentally regulated genes

Nature Genetics

Volumn 47, Issue 10, 2015, Pages 1158-1167

  Pérez Lluch, Sílvia ^a,b,c   Blanco, Enrique ^a,c   Tilgner, Hagen ^a,b,e   Curado, Joao ^a,b,d   Ruiz Romero, Marina ^c   Corominas, Montserrat ^c   Guigó, Roderic ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

^d UNIVERSITY OF PORTO   (Portugal)

^e STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTION FACTOR; CHROMATIN; HISTONE;

ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; CHROMATIN; CONTROLLED STUDY; DROSOPHILA; FEMALE; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENETIC STABILITY; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HISTONE MODIFICATION; IMAGINAL DISC; INSECT DEVELOPMENT; MALE; MAMMAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; WORM; ANIMAL; CHROMATIN IMMUNOPRECIPITATION; HUMAN; METABOLISM; POLYMERASE CHAIN REACTION; RNA PROCESSING;

ALTERNATIVE SPLICING; ANIMALS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HISTONES; HUMANS; POLYMERASE CHAIN REACTION; RNA PROCESSING, POST-TRANSCRIPTIONAL; TRANSCRIPTION, GENETIC;

EID: 84942983931     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3381     Document Type: Article

References (67)

1. Li B., Carey M., & Workman J.L. The role of chromatin during transcription. Cell 128, 707-719 (2007
2. Black J.C., Van Rechem C., & Whetstine J.R. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol. Cell 48, 491-507 (2012
3. Wagner E.J., & Carpenter P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell Biol. 13, 115-126 (2012
4. Dong X., et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 13, R53 (2012
5. Karlić, R., Chung H.R., Lasserre J., Vlahovicek K., & Vingron M. Histone modification levels are predictive for gene expression. Proc. Natl. Acad. Sci. USA 107, 2926-2931 (2010
6. Nègre N., et al. A cis-regulatory map of the drosophila genome. Nature 471, 527-531 (2011
7. Hödl M., & Basler K. Transcription in the absence of histone H3.2 and H3K4 methylation. Curr. Biol. 22, 2253-2257 (2012
8. Chen K., et al. A global change in RNA polymerase II pausing during the drosophila midblastula transition. eLife 2, e00861 (2013
9. Zhang H., Gao L., Anandhakumar J., & Gross D.S. Uncoupling transcription from covalent histone modification. PLoS Genet. 10, e1004202 (2014
10. Graveley B.R., et al. The developmental transcriptome of drosophila melanogaster. Nature 471, 473-479 (2011
11. Roy S., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010
12. Tweedie S., et al. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37, D555-D559 (2009
13. Spencer W.C., et al. A spatial and temporal map of C. elegans gene expression. Genome Res. 21, 325-341 (2011
14. Kundaje A., et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015
15. Yue F., et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515, 355-364 (2014
16. Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007
17. Pérez-Lluch S., et al. Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. Nucleic Acids Res. 39, 4628-4639 (2011
18. Teves S.S., & Henikoff S. Transcription-generated torsional stress destabilizes nucleosomes. Nat. Struct. Mol. Biol. 21, 88-94 (2014
19. Luque C.M., & Milan M. Growth control in the proliferative region of the drosophila eye-head primordium: the elbow-noc gene complex. Dev. Biol. 301, 327-339 (2007
20. Weihe U., Dorfman R., Wernet M.F., Cohen S.M., & Milan M. Proximodistal subdivision of drosophila legs and wings: the elbow-no ocelli gene complex. Development 131, 767-774 (2004
21. Ng M., Diaz-Benjumea F.J., & Cohen S.M. Nubbin encodes a POU-domain protein required for proximal-distal patterning in the drosophila wing. Development 121, 589-599 (1995
22. Beltran S., Angulo M., Pignatelli M., Serras F., & Corominas M. Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. Genome Biol. 8, R67 (2007
23. Beltran S., et al. Transcriptional network controlled by the trithorax-group gene ash2 in drosophila melanogaster. Proc. Natl. Acad. Sci. USA 100, 3293-3298 (2003
24. Zeitlinger J., & Stark A. Developmental gene regulation in the era of genomics. Dev. Biol. 339, 230-239 (2010
25. Stark A., et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232 (2007
26. Carninci P., et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626-635 (2006
27. Gaertner B., et al. Poised RNA polymerase II changes over developmental time and prepares genes for future expression. Cell Rep. 2, 1670-1683 (2012
28. Hoskins R.A., et al. Genome-wide analysis of promoter architecture in drosophila melanogaster. Genome Res. 21, 182-192 (2011
29. Rach E.A., Yuan H.Y., Majoros W.H., Tomancak P., & Ohler U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the drosophila genome. Genome Biol. 10, R73 (2009
30. Ni T., et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods 7, 521-527 (2010
31. Lenhard B., Sandelin A., & Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 13, 233-245 (2012
32. Teves S.S., & Henikoff S. The heat shock response: a case study of chromatin dynamics in gene regulation. Biochem. Cell Biol. 91, 42-48 (2013
33. Juven-Gershon T., & Kadonaga J.T. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev. Biol. 339, 225-229 (2010
34. Farley E., & Levine M. HOT DNAs: a novel class of developmental enhancers. Genes Dev. 26, 873-876 (2012
35. Gerstein M.B., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787 (2010
36. Froldi F., et al. The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells. Genes Dev. 29, 129-143 (2015
37. Georlette D., et al. Genomic profiling and expression studies reveal both positive and negative activities for the drosophila Myb MuvB/dREAM complex in proliferating cells. Genes Dev. 21, 2880-2896 (2007
38. Pennington K.L., Marr S.K., Chirn G.W., & Marr M.T. II. Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription. Proc. Natl. Acad. Sci. USA 110, 7678-7683 (2013
39. Piñeyro D., Blanch M., Badal M., Kosoy A., & Bernues J. GAGA factor repression of transcription is a rare event but the negative regulation of Trl is conserved in drosophila species. Biochim. Biophys. Acta 1829, 1056-1065 (2013
40. Turkel N., et al. The BTB-zinc finger transcription factor Abrupt acts as an epithelial oncogene in drosophila melanogaster through maintaining a progenitor-like cell state. PLoS Genet. 9, e1003627 (2013
41. Filion G.J., et al. Systematic protein location mapping reveals five principal chromatin types in drosophila cells. Cell 143, 212-224 (2010
42. Kharchenko P.V., et al. Comprehensive analysis of the chromatin landscape in drosophila melanogaster. Nature 471, 480-485 (2011
43. Ho J.W., et al. Comparative analysis of metazoan chromatin organization. Nature 512, 449-452 (2014
44. Sexton T., et al. Three-dimensional folding and functional organization principles of the drosophila genome. Cell 148, 458-472 (2012
45. Guelen L., et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948-951 (2008
46. Van Bemmel J.G., et al. The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the drosophila genome. PLoS ONE 5, e15013 (2010
47. Schwartz S., Meshorer E., & Ast G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16, 990-995 (2009
48. Tilgner H., et al. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 16, 996-1001 (2009
49. de Almeida S.F., et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat. Struct. Mol. Biol. 18, 977-983 (2011
50. Luco R.F., et al. Regulation of alternative splicing by histone modifications. Science 327, 996-1000 (2010
51. Sims R.J. III, et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell 28, 665-676 (2007
52. Delest A., Sexton T., & Cavalli G. Polycomb: a paradigm for genome organization from one to three dimensions. Curr. Opin. Cell Biol. 24, 405-414 (2012
53. Espada J., & Esteller M. DNA methylation and the functional organization of the nuclear compartment. Semin. Cell Dev. Biol. 21, 238-246 (2010
54. Gan Q., et al. Dynamic regulation of alternative splicing and chromatin structure in drosophila gonads revealed by RNA-seq. Cell Res. 20, 763-783 (2010
55. Ciabrelli F., & Cavalli G. Chromatin-driven behavior of topologically associating domains. J. Mol. Biol. 427, 608-625 (2015
56. Karolchik D., et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36, D773-D779 (2008
57. Xu T., & Rubin G.M. Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 117, 1223-1237 (1993
58. Cagan R.L., Kramer H., Hart A.C., & Zipursky S.L. The bride of sevenless and sevenless interaction: internalization of a transmembrane ligand. Cell 69, 393-399 (1992
59. Derrien T., et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012
60. Montgomery S.B., et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777 (2010
61. Blanco E., Messeguer X., Smith T.F., & Guigo R. Transcription factor map alignment of promoter regions. PLoS Comput. Biol. 2, e49 (2006
62. 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
63. Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 9, 326-332 (2008
64. Siepel A., et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005
65. Zhu L.J., et al. FlyFactorSurvey: a database of drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 39, D111-D117 (2011
66. Ernst J., & Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216 (2012
67. Cherbas L., et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. 21, 301-314 (2011