Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

Nature

Volumn 504, Issue 7479, 2013, Pages 306-310

  Zhang, Yubo ^a,g   Wong, Chee Hong ^a   Birnbaum, Ramon Y ^b,f   Li, Guoliang ^c,d   Favaro, Rebecca ^e   Ngan, Chew Yee ^a   Lim, Joanne ^d   Tai, Eunice ^d   Poh, Huay Mei ^d   Wong, Eleanor ^d   Mulawadi, Fabianus Hendriyan ^d   Sung, Wing Kin ^d   Nicolis, Silvia ^e   Ahituv, Nadav ^b   Ruan, Yijun ^c   Wei, Chia Lin ^a,d  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CONNECTICUT   (United States)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

^e UNIVERSITY OF MILANO BICOCCA   (Italy)

^f BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^g NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; RNA POLYMERASE II;

CONNECTIVITY; CYTOLOGY; ENZYME ACTIVITY; GENE EXPRESSION; GENOME; PROTEIN; RNA; RODENT;

ANIMAL CELL; ANTIGEN RECOGNITION; ARTICLE; CELL LINEAGE; CHROMATIN STRUCTURE; CIS TRANS ISOMERISM; CONTROLLED STUDY; EMBRYO; EMBRYONIC STEM CELL; ENHANCER REGION; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENETIC TRANSCRIPTION; GENOME; MOUSE; NEURAL STEM CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION;

ANIMALS; CELL LINE; CELL LINEAGE; CHROMATIN; EMBRYONIC STEM CELLS; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; IN SITU HYBRIDIZATION, FLUORESCENCE; MICE; NEURAL STEM CELLS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; TRANSCRIPTION, GENETIC; ZEBRAFISH;

EID: 84890432056     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature12716     Document Type: Article

References (30)

1. Neph, S. et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274-1286 (2012)
2. Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009)
3. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84-98 (2012)
4. Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genet. 43, 630-638 (2011)
5. Fullwood, M. J. et al. An oestrogen-receptor-a-bound human chromatin interactome. Nature 462, 58-64 (2009)
6. Phatnani, H. P. & Greenleaf, A. L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922-2936 (2006)
7. Evans, M. J. & Kaufman, M. H. Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154-156 (1981)
8. Conti, L. et al. Niche-independent symmetrical self-renewal of amammalian tissue stem cell. PLoS Biol. 3, e283 (2005)
9. Zappone, M. V. et al. Sox2 regulatory sequences direct expression of a b-geo transgene to telencephalic neural stemcells and precursors of themouseembryo, revealing regionalization of gene expression in CNS stem cells. Development 127, 2367-2382 (2000)
10. Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R. & Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature 435, 637-645 (2005)
11. Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012)
12. Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008)
13. Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010)
14. Hardison, R. C. & Taylor, J. Genomic approaches towards finding cis-regulatory modules in animals. Nature Rev. Genet. 13, 469-483 (2012)
15. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006)
16. Rada-Iglesias, A. et al. Auniquechromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011)
17. Li, Q. et al. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev. Biol. 337, 484-495 (2010)
18. Nolis, I. K. et al. Transcription factors mediate long-range enhancer-promoter interactions. Proc. Natl Acad. Sci. USA 106, 20222-20227 (2009)
19. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917-1920 (2007)
20. Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567-582 (2008)
21. Ring, K. L. et al. Direct reprogramming of mouse and human fibroblasts into multipotent neural stem cells with a single factor. Cell Stem Cell 11, 100-109 (2012)
22. Pollard, S. M., Wallbank, R., Tomlinson, S., Grotewold, L. & Smith, A. Fibroblast growth factor induces a neural stem cell phenotype in foetal forebrain progenitors and during embryonic stem cell differentiation. Mol. Cell. Neurosci. 38, 393-403 (2008)
23. Ligon, K. L. et al. Olig2-regulated lineage-restricted pathway controls replication competence in neural stem cells and malignant glioma. Neuron 53, 503-517 (2007)
24. Levine, M. Paused RNA polymerase II as a developmental checkpoint. Cell 145, 502-511 (2011)
25. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012)
26. Li, G. et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22 (2010)
27. Bastian, M., Heymann, S. & Jacomy, M. Gephi: an open source software for exploring and manipulating networks http://www. aaai. org/ocs/index. php/ ICWSM/09/paper/view/154 and https://gephi. org/users/publications/ (International AAAI Conference on Weblogs and Social Media, 2009
28. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008)
29. Bolli, N. et al. Expression of the cytoplasmic NPM1 mutant (NPMc1) causes the expansion of hematopoietic cells in zebrafish. Blood 115, 3329-3340 (2010)
30. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005)