Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome

Nature Communications

Volumn 6, Issue , 2015, Pages

  Naville, Magali ^a,b,c   Ishibashi, Minaka ^d   Ferg, Marco ^e   Bengani, Hemant ^f   Rinkwitz, Silke ^d   Krecsmarik, Monika ^g   Hawkins, Thomas A ^h   Wilson, Stephen W ^h   Manning, Elizabeth ^d   Chilamakuri, Chandra S R ⁱ   Wilson, David I ^j   Louis, Alexandra ^a,b,c   Lucy Raymond, F ^k   Rastegar, Sepand ^e   Strähle, Uwe ^e   Lenhard, Boris ^l   Bally Cuif, Laure ^g   Van Heyningen, Veronica ^f   Fitzpatrick, David R ^f   Becker, Thomas S ^d,m   Roest Crollius, Hugues ^a,b,c   more..

^a PSL RESEARCH UNIVERSITY   (France)

^b CNRS   (France)

^c INSERM   (France)

^d UNIVERSITY OF SYDNEY   (Australia)

^e KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^f UNIVERSITY OF EDINBURGH   (United Kingdom)

^g CNRS   (France)

^h UNIVERSITY COLLEGE LONDON   (United Kingdom)

ⁱ OSLO UNIVERSITY HOSPITAL   (Norway)

^j SOUTHAMPTON GENERAL HOSPITAL   (United Kingdom)

^k UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^l MRC CLINICAL SCIENCES CENTRE   (United Kingdom)

^m UNIVERSITY OF BERGEN   (Norway)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ELEMENT; GREEN FLUORESCENT PROTEIN; TRANSCRIPTION FACTOR;

CHROMOSOME; CYPRINID; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOMICS;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BRAIN DEVELOPMENT; CHROMATIN; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; GENE EXPRESSION; GENE INTERACTION; GENE REARRANGEMENT; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC IDENTIFICATION; GENETIC REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN GENOME; NONHUMAN; SCORING SYSTEM; SEQUENCE ALIGNMENT; TRANSGENICS; X CHROMOSOME; ZEBRA FISH; ANIMAL; GENETIC LINKAGE; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; TRANSGENIC ANIMAL;

DANIO RERIO;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CHROMOSOMES, HUMAN, X; ENHANCER ELEMENTS, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE REARRANGEMENT; GENETIC LINKAGE; HUMANS; SELECTION, GENETIC; ZEBRAFISH;

EID: 84928630490     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7904     Document Type: Article

References (40)

1. Benko, S. et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat. Genet. 41, 359-364 (2009
2. Lettice, L. A. et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725-1735 (2003
3. Goode, D. K., Snell, P., Smith, S. F., Cooke, J. E. & Elgar, G. Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3. Genomics 86, 172-181 (2005
4. Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545-555 (2007
5. Mongin, E., Dewar, K. & Blanchette, M. Mapping association between longrange cis-regulatory regions and their target genes using synteny. J. Comput. Biol. 18, 1115-1130 (2011
6. Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004
7. Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 7, 476-482 (2011
8. Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011
9. Blow, M. J. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806-810 (2010
10. Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009
11. Stevenson, R. E. & Schwartz, C. E. X-linked intellectual disability: unique vulnerability of the male genome. Dev. Disabil. Res. Rev. 15, 361-368 (2009
12. Sprague, J. et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 34, D581-D585 (2006
13. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84-98 (2012
14. Fong, A. P. et al. Genetic and epigenetic determinants of neurogenesis and myogenesis. Dev. Cell 22, 721-735 (2012
15. Ince-Dunn, G. et al. Regulation of thalamocortical patterning and synaptic maturation by NeuroD2. Neuron 49, 683-695 (2006
16. Narayanan, G. et al. Single-cell mRNA profiling identifies progenitor subclasses in neurospheres. Stem Cells Dev. 21, 3351-3362 (2012
17. Chepelev, I., Wei, G., Wangsa, D., Tang, Q. & Zhao, K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 22, 490-503 (2012
18. Merkenschlager, M. & Odom, D. T. CTCF and cohesin: linking gene regulatory elements with their targets. Cell 152, 1285-1297 (2013).
19. Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014
20. Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32 (2005
21. Benko, S. et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat. Genet. 41, 359-364 (2009
22. Smemo, S. et al. Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease. Hum. Mol. Genet. 21, 3255-3263 (2012
23. Weedon, M. N. et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat. Genet. 46, 61-64 (2014
24. Noonan, J. P. & McCallion, A. S. Genomics of long-range regulatory elements. Annu. Rev. Genomics Hum. Genet. 11, 1-23 (2010
25. Flicek, P. et al. Ensembl 2012. Nucleic Acids Res. 40, D84-D90 (2012
26. Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012
27. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000
28. Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901-1904 (2002
29. Toedling, J. et al. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 8 (2007
30. Ishibashi, M., Mechaly, A. S., Becker, T. S. & Rinkwitz, S. Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity. Methods. 62, 216-225 (2013
31. Marz, M. et al. Heterogeneity in progenitor cell subtypes in the ventricular zone of the zebrafish adult telencephalon. Glia 58, 870-888 (2010
32. Turner, K. J., Bracewell, T. G. & Hawkins, T. A. Anatomical dissection of zebrafish brain development. Methods Mol. Biol. 1082, 197-214 (2014
33. Lauter, G., Soll, I. & Hauptmann, G. Sensitive whole-mount fluorescent in situ hybridization in zebrafish using enhanced tyramide signal amplification. Methods Mol. Biol. 1082, 175-185 (2014
34. Thisse, C. & Thisse, B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat. Protoc. 3, 59-69 (2008
35. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009
36. Thomas-Chollier, M. et al. RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 39, W86-W91 (2011
37. Wingender, E. et al. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29, 281-283 (2001
38. Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013
39. Mathelier, A. et al. JASPAR 2014: an extensively expanded and updated openaccess database of transcription factor binding profiles. Nucleic Acids Res. 42, D142-D147 (2014
40. Rothenaigner, I. et al. Clonal analysis by distinct viral vectors identifies bona fide neural stem cells in the adult zebrafish telencephalon and characterizes their division properties and fate. Development 138, 1459-1469 (2011).