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PMID: 18176564 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Nature genetics ·Vol. 40 ·No. 2 ·2008-02-00 ·Pages 158-60

Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA

Abstract

Extended perfect human-rodent sequence identity of at least 200 base pairs (ultraconservation) is potentially indicative of evolutionary or functional uniqueness. We used a transgenic mouse assay to compare the embryonic enhancer activity of 231 noncoding ultraconserved human genome regions with that of 206 extremely conserved regions lacking ultraconservation. Developmental enhancers were equally prevalent in both populations, suggesting instead that ultraconservation identifies a small, functionally indistinct subset of similarly constrained cis-regulatory elements.

MeSH Terms
Animals Base Pairing Base Sequence Conserved Sequence/genetics Embryo, Mammalian Enhancer Elements, Genetic Evolution, Molecular Gene Expression Regulation, Developmental Genes, Reporter Genome, Human Genomics/methods Humans Mice Mice, Transgenic Molecular Sequence Data Nervous System/embryology,metabolism Regulatory Sequences, Nucleic Acid Selection, Genetic Species Specificity Transcription, Genetic
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Visel Axel
Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Prabhakar Shyam
Akiyama Jennifer A
Shoukry Malak
Lewis Keith D
Holt Amy
Plajzer-Frick Ingrid
Afzal Veena
Rubin Edward M
Pennacchio Len A
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.2007.55
Published
2008-02-00
Epub
2008-00-06
Pages
158-60
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC2647775
Subset
IM
Grants
NHGRI NIH HHS · R01 HG003988 · United States
NHLBI NIH HHS · HL066681 · United States
NHGRI NIH HHS · HG003988 · United States
NHGRI NIH HHS · R01 HG003988-02 · United States
NHLBI NIH HHS · U01 HL066681 · United States
External Links
PubMed source DOI: 10.1038/ng.2007.55 PMC Full Text View journal details
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