title: Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
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.
authors.affiliation: Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Axel
authors.initials: A
authors.lastname: Visel
authors.forename: Shyam
authors.initials: S
authors.lastname: Prabhakar
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Akiyama
authors.forename: Malak
authors.initials: M
authors.lastname: Shoukry
authors.forename: Keith D
authors.initials: KD
authors.lastname: Lewis
authors.forename: Amy
authors.initials: A
authors.lastname: Holt
authors.forename: Ingrid
authors.initials: I
authors.lastname: Plajzer-Frick
authors.forename: Veena
authors.initials: V
authors.lastname: Afzal
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics*; D004622:Embryo, Mammalian; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D017930:Genes, Reporter; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D051379:Mice; D008822:Mice, Transgenic; D008969:Molecular Sequence Data; D009420:Nervous System / Q000196:embryology / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012641:Selection, Genetic; D013045:Species Specificity; D014158:Transcription, Genetic