Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
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.
Visel
Axel
A
Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Prabhakar
Shyam
S
Akiyama
Jennifer A
JA
Shoukry
Malak
M
Lewis
Keith D
KD
Holt
Amy
A
Plajzer-Frick
Ingrid
I
Afzal
Veena
V
Rubin
Edward M
EM
Pennacchio
Len A
LA
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