Ultraconservation identifies a small subset of extremely constrained developmental enhancers

被引：253

作者：

Visel, Axel ^{[1
]}

Prabhakar, Shyam ^{[1
]}

Akiyama, Jennifer A. ^{[1
]}

Shoukry, Malak ^{[1
]}

Lewis, Keith D. ^{[1
]}

Holt, Amy ^{[1
]}

Plajzer-Frick, Ingrid ^{[1
]}

Afzal, Veena ^{[1
]}

Rubin, Edward M. ^{[1
,2
]}

Pennacchio, Len A. ^{[1
,2
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA

[2] US Dept Energy Joint Genome Inst, Walnut Creek, CA 94598 USA

来源：

NATURE GENETICS | 2008年 / 40卷 / 02期

关键词：

D O I：

10.1038/ng.2007.55

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：158 / 160

页数：3

共 15 条

[1] Deletion of ultraconserved elements yields viable mice [J].

Ahituv, Nadav ;

Zhu, Yiwen ;

Visel, Axel ;

Holt, Amy ;

Afzal, Veena ;

Pennacchio, Len A. ;

Rubin, Edward M. .

PLOS BIOLOGY, 2007, 5 (09) :1906-1911

[2] Ultraconserved elements in the human genome [J].

Bejerano, G ;

Pheasant, M ;

Makunin, I ;

Stephen, S ;

Kent, WJ ;

Mattick, JS ;

Haussler, D .

SCIENCE, 2004, 304 (5675) :1321-1325

[3] Distribution and intensity of constraint in mammalian genomic sequence [J].

Cooper, GM ;

Stone, EA ;

Asimenos, G ;

Green, ED ;

Batzoglou, S ;

Sidow, A .

GENOME RESEARCH, 2005, 15 (07) :901-913

[4] A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts [J].

de la Calle-Mustienes, E ;

Feijóo, CG ;

Manzanares, M ;

Tena, JJ ;

Rodríguez-Seguel, E ;

Letizia, A ;

Allende, ML ;

Gómez-Skarmeta, JL .

GENOME RESEARCH, 2005, 15 (08) :1061-1072

[5] Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants [J].

Derti, Adnan ;

Roth, Frederick P. ;

Church, George M. ;

Wu, C-ting .

NATURE GENETICS, 2006, 38 (10) :1216-1220

[6] Conserved noncoding sequences are selectively constrained and not mutation cold spots [J].

Drake, JA ;

Bird, C ;

Nemesh, J ;

Thomas, DJ ;

Newton-Cheh, C ;

Reymond, A ;

Excoffier, L ;

Attar, H ;

Antonarakis, SE ;

Dermitzakis, ET ;

Hirschhorn, JN .

NATURE GENETICS, 2006, 38 (02) :223-227

[7] Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons [J].

Ghanem, Noel ;

Yu, Man ;

Long, Jason ;

Hatch, Gary ;

Rubenstein, John L. R. ;

Ekker, Marc .

JOURNAL OF NEUROSCIENCE, 2007, 27 (19) :5012-5022

[8] Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome [J].

Hardison, RC ;

Oeltjen, J ;

Miller, W .

GENOME RESEARCH, 1997, 7 (10) :959-966

[9] Human genome ultraconserved elements are ultraselected [J].

Katzman, Sol ;

Kern, Andrew D. ;

Bejerano, Gill ;

Fewell, Ginger ;

Fulton, Lucinda ;

Wilson, Richard K. ;

Salama, Sofie R. ;

Haussler, David .

SCIENCE, 2007, 317 (5840) :915-915

[10] Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression [J].

Paparidis, Zissis ;

Abbasi, Amir Ali ;

Malik, Sajid ;

Goode, Debbie K. ;

Callaway, Heather ;

Elgar, Greg ;

deGraaff, Esther ;

Lopez-Rios, Javier ;

Zeller, Rolf ;

Grzeschik, Karl-Heinz .

DEVELOPMENT GROWTH & DIFFERENTIATION, 2007, 49 (06) :543-553

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