Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

被引：117

作者：

Barolo, Scott ^{[1
]}

机构：

[1] Univ Michigan, Sch Med, Dept Cell & Dev Biol, Ann Arbor, MI 48109 USA

来源：

BIOESSAYS | 2012年 / 34卷 / 02期

关键词：

cis-regulatory elements; enhancers; evolution; genomics; transcriptional regulation; DROSOPHILA-EMBRYO; GENE-EXPRESSION; MORPHOGEN GRADIENT; TRANSCRIPTIONAL ENHANCERS; MORPHOLOGICAL EVOLUTION; TARGETED MUTAGENESIS; TRANSGENIC ANALYSIS; SEPARATE ENHANCERS; CONTROL ELEMENTS; SHH EXPRESSION;

D O I：

10.1002/bies.201100121

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

This paper, in the form of a frequently asked questions page (FAQ), addresses outstanding questions about shadow enhancers, quasi-redundant cis-regulatory elements, and their proposed roles in transcriptional control. Questions include: What exactly are shadow enhancers? How many genes have shadow/redundant/distributed enhancers? How redundant are these elements? What is the function of distributed enhancers? How modular are enhancers? Is it useful to study a single enhancer in isolation? In addition, a revised definition of shadow enhancers is proposed, and possible mechanisms of shadow enhancer function and evolution are discussed.

引用

页码：135 / 141

页数：7

共 91 条

[1] Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development [J].

Abbasi, Amir A. ;

Paparidis, Zissis ;

Malik, Sajid ;

Bangs, Fiona ;

Schmidt, Ansgar ;

Koch, Sabine ;

Lopez-Rios, Javier ;

Grzeschik, Karl-Heinz .

BMC DEVELOPMENTAL BIOLOGY, 2010, 10

[2] Dissection of cis-regulatory elements of the Drosophila gene Serrate [J].

Bachmann, A ;

Knust, E .

DEVELOPMENT GENES AND EVOLUTION, 1998, 208 (06) :346-351

[3] Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element [J].

Barriere, Antoine ;

Gordon, Kacy L. ;

Ruvinsky, Ilya .

PLOS GENETICS, 2011, 7 (06)

[4] In Vivo Redundant Function of the 3′ IgH Regulatory Element HS3b in the Mouse [J].

Bebin, Anne-Gaelle ;

Carrion, Claire ;

Marquet, Marie ;

Cogne, Nadine ;

Lecardeur, Sandrine ;

Cogne, Michel ;

Pinaud, Eric .

JOURNAL OF IMMUNOLOGY, 2010, 184 (07) :3710-3717

[5] Activation of a floral homeotic gene in Arabidopsis [J].

Busch, MA ;

Bomblies, K ;

Weigel, D .

SCIENCE, 1999, 285 (5427) :585-587

[6] ULTRABITHORAX PROTEIN EXPRESSION IN BREAKPOINT MUTANTS - LOCALIZATION OF SINGLE, COOPERATIVE AND REDUNDANT CIS REGULATORY ELEMENTS [J].

CAMPRODON, FJ ;

CASTELLIGAIR, JE .

ROUXS ARCHIVES OF DEVELOPMENTAL BIOLOGY, 1994, 203 (7-8) :411-421

[7] Conservation of enhancer location in divergent insects [J].

Cande, Jessica ;

Goltsev, Yury ;

Levine, Michael S. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (34) :14414-14419

[8] Essential and redundant functions of the MyoD distal regulatory region revealed by targeted mutagenesis [J].

Chen, JCJ ;

Ramachandran, R ;

Goldhamer, DJ .

DEVELOPMENTAL BIOLOGY, 2002, 245 (01) :213-223

[9] CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors [J].

Corbo, Joseph C. ;

Lawrence, Karen A. ;

Karlstetter, Marcus ;

Myers, Connie A. ;

Abdelaziz, Musa ;

Dirkes, William ;

Weigelt, Karin ;

Seifert, Martin ;

Benes, Vladimir ;

Fritsche, Lars G. ;

Weber, Bernhard H. F. ;

Langmann, Thomas .

GENOME RESEARCH, 2010, 20 (11) :1512-1525

[10] THE CELL-SPECIFIC ENHANCER OF THE MOUSE TRANSTHYRETIN (PREALBUMIN) GENE BINDS A COMMON FACTOR AT ONE SITE AND A LIVER-SPECIFIC FACTOR(S) AT 2 OTHER SITES [J].

COSTA, RH ;

LAI, E ;

GRAYSON, DR ;

DARNELL, JE .

MOLECULAR AND CELLULAR BIOLOGY, 1988, 8 (01) :81-90

← 1 2 3 4 5 6 7 8 9 10 →