Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.

Abstract:

:We present new approaches to cis-regulatory module (CRM) discovery in the common scenario where relevant transcription factors and/or motifs are unknown. Beginning with a small list of CRMs mediating a common gene expression pattern, we search genome-wide for CRMs with similar functionality, using new statistical scores and without requiring known motifs or accurate motif discovery. We cross-validate our predictions on 31 regulatory networks in Drosophila and through correlations with gene expression data. Five predicted modules tested using an in vivo reporter gene assay all show tissue-specific regulatory activity. We also demonstrate our methods' ability to predict mammalian tissue-specific enhancers. Finally, we predict human CRMs that regulate early blood and cardiovascular development. In vivo transgenic mouse analysis of two predicted CRMs demonstrates that both have appropriate enhancer activity. Overall, 7/7 predictions were validated successfully in vivo, demonstrating the effectiveness of our approach for insect and mammalian genomes.

journal_name

Dev Cell

journal_title

Developmental cell

authors

Kantorovitz MR,Kazemian M,Kinston S,Miranda-Saavedra D,Zhu Q,Robinson GE,Göttgens B,Halfon MS,Sinha S

doi

10.1016/j.devcel.2009.09.002

subject

Has Abstract

pub_date

2009-10-01 00:00:00

pages

568-79

issue

4

eissn

1534-5807

issn

1878-1551

pii

S1534-5807(09)00384-0

journal_volume

17

pub_type

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