Universität zu Köln

Nourmohammad, Armita and Laessig, Michael (2011). Formation of Regulatory Modules by Local Sequence Duplication. PLoS Comput. Biol., 7 (10). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1553-7358

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Abstract

Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Nourmohammad, Armita UNSPECIFIED UNSPECIFIED UNSPECIFIED Laessig, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-487625
DOI:	10.1371/journal.pcbi.1002167
Journal or Publication Title:	PLoS Comput. Biol.
Volume:	7
Number:	10
Date:	2011
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1553-7358
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language FACTOR-BINDING-SITES; TANDEM REPEATS; DROSOPHILA-MELANOGASTER; GENOME; GENE; EVOLUTION; DATABASE; ENERGY; IDENTIFICATION; CONSERVATION Multiple languages Biochemical Research Methods; Mathematical & Computational Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/48762