De Novo Cis-regulatory Module Elicitation for Eukaryotic Genomes

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2005 May 11

PMID 15883375

Citations 63

Authors

Mayetri Gupta

Jun S Liu

Affiliations

Soon will be listed here.

Abstract

Transcription regulation is controlled by coordinated binding of one or more transcription factors in the promoter regions of genes. In many species, especially higher eukaryotes, transcription factor binding sites tend to occur as homotypic or heterotypic clusters, also known as cis-regulatory modules. The number of sites and distances between the sites, however, vary greatly in a module. We propose a statistical model to describe the underlying cluster structure as well as individual motif conservation and develop a Monte Carlo motif screening strategy for predicting novel regulatory modules in upstream sequences of coregulated genes. We demonstrate the power of the method with examples ranging from bacterial to insect and human genomes.

Citing Articles

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Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants.

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Sequence motif finder using memetic algorithm.

Garbelini J, Kashiwabara A, Sanches D BMC Bioinformatics. 2018; 19(1):4.

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Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

Acevedo-Luna N, Marino-Ramirez L, Halbert A, Hansen U, Landsman D, Spouge J BMC Bioinformatics. 2016; 17(1):479.

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A Conserved cis-Regulatory Module Determines Germline Fate through Activation of the Transcription Factor DUO1 Promoter.

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