Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers

We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene express...

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Bibliographic Details
Published in:PLoS computational biology 2011-12, Vol.7 (12), p.e1002256-e1002256
Main Authors: Kwon, Andrew T, Chou, Alice Yi, Arenillas, David J, Wasserman, Wyeth W
Format: Article
Language:English
Subjects:
Animals
Base Composition
Binding sites
Biology
Cell culture
Chromatin Immunoprecipitation
Computational Biology - methods
Computer Simulation
Conserved Sequence
Gene expression
Genetics
Genome
Genomes
Histones - genetics
Human genome
Humans
Medical research
Mice
Models, Genetic
Models, Statistical
Muscle Fibers, Skeletal - physiology
Muscle, Skeletal - physiology
Muscles
Musculoskeletal system
MyoD Protein - genetics
NIH 3T3 Cells
Nucleotides
Phylogeny
Physiological aspects
Proteins
Regulatory Sequences, Nucleic Acid
Reproducibility of Results
Sequence Analysis, DNA
Statistical analysis
Statistical methods
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Summary:We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1002256