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Genomic approaches towards finding cis-regulatory modules in animals
Ross C Hardison1, James Taylor
1Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, 304 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. rch8@psu.edu
Nature Reviews. Genetics
|June 19, 2012
Summary
Identifying cis-regulatory modules (CRMs) is crucial for understanding gene expression. The most reliable method for predicting CRMs involves analyzing diagnostic biochemical marks, supported by motif and conservation pattern analysis.
Area of Science:
- Genomics
- Developmental Biology
- Molecular Biology
Background:
- Differential gene expression drives animal development and cell differentiation.
- Identifying cis-regulatory modules (CRMs) that regulate gene expression is a significant challenge.
- CRMs are DNA sequences controlling gene activity.
Purpose of the Study:
- To evaluate methods for comprehensively and accurately identifying cis-regulatory modules (CRMs).
- To determine the most reliable features for predicting CRM locations and functions.
Main Methods:
- Analysis of transcription factor binding site motifs.
- Assessment of evolutionary constraints on non-coding DNA.
- Evaluation of biochemical marks associated with CRMs, including histone modifications and protein occupancy.
Main Results:
- Predicting CRMs using clusters of transcription factor binding site motifs, evolutionary conservation, and biochemical marks were compared.
- Identifying diagnostic biochemical marks emerged as the most reliable method for CRM prediction.
- Analysis of motifs and conservation patterns within predicted CRMs enhances understanding.
Conclusions:
- Biochemical marks are the most effective diagnostic feature for identifying CRMs.
- A combination of motif analysis, evolutionary conservation, and biochemical data provides a robust approach to understanding gene regulation.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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