Regulatory elements in molecular networks
- 17 January 2017
- journal article
- review article
- Published by Wiley in WIREs Mechanisms of Disease
- Vol. 9 (3)
Abstract
Regulatory elements determine the connectivity of molecular networks and mediate a variety of regulatory processes ranging from DNA looping to transcriptional, posttranscriptional, and posttranslational regulation. This review highlights our current understanding of the different types of regulatory elements found in molecular networks with a focus on DNA regulatory elements. We highlight technical advances and current challenges for the mapping of regulatory elements at the genome‐wide scale, and describe new computational methods to uncover these elements via reconstructing regulatory networks from large genomic datasets. WIREs Syst Biol Med 2017, 9:e1374. doi: 10.1002/wsbm.1374This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory BiologyKeywords
Funding Information
- National Science Foundation (DB1054964)
- National Institutes of Health (R01CA194547)
This publication has 79 references indexed in Scilit:
- Architecture of the human regulatory network derived from ENCODE dataNature, 2012
- Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop CodonsCell, 2012
- Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide ResolutionCell, 2011
- Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox ProteinsCell, 2011
- Targeting Androgen Receptor in Estrogen Receptor-Negative Breast CancerCancer Cell, 2011
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- Revealing Global Regulatory Perturbations across Human CancersMolecular Cell, 2009
- The role of DNA shape in protein–DNA recognitionNature, 2009
- High-Resolution Mapping and Characterization of Open Chromatin across the GenomeCell, 2008
- A Universal Framework for Regulatory Element Discovery across All Genomes and Data TypesMolecular Cell, 2007