Regulatory elements in molecular networks

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.1374 For further resources related to this article, please visit the WIREs website.

Figure 1

Examples of putative regulatory elements mapped by ATACseq and identified by HOMER motif analysis. ATACseq insertion tracks in naïve B (NB, light blue) and germinal center B-cells (CB, orange). ChIP-seq signal in CB for the transcription factors PU.1, BCL6, BCOR, SMRT, and CTCF, and ChIP-seq for activated histone H3K27ac and H3K4me2 chromatin marks in CB (red) and NB (blue) from Jiang et, al (79), and HiC normalized interactions in CB (red) and NB (blue) from Bunting et. al (52).