Work

Uncovering Transcription Factor Modules Using One- and Three-dimensional Analyses

Year: 2012

Type: review

Abstract: Transcriptional regulation is a critical mediator of many normal cellular processes, as well as disease progression. Transcription factors (TFs) often co-localize at cis-regulatory elements on the DNA, form protein complexes, and collaboratively regulate gene expression. Machine learning and Bayesian approaches have been used to identify TF modules in a one-dimensional context. However, recent studies using high throughput technologies have shown that TF interactions should also be considered in three-dimensional nuclear space. Here, we describe methods for identifying TF modules and discuss how moving from a one-dimensional to a three-dimensional paradigm, along with integrated experimental and computational approaches, can lead to a better understanding of TF association networks.

Source: Journal of Biological Chemistry

DOI: 10.1074/jbc.r111.309229

Authors: Xun Lan, Peggy J. Farnham, Victor X. Jin

Institutions: The Ohio State University, University of Southern California, USC Norris Comprehensive Cancer Center

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,430