BAYESIAN NETWORK ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME DYNAMICS AND TRANSCRIPTIONAL REGULATORY FACTORS

Bich Hai Ho, Ngoc Tu Le, Tu Bao Ho

Abstract

Intergenic regions are unstable, owing to trans-regulatory factors that regulate chromatin structure. Nucleosome organization at promoter has been shown to exhibit distinct patterns corresponding to the level of gene expression. Post-translational modifications (PTMs) of histone proteins and transcriptional regulators, including chromatin remodeling complexes (CRCs), general transcription factors (GTFs), and RNA polymerase II (PolII), are presumably related to the establishment of such nucleosome dynamics. However, their concrete relationships, especially in gene regulation, remain elusive. We, therefore, sought to understand the functional linkages among these factors and nucleosome dynamics by deriving a Bayesian network (BN)-based model representing their interactions. Based on the recovered network, learnt from 8 PTMs and 15 transcriptional regulators at 4034 S.cerevisiae promoters, we speculate that nucleosome organization at promoter is intentionally volatile in various regulatory pathways. Notably, interactions of CRCs/GTFs and H3 histone methylation were inferred to co-function with nucleosome dynamics in gene repression and pre-initiation complex (PIC) formation. Our results affirm the hypothesis that extrinsic factors take part in regulating nucleosome dynamics. More thorough investigation can be made by adding more factors and using our proposed method.

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Paper Citation


in Harvard Style

Ho B., Le N. and Ho T. (2012). BAYESIAN NETWORK ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME DYNAMICS AND TRANSCRIPTIONAL REGULATORY FACTORS . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 299-302. DOI: 10.5220/0003773502990302


in Bibtex Style

@conference{bioinformatics12,
author={Bich Hai Ho and Ngoc Tu Le and Tu Bao Ho},
title={BAYESIAN NETWORK ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME DYNAMICS AND TRANSCRIPTIONAL REGULATORY FACTORS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={299-302},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003773502990302},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - BAYESIAN NETWORK ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME DYNAMICS AND TRANSCRIPTIONAL REGULATORY FACTORS
SN - 978-989-8425-90-4
AU - Ho B.
AU - Le N.
AU - Ho T.
PY - 2012
SP - 299
EP - 302
DO - 10.5220/0003773502990302