Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs

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Item Type:	Article
Title:	Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs
Creators Name:	Majoros, W.H. and Ohler, U.
Abstract:	The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.
Keywords:	Base Sequence, Computational Biology, Computer Simulation, DNA Sequence Analysis, Gene Expression Regulation, Markov Chains, Molecular Evolution, Molecular Sequence Data, Phylogeny, ROC Curve, Sequence Alignment, Transcriptional Regulatory Elements, Animals, Drosophila melanogaster
Source:	PLoS Computational Biology
ISSN:	1553-734X
Publisher:	Public Library of Science
Volume:	6
Number:	12
Page Range:	e1001037
Date:	16 December 2010
Official Publication:	https://doi.org/10.1371/journal.pcbi.1001037
PubMed:	View item in PubMed

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