Universität zu Köln

Glas, Julia, Duemcke, Sebastian, Zacher, Benedikt, Poron, Don, Gagneur, Julien ORCID: 0000-0002-8924-8365 and Tresch, Achim (2016). Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model. Nucleic Acids Res., 44 (5). OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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Abstract

Hidden Markov models (HMMs) have been extensively used to dissect the genome into functionally distinct regions using data such as RNA expression or DNA binding measurements. It is a challenge to disentangle processes occurring on complementary strands of the same genomic region. We present the double-stranded HMM (dsHMM), a model for the strand-specific analysis of genomic processes. We applied dsHMM to yeast using strand specific transcription data, nucleosome data, and protein binding data for a set of 11 factors associated with the regulation of transcription. The resulting annotation recovers the mRNA transcription cycle (initiation, elongation, termination) while correctly predicting strand-specificity and directionality of the transcription process. We find that pre-initiation complex formation is an essentially undirected process, giving rise to a large number of bidirectional promoters and to pervasive antisense transcription. Notably, 12% of all transcriptionally active positions showed simultaneous activity on both strands. Furthermore, dsHMM reveals that antisense transcription is specifically suppressed by Nrd1, a yeast termination factor.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Glas, Julia UNSPECIFIED UNSPECIFIED UNSPECIFIED Duemcke, Sebastian UNSPECIFIED UNSPECIFIED UNSPECIFIED Zacher, Benedikt UNSPECIFIED UNSPECIFIED UNSPECIFIED Poron, Don UNSPECIFIED UNSPECIFIED UNSPECIFIED Gagneur, Julien UNSPECIFIED orcid.org/0000-0002-8924-8365 UNSPECIFIED Tresch, Achim UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-281181
DOI:	10.1093/nar/gkv1184
Journal or Publication Title:	Nucleic Acids Res.
Volume:	44
Number:	5
Date:	2016
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1362-4962
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RNA-POLYMERASE-II; BIDIRECTIONAL PROMOTERS; CHROMATIN STATES; TRANSCRIPTION; ANNOTATION; DISCOVERY; YEAST; IDENTIFICATION; SEGMENTATION; TERMINATION Multiple languages Biochemistry & Molecular Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/28118