Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model
Glas J, Duemcke S, Zacher B, Poron D, Gagneur J, Tresch A (2015)
Publication Type: Journal article
Publication year: 2015
Journal
Book Volume: 44
Pages Range: e44-
Journal Issue: 5
DOI: 10.1093/nar/gkv1184
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.
Involved external institutions
Ludwig-Maximilians-Universität (LMU)
Germany (DE)
Max-Planck-Institut für Pflanzenzüchtungsforschung / Max Planck Institute for Plant Breeding Research
Germany (DE)
Universität zu Köln
Germany (DE)
Germany (DE)
Max-Planck-Institut für Pflanzenzüchtungsforschung / Max Planck Institute for Plant Breeding Research
Germany (DE)
Universität zu Köln
Germany (DE)
How to cite
APA:
Glas, J., Duemcke, S., Zacher, B., Poron, D., Gagneur, J., & Tresch, A. (2015). Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model. Nucleic Acids Research, 44(5), e44-. https://doi.org/10.1093/nar/gkv1184
MLA:
Glas, Julia, et al. "Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model." Nucleic Acids Research 44.5 (2015): e44-.
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