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Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A - Mol. Syst. Biol. (2014)

Bottom Line: To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic states from occupancy profiles de novo.Application to RNA polymerase II-associated factors in yeast and chromatin modifications in human T cells recovers the majority of transcribed loci, reveals gene-specific variations in the yeast transcription cycle and indicates the existence of directed chromatin state patterns at transcribed, but not at repressed, regions in the human genome.We anticipate bidirectional HMMs to significantly improve the analyses of genome-associated directed processes.

View Article: PubMed Central - PubMed

Affiliation: Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Institute for Genetics, University of Cologne, Cologne, Germany.

No MeSH data available.


Related in: MedlinePlus

De novo annotation of directed genomic states from genomewide transcription data in yeast using bdHMMInputs for the bdHMM are the following, from top to bottom: strand-specific wild-type RNA levels, occupancy maps of nucleosomes, 3 termination factors, 6 elongation factors, 3 capping factors, 2 initiation factors, 4 CTD modifcations and 1 core Pol II member (Rpb3). Inferred directed genomic states are shown as colored boxes in the lowest track (see color legend beneath) where expressed states on the + (respectively −) strand are positioned above (respectively under) the axis, and not expressed states are centered on the axis. Previous transcriptome annotation is shown in the 2nd track from the bottom.
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fig02: De novo annotation of directed genomic states from genomewide transcription data in yeast using bdHMMInputs for the bdHMM are the following, from top to bottom: strand-specific wild-type RNA levels, occupancy maps of nucleosomes, 3 termination factors, 6 elongation factors, 3 capping factors, 2 initiation factors, 4 CTD modifcations and 1 core Pol II member (Rpb3). Inferred directed genomic states are shown as colored boxes in the lowest track (see color legend beneath) where expressed states on the + (respectively −) strand are positioned above (respectively under) the axis, and not expressed states are centered on the axis. Previous transcriptome annotation is shown in the 2nd track from the bottom.

Mentions: We applied the bdHMM to ChIP data in S. cerevesiae, where high-resolution datasets for dozens of proteins of the transcription machinery are available. We compiled genomewide ChIP-chip experiments for transcription initiation factors (TFIIB, Kin28), elongation factors (Spt5, Spn1, Bur1, Spt16, Ctk1, Paf1), termination factors (Pcf11, Rna15, Nrd1), Pol II and various modifications of its C-terminal domain (CTD) (Tyr1P, Ser2P, Ser5P, Ser7P) and nucleosomes (Lee et al, 2007; Mayer et al2010, 2012; Lidschreiber et al, 2013). The dataset was complemented by strand-specific mRNA expression data (Xu et al, 2009) (Fig2).


Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A - Mol. Syst. Biol. (2014)

De novo annotation of directed genomic states from genomewide transcription data in yeast using bdHMMInputs for the bdHMM are the following, from top to bottom: strand-specific wild-type RNA levels, occupancy maps of nucleosomes, 3 termination factors, 6 elongation factors, 3 capping factors, 2 initiation factors, 4 CTD modifcations and 1 core Pol II member (Rpb3). Inferred directed genomic states are shown as colored boxes in the lowest track (see color legend beneath) where expressed states on the + (respectively −) strand are positioned above (respectively under) the axis, and not expressed states are centered on the axis. Previous transcriptome annotation is shown in the 2nd track from the bottom.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4300491&req=5

fig02: De novo annotation of directed genomic states from genomewide transcription data in yeast using bdHMMInputs for the bdHMM are the following, from top to bottom: strand-specific wild-type RNA levels, occupancy maps of nucleosomes, 3 termination factors, 6 elongation factors, 3 capping factors, 2 initiation factors, 4 CTD modifcations and 1 core Pol II member (Rpb3). Inferred directed genomic states are shown as colored boxes in the lowest track (see color legend beneath) where expressed states on the + (respectively −) strand are positioned above (respectively under) the axis, and not expressed states are centered on the axis. Previous transcriptome annotation is shown in the 2nd track from the bottom.
Mentions: We applied the bdHMM to ChIP data in S. cerevesiae, where high-resolution datasets for dozens of proteins of the transcription machinery are available. We compiled genomewide ChIP-chip experiments for transcription initiation factors (TFIIB, Kin28), elongation factors (Spt5, Spn1, Bur1, Spt16, Ctk1, Paf1), termination factors (Pcf11, Rna15, Nrd1), Pol II and various modifications of its C-terminal domain (CTD) (Tyr1P, Ser2P, Ser5P, Ser7P) and nucleosomes (Lee et al, 2007; Mayer et al2010, 2012; Lidschreiber et al, 2013). The dataset was complemented by strand-specific mRNA expression data (Xu et al, 2009) (Fig2).

Bottom Line: To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic states from occupancy profiles de novo.Application to RNA polymerase II-associated factors in yeast and chromatin modifications in human T cells recovers the majority of transcribed loci, reveals gene-specific variations in the yeast transcription cycle and indicates the existence of directed chromatin state patterns at transcribed, but not at repressed, regions in the human genome.We anticipate bidirectional HMMs to significantly improve the analyses of genome-associated directed processes.

View Article: PubMed Central - PubMed

Affiliation: Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Institute for Genetics, University of Cologne, Cologne, Germany.

No MeSH data available.


Related in: MedlinePlus