PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks

2017 ◽  
Vol 16 (5) ◽  
pp. 1988-2003 ◽  
Author(s):  
Aidan P. Tay ◽  
Chi Nam Ignatius Pang ◽  
Daniel L. Winter ◽  
Marc R. Wilkins
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Post Translational Modifications

scholarly journals A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination

2021 ◽  
pp. gr.275368.121 ◽  
Author(s):  
Desislava P Staneva ◽  
Roberta Carloni ◽  
Tatsiana Auchynnikava ◽  
Pin Tong ◽  
Jeyaprakash A Arulanandam ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Protein Interaction ◽  
Transcription Initiation ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Systematic Analysis ◽  
Post Translational Modifications ◽  
Chromatin Regulators ◽  
Regulatory Machinery ◽  
Rnapii Transcription

Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by ‘writer’ and ‘eraser’ enzymes, respectively. Nucleosomal PTMs are recognised by a variety of ‘reader’ proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite’s bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.

scholarly journals A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination

2021 ◽  
Author(s):  
Desislava P. Staneva ◽  
Roberta Carloni ◽  
Tatsiana Auchynnikava ◽  
Pin Tong ◽  
Juri Rappsilber ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Protein Interaction ◽  
Transcription Initiation ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Systematic Analysis ◽  
Post Translational Modifications ◽  
Chromatin Regulators ◽  
Regulatory Machinery ◽  
Rnapii Transcription

AbstractNucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by ‘writer’ and ‘eraser’ enzymes, respectively. Nucleosomal PTMs are recognised by a variety of ‘reader’ proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 68 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 63 of them in the parasite’s bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.

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