Depletion of Trypanosome CTR9 Leads to Gene Expression Defects

The Paf complex of Opisthokonts and plants contains at least five subunits: Paf1, Cdc73, Rtf1, Ctr9, and Leo1. Mutations in, or loss of Paf complex subunits have been shown to cause defects in histone modification, mRNA polyadenylation, and transcription by RNA polymerase I and RNA polymerase II. We...

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Published inPloS one Vol. 7; no. 4; p. e34256
Main Authors Ouna, Benard A., Nyambega, Benson, Manful, Theresa, Helbig, Claudia, Males, Matilda, Fadda, Abeer, Clayton, Christine
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 20.04.2012
Public Library of Science (PLoS)
Subjects
Acids
Animals
Biochemistry
Biology
Cell Cycle Proteins - genetics
Cell Cycle Proteins - metabolism
Chromatin
Defects
DNA methylation
DNA-directed RNA polymerase
Epigenetics
Gene Expression
Genes
Genomes
Homology
Kinases
Metabolism
Mutation
Platelet-activating factor
Polyadenylation
Protein binding
Proteins
Ribonucleic acid
RNA
RNA modification
RNA polymerase II
RNA polymerases
RNA, Messenger - genetics
RNA, Messenger - metabolism
RNA-binding protein
RNA-mediated interference
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Transcription
Transcription (Genetics)
Transcription factors
Transcription, Genetic
Transcriptional Elongation Factors - genetics
Transcriptional Elongation Factors - metabolism
Trypanosoma - genetics
Trypanosoma - metabolism
Trypanosoma brucei
Trypanosome
Yeast
Germany
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Summary:The Paf complex of Opisthokonts and plants contains at least five subunits: Paf1, Cdc73, Rtf1, Ctr9, and Leo1. Mutations in, or loss of Paf complex subunits have been shown to cause defects in histone modification, mRNA polyadenylation, and transcription by RNA polymerase I and RNA polymerase II. We here investigated trypanosome CTR9, which is essential for trypanosome survival. The results of tandem affinity purification suggested that trypanosome CTR9 associates with homologues of Leo1 and Cdc73; genes encoding homologues of Rtf1 and Paf1 were not found. RNAi targeting CTR9 resulted in at least ten-fold decreases in 131 essential mRNAs: they included several that are required for gene expression and its control, such as those encoding subunits of RNA polymerases, exoribonucleases that target mRNA, RNA helicases and RNA-binding proteins. Simultaneously, some genes from regions subject to chromatin silencing were derepressed, possibly as a secondary effect of the loss of two proteins that are required for silencing, ISWI and NLP1.
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Current address: Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
Current address: Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
Conceived and designed the experiments: BO BN TM CH MM CC. Performed the experiments: BO BN TM CH MM. Analyzed the data: BO BN TM MM AF CC. Contributed reagents/materials/analysis tools: AF. Wrote the paper: BO BN TM AF CC. Did the initial RNAi, prepared the RNA for RNASeq: BN. Did the TAP purification, the RBPI co-immunoprecipitation, and some initial Northern blots, which were completed by CH and MM (who also attempted RT-PCRs): BO. Made the plasmids: BO BN. Did the Cell fractionation: BN. Repeated the Cell fractionation: TM BO. Aligned and Analysed the RNASeq data: TM AF. Further investigated the functional implications of the results: BO CC.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0034256