The SPARC complex defines RNAPII promoters in Trypanosoma brucei
- University of Edinburgh, United Kingdom
- The Francis Crick Institute, United Kingdom
- Technische Universität, Germany
Abstract
Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here we report that SET27 and CRD1, together with four previously uncharacterized constituents, form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. SET27 loss leads to aberrant RNAPII recruitment to promoter sites, accumulation of polyadenylated transcripts upstream of normal transcription start sites, and conversion of some normally unidirectional promoters to bidirectional promoters. Transcriptome analysis in the absence of SET27 revealed upregulated mRNA expression in the vicinity of SPARC peaks within the main body of chromosomes in addition to derepression of genes encoding variant surface glycoproteins (VSGs) located in subtelomeric regions. These analyses uncover a novel chromatin-associated complex required to establish accurate promoter position and directionality.
Data availability
The sequencing data generated in this study can be accessed on the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) with accession number GSE208037.The proteomics data generated in this study can be accessed on the Proteomics Identification Database (PRIDE; https://www.ebi.ac.uk/pride/) with accession number PXD036454.
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The SPARC complex defines RNAPII promoters in Trypanosoma bruceiNCBI Gene Expression Omnibus, GSE208037.
Article and author information
Author details
Funding
Medical Research Council (MR/T04702X/1)
- Desislava P Staneva
- Keith R Matthews
- Robin C Allshire
Wellcome Trust (22171)
- Keith R Matthews
Wellcome Trust (200885)
- Desislava P Staneva
- Tatsiana Auchynnikava
- Robin C Allshire
Wellcome Trust (224358)
- Desislava P Staneva
- Tatsiana Auchynnikava
- Robin C Allshire
Wellcome Trust (222516)
- Stefan Bresson
- David Tollervey
Wellcome Trust (202811)
- A Arockia Jeyaprakash
Wellcome Trust (108504)
- Juri Rappsilber
Wellcome Trust (203149)
- Christos Spanos
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Staneva et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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The SPARC complex defines RNAPII promoters in Trypanosoma brucei
eLife 11:e83135.
https://doi.org/10.7554/eLife.83135
Further reading
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- Chromosomes and Gene Expression
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- Chromosomes and Gene Expression
- Developmental Biology
About 70% of human cleavage stage embryos show chromosomal mosaicism, falling to 20% in blastocysts. Chromosomally mosaic human blastocysts can implant and lead to healthy new-borns with normal karyotypes. Studies in mouse embryos and human gastruloids showed that aneuploid cells are eliminated from the epiblast by p53-mediated apoptosis while being tolerated in the trophectoderm. These observations suggest a selective loss of aneuploid cells from human embryos, but the underlying mechanisms are not yet fully understood. Here, we investigated the cellular consequences of aneuploidy in a total of 125 human blastocysts. RNA-sequencing of trophectoderm cells showed activated p53 pathway and apoptosis proportionate to the level of chromosomal imbalance. Immunostaining corroborated that aneuploidy triggers proteotoxic stress, autophagy, p53-signaling, and apoptosis independent from DNA damage. Total cell numbers were lower in aneuploid embryos, due to a decline both in trophectoderm and in epiblast/primitive endoderm cell numbers. While lower cell numbers in trophectoderm may be attributed to apoptosis, aneuploidy impaired the second lineage segregation, particularly primitive endoderm formation. This might be reinforced by retention of NANOG. Our findings might explain why fully aneuploid embryos fail to further develop and we hypothesize that the same mechanisms lead to the removal of aneuploid cells from mosaic embryos.
