CoChat
Sign Up
PreprintCited by 13Genomics and Chromatin DynamicsTrypanosoma species research and implicationsNuclear Structure and Function

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

The SPARC complex defines RNAPII promoters in Trypanosoma brucei

Open access
Staneva, Desislava P., Bresson, Stefan, Auchynnikava, Tatsiana, Spanos, Christos, Rappsilber, Juri, Jeyaprakash, A. Arockia, Tollervey, David, Matthews, Keith R., Allshire, Robin C.·2022·eLife
DOI 10.1101/2022.07.14.499694PMC PMC9566855

Preprint — published as 10.7554/elife.83135 · Paper page

Open this paper in CoChat — free account

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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2022.07.14.499694

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 53

  1. 10.1016/S0968-0004(00)88957-4 · DOI
  2. 10.1093/nar/23.16.3168 · DOI
  3. 10.1098/rsob.130023 · DOI
  4. 10.1242/jcs.242271 · DOI
  5. 10.1038/s41594-019-0290-2 · DOI
  6. 10.1126/science.1085703 · DOI
  7. 10.1098/rsos.170095 · DOI
  8. 10.1016/j.molbiopara.2005.05.008 · DOI
  9. 10.1126/science.1112642 · DOI
  10. 10.1098/rsob.190072 · DOI
  11. 10.1128/MMBR.00024-10 · DOI
  12. 10.1111/mmi.12812 · DOI
  13. 10.1186/gb-2005-6-8-227 · DOI
  14. 10.1016/j.molcel.2004.12.022 · DOI
  15. 10.1038/nprot.2012.101 · DOI
  16. 10.1038/nrg2337 · DOI
  17. 10.1002/cpbi.108 · DOI · Paper page
  18. 10.1093/nar/gkq366 · DOI · Paper page
  19. 10.1016/j.molbiopara.2014.05.001 · DOI
  20. 10.1002/bies.201600095 · DOI
  21. 10.1128/mSphere.01204-20 · DOI
  22. 10.1016/j.molbiopara.2007.06.010 · DOI
  23. 10.1371/journal.pgen.1008390 · DOI
  24. 10.1101/SQB.1987.052.01.054 · DOI
  25. 10.1371/journal.ppat.1001090 · DOI
  26. 10.1038/s41467-020-15274-0 · DOI
  27. 10.1038/nmeth.1923 · DOI · Paper page
  28. 10.1093/bioinformatics/btt656 · DOI · Paper page
  29. 10.1242/jcs.01649 · DOI
  30. 10.1101/gad.8.4.491 · DOI
  31. 10.1186/s13059-020-02164-3 · DOI
  32. 10.2217/fmb.11.20 · DOI
  33. 10.1038/s41592-022-01488-1 · DOI · Paper page
  34. 10.1038/s41586-018-0619-8 · DOI
  35. 10.1016/0168-9525(90)90303-N · DOI
  36. 10.1038/nprot.2007.261 · DOI · Paper page
  37. 10.1038/nbt.1754 · DOI · Paper page
  38. 10.1093/bioinformatics/btp616 · DOI · Paper page
  39. 10.1186/gb-2010-11-3-r25 · DOI · Paper page
  40. 10.1371/journal.pbio.1002316 · DOI
  41. 10.1371/journal.pgen.1005762 · DOI
  42. 10.1101/gr.1239303 · DOI · Paper page
  43. 10.1146/annurev-biochem-051710-134100 · DOI · Paper page
  44. 10.1101/gad.1790409 · DOI
  45. 10.1093/nar/19.4.789 · DOI
  46. 10.12688/f1000research.10342.2 · DOI
  47. 10.1093/nar/gki408 · DOI
  48. 10.1101/gr.275368.121 · DOI
  49. 10.1038/nmeth.3901 · DOI · Paper page
  50. 10.1016/j.molbiopara.2010.03.013 · DOI
  51. 10.1016/j.bbrc.2021.07.017 · DOI
  52. 2009, Universal sample preparation method for proteome analysis, Nature methods, 6, 359, 10.1038/nmeth.1322 · DOI · Paper page
  53. 10.1016/j.jmb.2017.12.007 · DOI · Paper page

Metadata

Authors
Staneva, D. P., Bresson, S., Auchynnikava, T., Spanos, C., Rappsilber, J., Jeyaprakash, A. A., Tollervey, D., Matthews, K. R., & Allshire, R. C.
Affiliations
  • Wellcome Centre for Cell Biology (GB)
  • The Francis Crick Institute (GB)
  • University of Edinburgh (GB)
Corresponding author
  • Matthews, Keith R.
  • Allshire, Robin C.
ORCID
Venue
eLife
Publisher
openRxiv
Published
2022-07-15
Volume
11
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2022.07.14.499694
PMC
PMC9566855
OpenAlex
W4297458009
Cited by
13
References
1
Citations by year
2026: 2 · 2025: 3 · 2024: 4 · 2023: 3 · 2022: 1
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Wellcome Trust (222516, 224358, 222516/Z/21/Z, 200885, 221717, 202811/Z/16/Z, 202811, 22171, 108504, 200885/Z/16/Z, 224358/Z/21/Z, 203149, 221717/Z/20/Z)
  • Medical Research Council Canada (MR/T04702X/1)
  • Medical Research Council (MR/T04702X/1, 203149)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Health Sciences › Medicine › Epidemiology › Trypanosoma species research and implications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
bidirectional promoter, histone methyltransferase, Trypanosoma brucei, variant surface glycoprotein, subtelomeric regions, polyadenylated transcripts, transcriptional derepression
MeSH terms
Histone Methyltransferases, Chromatin, Heterochromatin, RNA Polymerase II, RNA, Messenger, Transcription, Genetic, Trypanosoma brucei brucei, Variant Surface Glycoproteins, Trypanosoma

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review