Cited by 67RNA Research and SplicingRNA regulation and diseaseRNA and protein synthesis mechanisms

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster

Open access
Liu, Xiaochuan, Freitas, Jaime, Zheng, Dinghai, Oliveira, Marta S., Hoque, Mainul, Martins, Torcato, Henriques, Telmo, Tian, Bin +1 more·2017·RNA

Abstract

Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3′UTRs and/or coding sequences from a single gene. Here, using 3′ region extraction and deep sequencing (3′READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster, expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis-element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3′UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3′UTRs and in introns, consistent with the “first come, first served” model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate.

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 · 10.1261/rna.062661.117

Cites

65 of 65 references verified0 citation errors · 0 not checkable

Statistics

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

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • A slow RNA Pol II mutant shows a tissue-specific effect on alternative polyadenylation in Drosophila head or body.

    “In addition, a slow RNA Pol II mutant shows a tissue‐specific effect on alternative polyadenylation as it affects poly(A) site usage differentially in the Drosophila head or body (Liu et al, 2017).”
  • On several genes possessing alternative poly(A) sites, a slow RNA Pol II mutant shows a switch to upstream poly(A) sites, while a fast mutant shows a slight downstream switch.

    “On several genes possessing alternative poly(A) sites, a slow RNA Pol II mutant shows a switch to the use of upstream poly(A) sites (Pinto et al, 2011; Liu et al, 2017; Geisberg et al, 2020; Yague‐Sanz et al, 2020), while a fast RNA Pol II mutant shows a slight downstream switch in poly(A) site usage (Geisberg et al, 2020).”

Self-check

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

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

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Liu, X., Freitas, J., Zheng, D., Oliveira, M. S., Hoque, M., Martins, T., Henriques, T., Tian, B., & Moreira, A.
Affiliations
  • Rutgers New Jersey Medical School (US)
  • Universidade do Porto (PT)
  • i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto (PT)
Corresponding author
  • Tian, Bin
  • Moreira, Alexandra
Venue
RNA
Published
2017-08-29
Volume
23
Issue
12
Pages
1807-1816
ISSN
  • 1355-8382 (ISSN-L)
  • 1469-9001
OpenAlex
W2751688575
Cited by
67
References
65
Citations by year
2026: 5 · 2025: 3 · 2024: 9 · 2023: 8 · 2022: 6 · 2021: 10 · 2020: 12 · 2019: 9 · 2018: 4 · 2012: 1
FWCI
2.79
Type
journal article
Language
en
Open access
Locations
  • RNA (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • National Institutes of Health (GM084089, Norte-01-0145-FEDER-000008)
  • Porto Neurosciences and Neurologic Disease Research Initiative
  • Norte Portugal Regional Operational Programme (NORTE 2020, FCOMP-01-0124-FEDER-028252, SFRH/BD/102002/2014)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
alternative polyadenylation, RNA polymerase II, Drosophila melanogaster, tissue-specific gene regulation, cis-regulatory elements
MeSH terms
Animals, Drosophila melanogaster, Male, RNA Polymerase II, Gene Expression Regulation, Fungal, Alternative Splicing, 3' Untranslated Regions, Polyadenylation, Animals, Genetically Modified, High-Throughput Nucleotide Sequencing, Transcription Elongation, Genetic

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