| Title |
Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing
|
|---|---|
| Published in |
Genome Biology, March 2018
|
| DOI | 10.1186/s13059-018-1418-0 |
| Pubmed ID | |
| Authors |
Seyed Yahya Anvar, Guy Allard, Elizabeth Tseng, Gloria M. Sheynkman, Eleonora de Klerk, Martijn Vermaat, Raymund H. Yin, Hans E. Johansson, Yavuz Ariyurek, Johan T. den Dunnen, Stephen W. Turner, Peter A. C. ‘t Hoen |
| Abstract |
The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing. |
X Demographics
The data shown below were collected from the profiles of 70 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 21 | 30% |
| Spain | 5 | 7% |
| France | 5 | 7% |
| United Kingdom | 4 | 6% |
| Canada | 2 | 3% |
| Australia | 2 | 3% |
| Germany | 2 | 3% |
| New Zealand | 1 | 1% |
| Italy | 1 | 1% |
| Other | 6 | 9% |
| Unknown | 21 | 30% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 36 | 51% |
| Members of the public | 32 | 46% |
| Science communicators (journalists, bloggers, editors) | 2 | 3% |
Mendeley readers
The data shown below were compiled from readership statistics for 191 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 191 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 43 | 23% |
| Student > Ph. D. Student | 42 | 22% |
| Student > Master | 21 | 11% |
| Student > Postgraduate | 13 | 7% |
| Student > Bachelor | 11 | 6% |
| Other | 32 | 17% |
| Unknown | 29 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 81 | 42% |
| Agricultural and Biological Sciences | 41 | 21% |
| Computer Science | 6 | 3% |
| Immunology and Microbiology | 5 | 3% |
| Neuroscience | 4 | 2% |
| Other | 17 | 9% |
| Unknown | 37 | 19% |
Attention Score in Context
This research output has an Altmetric Attention Score of 47. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 August 2022.
All research outputs
#883,768
of 25,382,440 outputs
Outputs from Genome Biology
#595
of 4,468 outputs
Outputs of similar age
#19,857
of 344,233 outputs
Outputs of similar age from Genome Biology
#7
of 38 outputs
Altmetric has tracked 25,382,440 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 96th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,468 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has done well, scoring higher than 86% of its peers.
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We're also able to compare this research output to 38 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 81% of its contemporaries.