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Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species

Overview of attention for article published in Genome Biology (Online Edition), November 2017
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (75th percentile)

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13 tweeters
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1 Facebook page

Citations

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55 Mendeley
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Title
Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species
Published in
Genome Biology (Online Edition), November 2017
DOI 10.1186/s13059-017-1358-0
Pubmed ID
Authors

Piero Sanfilippo, Jiayu Wen, Eric C. Lai

Abstract

Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control. Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends. These data broadly extend the annotated transcriptome, identify ~ 40,000 novel 3' termini, and reveal that two-thirds of Drosophila genes are subject to APA. Furthermore, we dramatically expand the numbers of genes known to be subject to tissue-specific APA, such as 3' untranslated region (UTR) lengthening in head and 3' UTR shortening in testis, and characterize new tissue and developmental 3' UTR patterns. Our thorough 3' UTR annotations permit reassessment of post-transcriptional regulatory networks, via conserved miRNA and RNA binding protein sites. To evaluate the evolutionary conservation and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis. We document broadly analogous tissue-specific APA trends in these species, but also observe significant alterations in 3' end usage across orthologs. We exploit the population of functionally evolving poly(A) sites to gain clear evidence that evolutionary divergence in core polyadenylation signal (PAS) and downstream sequence element (DSE) motifs drive broad alterations in 3' UTR isoform expression across the Drosophila phylogeny. These data provide a critical resource for the Drosophila community and offer many insights into the complex control of alternative tissue-specific 3' UTR formation and its consequences for post-transcriptional regulatory networks.

Twitter Demographics

The data shown below were collected from the profiles of 13 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 55 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 55 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 20%
Student > Ph. D. Student 7 13%
Student > Master 7 13%
Student > Bachelor 6 11%
Professor > Associate Professor 5 9%
Other 11 20%
Unknown 8 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 22 40%
Agricultural and Biological Sciences 13 24%
Computer Science 3 5%
Engineering 2 4%
Unspecified 1 2%
Other 2 4%
Unknown 12 22%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. 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 14 February 2018.
All research outputs
#3,219,516
of 16,254,026 outputs
Outputs from Genome Biology (Online Edition)
#2,136
of 3,449 outputs
Outputs of similar age
#101,954
of 413,524 outputs
Outputs of similar age from Genome Biology (Online Edition)
#196
of 241 outputs
Altmetric has tracked 16,254,026 research outputs across all sources so far. Compared to these this one has done well and is in the 76th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,449 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 26.1. This one is in the 36th percentile – i.e., 36% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 413,524 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 75% of its contemporaries.
We're also able to compare this research output to 241 others from the same source and published within six weeks on either side of this one. This one is in the 18th percentile – i.e., 18% of its contemporaries scored the same or lower than it.