↓ Skip to main content

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Overview of attention for article published in Genome Biology, October 2017
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (91st percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

news
2 news outlets
twitter
22 X users

Citations

dimensions_citation
31 Dimensions

Readers on

mendeley
76 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Published in
Genome Biology, October 2017
DOI 10.1186/s13059-017-1335-7
Pubmed ID
Authors

Dei M. Elurbe, Sarita S. Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Ozren Bogdanovic, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra

Abstract

Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers comprise transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos. The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and non-allelic homologous recombination and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole-genome duplication.

X Demographics

X Demographics

The data shown below were collected from the profiles of 22 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 76 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 76 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 20%
Student > Bachelor 13 17%
Researcher 11 14%
Student > Master 10 13%
Professor > Associate Professor 4 5%
Other 12 16%
Unknown 11 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 27 36%
Agricultural and Biological Sciences 21 28%
Engineering 3 4%
Environmental Science 2 3%
Computer Science 2 3%
Other 3 4%
Unknown 18 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 28. 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 20 April 2020.
All research outputs
#1,394,896
of 25,394,764 outputs
Outputs from Genome Biology
#1,103
of 4,470 outputs
Outputs of similar age
#28,338
of 338,315 outputs
Outputs of similar age from Genome Biology
#33
of 60 outputs
Altmetric has tracked 25,394,764 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,470 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 75% of its peers.
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 338,315 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 91% of its contemporaries.
We're also able to compare this research output to 60 others from the same source and published within six weeks on either side of this one. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.