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Identification of REST targets in the Xenopus tropicalis genome

Overview of attention for article published in BMC Genomics, May 2015
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Title
Identification of REST targets in the Xenopus tropicalis genome
Published in
BMC Genomics, May 2015
DOI 10.1186/s12864-015-1591-4
Pubmed ID
Authors

Banu Saritas-Yildirim, Christopher P Childers, Christine G Elsik, Elena M Silva

Abstract

A major role of REST (repressor element-1 silencing transcription factor) is to inhibit the expression of neuronal genes in neural stem cells and non-neuronal cells by binding to a 21 bp consensus sequence and recruiting epigenetic and regulatory cofactors to gene regulatory regions. In neural stem cells, REST silences differentiation-promoting genes to prevent their premature expression and is central to the regulation of neurogenesis and the balance of neural stem cells and neurons. To understand the role of REST in vertebrate neurogenesis, we performed a genome-wide screen for REST targets in Xenopus tropicalis. We identified 742 neuron-restrictive silencer elements (NRSE) associated with 1396 genes that are enriched in neuronal function. Comparative analyses revealed that characteristics of NRSE motifs in frog are similar to those in mammals in terms of the distance to target genes, frequency of motifs and the repertoire of putative target genes. In addition, we identified four F-box ubiquitin ligases as putative REST targets and determined that they are expressed in neuronal tissues during Xenopus development. We identified a conserved core of putative target genes in human, mouse and frog that may be fundamental to REST function in vertebrates. We demonstrate that NRSE sites are associated with both protein-coding genes and lncRNAs in the human genome. Furthermore, we demonstrate that REST binding sites are abundant in low gene-occupancy regions of the human genome but this is not due to an increased association with non-coding RNAs. Our findings identify novel targets of REST and broaden the known mechanism of REST-mediated silencing in neurogenesis.

Twitter Demographics

The data shown below were collected from the profiles of 4 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 16 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 16 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 19%
Researcher 3 19%
Professor > Associate Professor 3 19%
Other 2 13%
Student > Master 1 6%
Other 2 13%
Unknown 2 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 6 38%
Biochemistry, Genetics and Molecular Biology 4 25%
Environmental Science 1 6%
Social Sciences 1 6%
Medicine and Dentistry 1 6%
Other 0 0%
Unknown 3 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 26 May 2015.
All research outputs
#11,729,004
of 19,211,930 outputs
Outputs from BMC Genomics
#5,132
of 9,730 outputs
Outputs of similar age
#119,592
of 241,097 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 19,211,930 research outputs across all sources so far. This one is in the 36th percentile – i.e., 36% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,730 research outputs from this source. They receive a mean Attention Score of 4.5. This one is in the 43rd percentile – i.e., 43% of its peers scored the same or lower than it.
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We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them