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DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells

Overview of attention for article published in Genome Biology, July 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)
  • Average Attention Score compared to outputs of the same age and source

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Title
DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Published in
Genome Biology, July 2018
DOI 10.1186/s13059-018-1464-7
Pubmed ID
Authors

Tianpeng Gu, Xueqiu Lin, Sean M. Cullen, Min Luo, Mira Jeong, Marcos Estecio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Stanley Qi, Jia-Jia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A. Goodell

Abstract

DNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5mC), which can be further oxidized by the TET dioxygenases to ultimately cause DNA demethylation. However, the genome-wide cooperation and functions of these two families of proteins, especially at large under-methylated regions, called canyons, remain largely unknown. Here we demonstrate that DNMT3A and TET1 function in a complementary and competitive manner in mouse embryonic stem cells to mediate proper epigenetic landscapes and gene expression. The longer isoform of DNMT3A, DNMT3A1, exhibits significant enrichment at distal promoters and canyon edges, but is excluded from proximal promoters and canyons where TET1 shows prominent binding. Deletion of Tet1 increases DNMT3A1 binding capacity at and around genes with wild-type TET1 binding. However, deletion of Dnmt3a has a minor effect on TET1 binding on chromatin, indicating that TET1 may limit DNA methylation partially by protecting its targets from DNMT3A and establishing boundaries for DNA methylation. Local CpG density may determine their complementary binding patterns and therefore that the methylation landscape is encoded in the DNA sequence. Furthermore, DNMT3A and TET1 impact histone modifications which in turn regulate gene expression. In particular, they regulate Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 enrichment to constrain gene expression from bivalent promoters. We conclude that DNMT3A and TET1 regulate the epigenome and gene expression at specific targets via their functional interplay.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 178 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 178 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 43 24%
Researcher 33 19%
Student > Master 24 13%
Student > Bachelor 18 10%
Other 7 4%
Other 18 10%
Unknown 35 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 78 44%
Agricultural and Biological Sciences 31 17%
Medicine and Dentistry 5 3%
Computer Science 4 2%
Immunology and Microbiology 4 2%
Other 18 10%
Unknown 38 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 23. 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 17 February 2020.
All research outputs
#1,649,482
of 25,394,764 outputs
Outputs from Genome Biology
#1,345
of 4,470 outputs
Outputs of similar age
#33,813
of 339,498 outputs
Outputs of similar age from Genome Biology
#37
of 64 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 93rd 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 gotten more attention than average, scoring higher than 69% 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 339,498 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 90% of its contemporaries.
We're also able to compare this research output to 64 others from the same source and published within six weeks on either side of this one. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.