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Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors

Overview of attention for article published in Cell Regeneration, January 2014
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  • Good Attention Score compared to outputs of the same age (67th percentile)

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4 tweeters

Citations

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16 Dimensions

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60 Mendeley
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Title
Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors
Published in
Cell Regeneration, January 2014
DOI 10.1186/2045-9769-3-4
Pubmed ID
Authors

Aline C Planello, Junfeng Ji, Vivek Sharma, Rajat Singhania, Faridah Mbabaali, Fabian Müller, Javier A Alfaro, Christoph Bock, Daniel D De Carvalho, Nizar N Batada

Abstract

The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

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 60 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Turkey 1 2%
Russia 1 2%
Brazil 1 2%
Unknown 56 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 15 25%
Student > Ph. D. Student 13 22%
Student > Bachelor 8 13%
Student > Master 6 10%
Professor 4 7%
Other 9 15%
Unknown 5 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 19 32%
Biochemistry, Genetics and Molecular Biology 18 30%
Medicine and Dentistry 6 10%
Neuroscience 3 5%
Immunology and Microbiology 1 2%
Other 6 10%
Unknown 7 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 06 March 2015.
All research outputs
#2,851,811
of 7,282,696 outputs
Outputs from Cell Regeneration
#21
of 35 outputs
Outputs of similar age
#55,047
of 173,612 outputs
Outputs of similar age from Cell Regeneration
#2
of 4 outputs
Altmetric has tracked 7,282,696 research outputs across all sources so far. This one has received more attention than most of these and is in the 60th percentile.
So far Altmetric has tracked 35 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.6. This one scored the same or higher as 14 of them.
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 173,612 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 67% of its contemporaries.
We're also able to compare this research output to 4 others from the same source and published within six weeks on either side of this one. This one has scored higher than 2 of them.