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Gene repositioning within the cell nucleus is not random and is determined by its genomic neighborhood

Overview of attention for article published in Epigenetics & Chromatin, September 2015
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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 (78th percentile)

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15 tweeters

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Title
Gene repositioning within the cell nucleus is not random and is determined by its genomic neighborhood
Published in
Epigenetics & Chromatin, September 2015
DOI 10.1186/s13072-015-0025-5
Pubmed ID
Authors

K. Laurence Jost, Bianca Bertulat, Alexander Rapp, Alessandro Brero, Tanja Hardt, Petra Domaing, Claudia Gösele, Herbert Schulz, Norbert Hübner, M. Cristina Cardoso

Abstract

Heterochromatin has been reported to be a major silencing compartment during development and differentiation. Prominent heterochromatin compartments are located at the nuclear periphery and inside the nucleus (e.g., pericentric heterochromatin). Whether the position of a gene in relation to some or all heterochromatin compartments matters remains a matter of debate, which we have addressed in this study. Answering this question demanded solving the technical challenges of 3D measurements and the large-scale morphological changes accompanying cellular differentiation. Here, we investigated the proximity effects of the nuclear periphery and pericentric heterochromatin on gene expression and additionally considered the effect of neighboring genomic features on a gene's nuclear position. Using a well-established myogenic in vitro differentiation system and a differentiation-independent heterochromatin remodeling system dependent on ectopic MeCP2 expression, we first identified genes with statistically significant expression changes by transcriptional profiling. We identified nuclear gene positions by 3D fluorescence in situ hybridization followed by 3D distance measurements toward constitutive and facultative heterochromatin domains. Single-cell-based normalization enabled us to acquire morphologically unbiased data and we finally correlated changes in gene positioning to changes in transcriptional profiles. We found no significant correlation of gene silencing and proximity to constitutive heterochromatin and a rather unexpected inverse correlation of gene activity and position relative to facultative heterochromatin at the nuclear periphery. In summary, our data question the hypothesis of heterochromatin as a general silencing compartment. Nonetheless, compared to a simulated random distribution, we found that genes are not randomly located within the nucleus. An analysis of neighboring genomic context revealed that gene location within the nucleus is rather dependent on CpG islands, GC content, gene density, and short and long interspersed nuclear elements, collectively known as RIDGE (regions of increased gene expression) properties. Although genes do not move away/to the heterochromatin upon up-/down-regulation, genomic regions with RIDGE properties are generally excluded from peripheral heterochromatin. Hence, we suggest that individual gene activity does not influence gene positioning, but rather chromosomal context matters for sub-nuclear location.

Twitter Demographics

The data shown below were collected from the profiles of 15 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 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 2 5%
Netherlands 1 3%
France 1 3%
Germany 1 3%
Unknown 32 86%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 35%
Researcher 9 24%
Student > Master 5 14%
Professor 3 8%
Student > Doctoral Student 1 3%
Other 1 3%
Unknown 5 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 46%
Biochemistry, Genetics and Molecular Biology 14 38%
Nursing and Health Professions 1 3%
Unknown 5 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 30 November 2015.
All research outputs
#3,141,147
of 16,530,799 outputs
Outputs from Epigenetics & Chromatin
#143
of 474 outputs
Outputs of similar age
#52,480
of 249,353 outputs
Outputs of similar age from Epigenetics & Chromatin
#1
of 1 outputs
Altmetric has tracked 16,530,799 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 474 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.5. 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 249,353 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 78% of its contemporaries.
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