| Title |
Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome
|
|---|---|
| Published in |
Protein & Cell, February 2016
|
| DOI | 10.1007/s13238-015-0240-7 |
| Pubmed ID | |
| Authors |
Zhuoya Gu, Ke Jin, M James C Crabbe, Yang Zhang, Xiaolin Liu, Yanyan Huang, Mengyi Hua, Peng Nan, Zhaolei Zhang, Yang Zhong |
| Abstract |
Transposable elements (TEs) have no longer been totally considered as "junk DNA" for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 10(16); IMR90 fibroblasts: r = 0.94, P < 2.2 × 10(16)) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10(-4); IMR90: r = 0.934, P = 2 × 10(-2); Promoter: hESC: r = 0.995, P = 3.8 × 10(-4); IMR90: r = 0.996, P = 3.2 × 10(-4)). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes. |
X Demographics
The data shown below were collected from the profiles of 5 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 20% |
| United Kingdom | 1 | 20% |
| France | 1 | 20% |
| Unknown | 2 | 40% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 4 | 80% |
| Scientists | 1 | 20% |
Mendeley readers
The data shown below were compiled from readership statistics for 52 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | 2% |
| United States | 1 | 2% |
| Russia | 1 | 2% |
| Unknown | 49 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 15 | 29% |
| Student > Ph. D. Student | 8 | 15% |
| Student > Master | 8 | 15% |
| Student > Bachelor | 6 | 12% |
| Professor | 4 | 8% |
| Other | 4 | 8% |
| Unknown | 7 | 13% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 20 | 38% |
| Agricultural and Biological Sciences | 20 | 38% |
| Computer Science | 1 | 2% |
| Physics and Astronomy | 1 | 2% |
| Social Sciences | 1 | 2% |
| Other | 0 | 0% |
| Unknown | 9 | 17% |
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 15 February 2016.
All research outputs
#13,222,124
of 22,844,985 outputs
Outputs from Protein & Cell
#391
of 738 outputs
Outputs of similar age
#188,432
of 400,522 outputs
Outputs of similar age from Protein & Cell
#11
of 17 outputs
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