| Title |
Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes
|
|---|---|
| Published in |
BMC Genomics, August 2017
|
| DOI | 10.1186/s12864-017-4078-7 |
| Pubmed ID | |
| Authors |
Yongcheng Dong, Ziyan Huang, Qifan Kuang, Zhining Wen, Zhibin Liu, Yizhou Li, Yi Yang, Menglong Li |
| Abstract |
TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes. In addition, TEs can influence the expression of nearby genes. The temporal and spatial influences of TEs remain unclear yet. To evaluate the TEs transcription patterns, we profiled their transcript levels in 11 organs for both sexes across four developmental stages of rat. The results show that most short interspersed elements (SINEs) are commonly expressed in all conditions, which are also the major TE types with commonly expression patterns. In contrast, long terminal repeats (LTRs) are more likely to exhibit specific expression patterns. The expression tendency of TEs and genes are similar in most cases. For example, few specific genes and TEs are in the liver, muscle and heart. However, TEs perform superior over genes on classing organ, which imply their higher organ specificity than genes. By associating the TEs with the closest genes in genome, we find their expression levels are correlated, independent of their distance in some cases. TEs sex-dependently associate with nearest genes. A gene would be associated with more than one TE. Our works can help to functionally annotate the genome and further understand the role of TEs in gene regulation. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Brazil | 1 | 33% |
| United States | 1 | 33% |
| Unknown | 1 | 33% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 67% |
| Scientists | 1 | 33% |
Mendeley readers
The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 19 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 3 | 16% |
| Student > Ph. D. Student | 3 | 16% |
| Other | 2 | 11% |
| Researcher | 2 | 11% |
| Student > Doctoral Student | 1 | 5% |
| Other | 2 | 11% |
| Unknown | 6 | 32% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 6 | 32% |
| Biochemistry, Genetics and Molecular Biology | 4 | 21% |
| Medicine and Dentistry | 2 | 11% |
| Unknown | 7 | 37% |
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 31 August 2017.
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#16,309,802
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Outputs of similar age from BMC Genomics
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