Question: Correlation Between Retrotransposons And Gene Expression
gravatar for roll
6.6 years ago by
United Kingdom
roll320 wrote:


I am trying to find the best way to analyse and see if there is a correlation between number of repeats(retrotransposons) in a gene and gene expression.

Is there any paper that is doing similar analysis?

gene expression • 1.8k views
ADD COMMENTlink modified 6.6 years ago by SES8.4k • written 6.6 years ago by roll320
gravatar for PoGibas
6.6 years ago by
PoGibas4.8k wrote:

Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Kelley D., Rinn J., Genome Biology, 2012.

ADD COMMENTlink written 6.6 years ago by PoGibas4.8k
gravatar for SES
6.6 years ago by
Vancouver, BC
SES8.4k wrote:

There are a lot of papers on the subject. It is widely accepted now that TEs play a significant role in modifying gene expression and regulatory networks. One of the best examples (in plants) is from rice (Naito et al. 2009, Nature):

There are some quantitative estimates of expression change due to insertion in that paper, and those analyses may give you some ideas. The specific mechanisms will vary by taxa though, so keep that in mind. For example, retrotransposons are ubiquitous in human genes but plant genomes seem to be less tolerant of large insertions into genes. I suggest you start with a review and see where that takes you. Here are a couple that may be helpful:

ADD COMMENTlink written 6.6 years ago by SES8.4k
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