Correlation Between Retrotransposons And Gene Expression
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8.5 years ago
roll ▴ 330

Hi,

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 • 2.1k views
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8.5 years ago
PoGibas 5.0k

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

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8.4 years ago
SES 8.5k

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:

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