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eRNA from RNASeq data

Hi, I am studing eRNA using RNASeq data and I would like to know how define the eRNA track. Is it sufficient to consider just enhancer regions or it is better consider ehnacer regions plus 2-3kb upstream-downstream of them? At moment I am considering the track downloaded from Enhancer Atlas.

rna-seq rnaseq enhancer rna
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updated by wuyc • wuyc • written by giorgio.giurato • giorgio.giurato

For "eRNA track" I mean the track against to count RNA-Seq reads. Is it sufficient consider the enahcer coordinates or is it necessary to enlarge each region?

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written by giorgio.giurato • giorgio.giurato

You can just consider enhancer region. But, its not as simple as counting the RNA reads mapped on to "enhancer" definition. You should be careful in defining eRNAs, and I would suggest to read the paper below to get an idea about defining eRNAs from RNA-Seq data.

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written by GouthamAtla GouthamAtla

If it solved your question, accept the answer so that the post will be "closed"

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written by GouthamAtla GouthamAtla

2 answers

I am not sure what do you mean by eRNA track , but to define eRNAs from RNA-Seq, you can get some inspiration from A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

Enhancers are usually 500 to 1000bp. Considering +/- 2 or 3kb is a bit too much.

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written by GouthamAtla GouthamAtla

Just check this pipeline for enhancer RNA quantification from RNA-seq,

http://fun-science.club/PET/

You can also check the paper: Wu, Y, Yang, Y, Gu, H, et al. Multi‐omics analysis reveals the functional transcription and potential translation of enhancers. Int. J. Cancer. 2020; 1– 15. https://doi.org/10.1002/ijc.33132

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written by wuyc • wuyc

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