Question: What is the common method(s) to detect eRNAs by using RNA-seq data?
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gravatar for hegelwyc
20 months ago by
hegelwyc0
hegelwyc0 wrote:

Dear researchers,

This question may have been asked before, sorry for that. I have read several related papers, in their method part, the detection criteria remains ambiguous.I am curious about the widely-used way to detect enhancer RNAs (eRNAs) by using a RNAseq data.

Kind regards.

rna-seq erna enhancer rna • 1.5k views
ADD COMMENTlink modified 20 months ago • written 20 months ago by hegelwyc0
1

Its difficult to find eRNAs through RNA-Seq data. The eRNAs are transcribed at very low levels and are usually do not contains polyA tails. You need to use something like CAGE-Seq to find eRNAs.

ADD REPLYlink written 20 months ago by geek_y9.8k
1

I have improved my answer below by adding a table of all possible methods, which include what both geek_y and I have been saying.

ADD REPLYlink modified 19 months ago • written 20 months ago by Kevin Blighe45k
5
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

I presume that you mean enhancer-RNAs. There have been some landmark studies looking at enhancers and enhancer RNAs.

To infer a non-coding RNA as an enhancer RNA, it's transcription has to coincide with an enhancer region. Enhancer regions can be inferred by the presence of H3K27-acetylation marks, i.e., through ChIP-chip or ChIP-seq studies. The expression and identification of the eRNA would have to be inferred through through a cDNA microarray or RNA-seq. Mehylation of H3K4me1 at enhancer regions is also important in regulating transcription at the site.

The interesting studies:


Edit: November 2nd 2017

Here is a list of methods that can be used:

  • Reverse transcription-PCR (RT-PCR)
  • RNA fluorescence in situ hybridization (RNA-FISH)
  • RNA polymerase II chromatin immunoprecipitation coupled with high-throughput sequencing (RNAPII ChIP–seq)
  • Global run-on sequencing (GRO-seq)
  • 5′GRO-seq or GRO-cap
  • BruUV-seq
  • RNA-seq (total)
  • RNA-seq (poly(A))
  • Cap analysis of gene expression (CAGE) followed by deep sequencing
  • Chromatin- bound RNA-seq
  • RNA-Seq in isolated 'transcription factories'
  • Native elongating transcript sequencing (NET-seq)
  • RNA capture sequencing (CaptureSeq)
  • Chromatin isolation by RNA purification (ChIRP-seq)

[source: http://www.nature.com/nrg/journal/v17/n4/fig_tab/nrg.2016.4_T1.html]

ADD COMMENTlink modified 20 months ago • written 20 months ago by Kevin Blighe45k

I guess, its not possible to detect eRNAs by microarray or traditional RNA-Seq data.

ADD REPLYlink written 20 months ago by geek_y9.8k
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Gracias por el comentario. As with everything in life, there is diversity, and eRNAs can be both polyadenylated and non-polyadenylated.

ADD REPLYlink modified 20 months ago • written 20 months ago by Kevin Blighe45k
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Thanks, the review you attached states that "Sometimes, by pure chance, the DNA around enhancers may harbor splicing acceptor and donor sites, even perhaps polyadenylation cassettes, in which case the corresponding eRNA becomes spliced, polyadenylated, and stable. These processed and stable eRNAs, now fitting the current defining criteria for lncRNAs".

Its a minute percentage that are polyadenylated.

ADD REPLYlink modified 20 months ago • written 20 months ago by geek_y9.8k

See my edited answer above. We are both correct in what we are saying.

ADD REPLYlink written 20 months ago by Kevin Blighe45k

Why are you so sure that it is not possible to detect these by cDNA microarray? If the eRNAs are known, then a specially-designed cDNA microarray will surely be capable of detecting these (but obviously not de novo identification of them). It will also detect the polyadenylated linc-RNAs that behave as enhancer RNAs.

ADD REPLYlink modified 15 months ago • written 20 months ago by Kevin Blighe45k
1

Sure. cDNA microarray could be used. Thankfully cDNA microarray is not mentioned in the nature reference paper. May be its a mistake that I assumed the OP wants to identify eRNAs from traditional RNA/Seq data.

ADD REPLYlink written 20 months ago by geek_y9.8k
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