linc noncoding RNA from chIPseq

Question

[kanwarjag]

We performed chipseq few years back and wonder can we use same data to identify long noncoding RNA wnrichment in the same dataset. I found number of papers for identification of lincRNA from RNA seq but not from Chip seq. My idea is if there is a dataset of lincRNA (mouse genome) and I map those coordinates to my chipseq data and apply a statistical model to find enrichment that may serve the purpose. However, I am not very confident about this procedure. Any thought is there is work flow to identify lincRNA from Chipseq data.

Thanks

Answer 1

[GouthamAtla]

As a first step, you can take the LncRNAs from the standard annotations, and check if there is any ChIP-Seq peak in the vicinity of any LncRNAs ( lets say within +/- 50kb ). LncRNAs are highly tissue specific, so you could focus on the LncRNAs that are relevant to the tissue/cells on which ChIP-Seq data is generated.