Author: trsrinivas

Lab’s first preprint is out!!!

Check it out here: https://www.biorxiv.org/content/10.1101/2020.08.17.253146v1

Here is a tweetorial on the paper:

Excited to share the first preprint from our lab!!! We started by asking a simple question of how proteins bound enhancers and ended up with really cool results on transcription factor cooperativity. 1/

We used short (<50 bp) MNase-protected fragments to identify TF binding at high-resolution in enhancers in Drosophila cells and found on average 4 (!!!) TF binding events within ~500 bp enhancers 2/

We found a way to use V-plots to ask if two of the TFs bound at the same time in these enhancers – and found most of the time they do! 3/

We orthogonally confirmed TFs binding at the same time using dSMF data generated by @arnaud_kr in the same cells

We also confirmed co-binding of TFs by comparing Native ChiP and CUT&RUN at GAGA factor (TRL) binding sites 5/

Finally, we saw cooperativity of TF binding at enhancers to correlate with BOTH nucleosome occupancy and turnover, pointing to cooperative binding as a means to displace nucleosomes from enhancers 6/

I want to thank my co-authors and collaboratorsr @satyaiiitm @KamiAhmad3. And this work wouldn't have been complete without amazing previous work from @AlexanderStark8 on STARR-seq and @arnaud_kr on dSMF!

Originally tweeted by Srinivas Ramachandran (@4everBiochemist) on August 18, 2020.

Srinivas selected as a Pew-Stewart Scholar

Very grateful for our research on plasma cell free-DNA to be recognized by the Pew Charitable Trusts and the Alexander and Margaret Stewart Trust.

https://www.pewtrusts.org/en/about/news-room/press-releases-and-statements/2020/06/15/5-pew-stewart-scholars-selected-to-spearhead-innovative-cancer-research

https://news.cuanschutz.edu/cancer-center/pew-stewart-scholar