Bianca won the trainee career development award for her abstract at the Molecular and Cellular Oncology retreat at University of Colorado Cancer Center!
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!
Check out his talk on youtube:
Alexis won the CRTEC innovation award from University of Colorado Cancer Center!
The lab welcomes Abby from beautiful North Carolina. Learn more about her here.
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.
Excited to welcome Grace and Kamesh to the lab! Read more about them in the member page.
Our paper describing a new histone H3 mutant used in chemical cleavage mapping is out in Genome Biology! This mutation along with phenanthroline makes histone H3 a site-specific nuclease, releasing exactly 51 bp from a single nucleosome. Center of the 51 bp fragment is the exact nucleosome position (no processing – WYSIWYG bp resolution).
Ramachandran Lab is officially open!