Great thread! I’d like to add that TFs can genuinely be located at nucleosomal DNA. If that is the case, you might be looking at a pioneering factor.

I get butterflies when omics technologies get married.

Great paper! The section on variable number tandem repeats within genes blew my mind. I have never heard of them before.

RIC-seq for global in situ profiling of RNA–RNA spatial interactions - Nature RNA in situ conformation sequencing (RIC-seq) enables the generation of three-dimensional interaction maps of RNA in cells, which sheds light on the interactions and regulatory functions of RNA.

Have you ever wondered how enhancers and gene promoters find each other? One possible explanation is the binding of enhancer RNA to target antisense promoter RNA. You can detect these non-coding RNA interactions using a relatively new biotechnology called in situ conformation sequencing (RIC-seq).

What brand of LLPS do you support? My circle is starting to explore transcriptional condensates so this got my attention.

#bioinformatics #biology #epigenetics

Did the method not work for ChIP-seq or MNase-seq? Surely there are low-entropy regions in MNase-seq because there should be equal nucleosome peaks throughout the genome. Seems like applying this method to other omics data could be low-hanging fruit for publication.

The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping - PubMed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a recent development for epigenome mapping, but its unique methodology can hamper proper quantitative analyses. As traditional normalization approaches have been shown to be inaccurate, we sought to determine endogenous normalization …

Have you performed CUT&RUN and forgot to add spike-in normalization? No worries! The CUT&RUN greenlist (pubmed.ncbi.nlm.nih.gov/38279652/) can accurately normalize your samples computationally by selecting low-entropy regions. The method looks accurate but I still have questions...