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Sources of variation in cell-type RNA-Seq profiles journals.plos.org/plosone/articl…

Enjoying #recomb2022 so far. If I know you and you're here, or arriving for the main conference, let me know!

Poster #19, this afternoon! #RECOMB2022

Almost every ⁦WestJet⁩ flight, out of Calgary this evening (YYC) is delayed. The Customer Service lineup, directly below this sign, has a massive line of well over 50 people. What an unfortunate mess.

Coby is looking for a postdoc opportunity in the U.S. next and wants to pivot from computational genomics to molecular evolution and has an interest in performant algorithms. If you have any leads I hope you will chat with him! #KSChromatin23 #KSEpigenetics23

My posters are located next to each-other, with the (fewer) Q8/#KSChromatin23 posters, in the far back of Salon C. Looking forward to chatting about them! #KSChromatin23 #KSEpigenetics23 Keystone Symposia

4/We developed a method to explicitly model how cytosine modifications on one side of a base pair or the other might affect transcription factor binding. To do this we simply expand the alphabet, adding m for methylcytosine, h for hydroxymethylcytosine, and so on.

11/For example, while previous literature reported that JUND is "uniformly inhibited by 5mC", our analysis suggests that a minority of JUND motifs have a slight preference for 5mC.

12/FEZF2 appears to have two completely different motifs, one which prefers modified cytosine, and another which prefers unmodified cytosine.

13/For OCT4, our expanded alphabet analysis revealed a potential preference for 5-hydroxymethylcytosine. Unlike some of the other preferences described above, we could not find this described in the literature.

17/This methodology gives us evidence of the epigenetic modification state of the DNA that is actually bound to OCT4. And, as it turns out, OCT4 motifs are indeed preferentially bound when the sequence is hydroxymethylated!

1/Now published Genome Biology! Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. By Coby Viner Charles Ishak Nic Walker Hui Shi Marcela Sjöberg Shu Yi (Roxana) Shen David Adams Anne Ferguson-Smith Daniel De Carvalho Sarah Hainer et al! genomebiology.biomedcentral.com/articles/10.11…

Expanded DNA alphabet for gene regulation🧬 Beyond A/C/G/T, a study by Coby Viner and collaborators, led by Michael Hoffman @michaelhoffman.bsky.social University Health Network, added symbols like “m” and “h” to the genetic alphabet as a new way to study epigenetic regulation. >>genomebiology.biomedcentral.com/articles/10.11…

Very nice paper by @cobvinyer and colleagues in Michael Hoffman @michaelhoffman.bsky.social's lab. Methylation and Hydroxy-methylation decoding is really starting to be unpicked.