Andy Katznelson
@andykatznelson.bsky.social
PhD student in the Zaret lab at Penn
Fairly sure my UG course used primate 16s rDNA or mitochondrial genes to learn tools of the trade. And then once more sophisticated, re-analysis of viral genomes to track epidemiological spread via character evolution etc.
March 25, 2025 at 7:49 PM
Fairly sure my UG course used primate 16s rDNA or mitochondrial genes to learn tools of the trade. And then once more sophisticated, re-analysis of viral genomes to track epidemiological spread via character evolution etc.
Structures of TFs bound to core histone (Sox2, Cramer, PU.1/FoxA1 Bai, OCT4 Halic, ect) shows a mechanistic solution for stable binding on nuc. Of course stable structures would be biased for in the cryoEM densities.
I do like the idea of transient interactions, but these are hard to study! By FRET?
I do like the idea of transient interactions, but these are hard to study! By FRET?
February 18, 2025 at 5:41 PM
Structures of TFs bound to core histone (Sox2, Cramer, PU.1/FoxA1 Bai, OCT4 Halic, ect) shows a mechanistic solution for stable binding on nuc. Of course stable structures would be biased for in the cryoEM densities.
I do like the idea of transient interactions, but these are hard to study! By FRET?
I do like the idea of transient interactions, but these are hard to study! By FRET?
Many have tested this! Most compelling IMO are that foxa1 re-ChIP’s with core histone, overlapping MNase-resistant chromatin (Iwafuchi/Zaret) pmc.ncbi.nlm.nih.gov/articles/PMC...
And C&R distinguish pioneering/nuc binding events by fragment size (Meers/Henikoff)
pmc.ncbi.nlm.nih.gov/articles/PMC...
And C&R distinguish pioneering/nuc binding events by fragment size (Meers/Henikoff)
pmc.ncbi.nlm.nih.gov/articles/PMC...
The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation
Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucle...
pmc.ncbi.nlm.nih.gov
February 18, 2025 at 4:01 PM
Many have tested this! Most compelling IMO are that foxa1 re-ChIP’s with core histone, overlapping MNase-resistant chromatin (Iwafuchi/Zaret) pmc.ncbi.nlm.nih.gov/articles/PMC...
And C&R distinguish pioneering/nuc binding events by fragment size (Meers/Henikoff)
pmc.ncbi.nlm.nih.gov/articles/PMC...
And C&R distinguish pioneering/nuc binding events by fragment size (Meers/Henikoff)
pmc.ncbi.nlm.nih.gov/articles/PMC...
Also… the Waymo seats are super comfy
January 6, 2025 at 11:50 PM
Also… the Waymo seats are super comfy
Hah, an n-of-1 of someone being inconvenienced seems better than the reality of hundreds of car deaths per day
January 6, 2025 at 11:49 PM
Hah, an n-of-1 of someone being inconvenienced seems better than the reality of hundreds of car deaths per day
Fantastic convo. And at times contained painful lessons that made me reflect on my own process. Thank you for this!!
December 20, 2024 at 3:34 PM
Fantastic convo. And at times contained painful lessons that made me reflect on my own process. Thank you for this!!
Wow, big congrats to Jailynn and co!
November 22, 2024 at 8:21 PM
Wow, big congrats to Jailynn and co!