Three @biorxivpreprint.bsky.social preprints on acute depletion of FACT in ES cells. First, from my colleague at Pitt Sarah Hainer's lab 1/ www.biorxiv.org/content/10.6...
27.02.2026 20:44
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Three @biorxivpreprint.bsky.social preprints on acute depletion of FACT in ES cells. First, from my colleague at Pitt Sarah Hainer's lab 1/ www.biorxiv.org/content/10.6...
Please send us feedback! Also, Rithika is beyond amazing and please watch for her applications in the near future :)
We are grateful to the Milne group for discussion of their data prior to posting and submission and encourage you to look at their beautiful work www.biorxiv.org/content/10.6...
We are grateful to the @dewitlab.bsky.social lab for sharing the SOX2-dTAG and NANOG-dTAG cell lines that served as nice controls (see Supp Fig. 3!)
We are grateful to @epicypher.bsky.social for sharing the Hia5 enzyme and assisting with Fiber-seq.
We are grateful to @flurylab.bsky.social and @groth-anja.bsky.social for sharing their SSRP1-dTAG cell line with us, and encourage you to take a peek at their amazing manuscript also online: www.biorxiv.org/content/10.6...
Together these data reveal a temporal cascade in which FACT depletion causes 5’ loss of nucleosomes and their associated histone modifications. This chromatin disruption occurs prior to transcriptional inhibition
More in the paper so take a look!
Ultimately, we observe transcriptional collapse and more specifically downregulation of genes. But this happens well after the initial reduction in nucleosome phasing observed.
So what impact does this have? Well, loss of histone recycling leads to a build up of RNAPII in the 5' end of genes and reduced transcription elongation, as indicated by changes to H3K36me3.
I told you that FACT's impact is greatest at highly transcribed locations, but does it require transcription? Again inspired by the Robert lab, we show that yes, FACT's function is dependent on transcription
This suggests that FACT loss is leading to a partially irreversible alteration to the epigenome.
Can we rescue this defect by bringing FACT back? Work led by our amazing undergraduate research Bryona Jackson found that there is only a partial restoration. Note for others: washing out dTAG doesn't always work, so we resorted to crafty ways of rescuing. But not full restoration.
Is the 5' nucleosome loss and increased TF invasion occurring at the same place? Yes! Over highly transcribed locations especially, which rely more on FACT activity
We corroborated our short read sequencing results with single molecule long read Fiber-seq and found reduce 5' and increased 3' nucleosomes in FACT depletion
How is this happening? Beautiful work from F. Robert group in budding yeast found FACT is important for recycling of histone PTMs, and inspired by this we hypothesized that chromatin opening would permit TF invasion. We found that 5' nucleosome phasing is lost over time in FACT depletion.
However, using rapid dTAG depletion and high resolution time course analysis, we find that FACT depletion results in TF impingement into gene bodies, in a sequence independent manner, but occurring more readily over highly transcribed genes.
Following up from our prior study that examined FACT function in ES cells (link.springer.com/article/10.1...) we asked whether FACT regulates transcription factor occupancy. Given that FACT loss leads to differentiation, our simple model was that FACT depletion would result in reduced TF occupancy.
Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...
Very sad news. Gail Martin (1944-2026) was a figure in developmental biology. She pioneered the field of ES cells.
A great colleague, a friend and a lovely person.
Happy Black History Month! I am sharing a permanent and continuously updated list of inspiring Black scientists! Check it out! Huge thank you to the folks who gathered this info. Thank you to @drstarbird.bsky.social and the rest of the Index Committee! www.wiley.com/en-us/resear...
* vaccines keep kids from dying
* guns cause kids to die
these are unassailable conclusions based on mountains of evidence
it is a crying shame that politicians pretend otherwise, endangering our kids and everyone else’s
Comment period ends on Monday for a proposed rule change that would terminate student visas after 4 years. It also puts limits on exchange visitors and reps of foreign media, and shortens the length of time at the end of the visa from 60 days to 30 days.
www.federalregister.gov/documents/20...
And while there were also minimal impacts on loops, our PCMC data suggest that BAF and INO80C are not general regulators of chromatin looping but may instead fine-tune regulatory interactions at distinct key developmental loci in ES cells.
Overall, our study suggests that esBAF and INO80 have limited influence on large-scale 3D genome architecture. However, subcompartment organization is sensitive to remodeler depletion, indicating a more nuanced role for these complexes in shaping chromatin topology at sub-megabase scales.
Enhancer-promoter loops impacted by BRG1 or INO80 loss are enriched for OCT4, SOX2, NANOG and SUZ12, and are described as bivalent locations.
For both these remodelers, these tend to be OSN bound and also Suz12 bound, and enriched as bivalent promoters. Together, these data suggest that the enhancer-promoter loops esBAF promotes and INO80C restricts are pluripotency and bivalency related.
Promoter capture microC (PCMC) enriches for TSS-based loops and shows decreased loops in Brg1 KD and increased loops in Ino80 KD
Therefore, to investigate the impact of these remodelers more directly on enhancer-promoter loops, we performed promoter capture microC (PCMC) and found that KD of BAF ATPase BRG1 results in decreases in some E-P loops and KD of INO80C ATPase Ino80 results in increases in some E-P loops.
Our Hi-C data detects limited TSS-based loops, but is enriched for CTCF-based (architectural) loops
Although we sequenced our Hi-C datasets deeply, we had a tough time calling non-architectural loops (most loops were CTCF-based, and not as many were TSS-based)
Hi-C data analyzed for TAD structures
Similar to work from the Schubeler lab for BAF, we find that loss of neither BAF nor INO80C impact TAD structures significantly.
We therefore thing that BRG1 and INO80 contribute to the maintenance of active subcompartment organization (we are saying "fine-tune"), with effects that are especially pronounced at loci where these remodelers bind and/or their loss impacts transcription.
