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Reposted by Sarah Hainer

Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 11d

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...

Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media

Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...

www.federalregister.gov

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Sarah Hainer @hainerlab.bsky.social · 20d

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.

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Sarah Hainer @hainerlab.bsky.social · 20d

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.

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Sarah Hainer @hainerlab.bsky.social · 20d

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.

Enhancer-promoter loops impacted by BRG1 or INO80 loss are enriched for OCT4, SOX2, NANOG and SUZ12, and are described as bivalent locations.

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Sarah Hainer @hainerlab.bsky.social · 20d

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.

Promoter capture microC (PCMC) enriches for TSS-based loops and shows decreased loops in Brg1 KD and increased loops in Ino80 KD

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Sarah Hainer @hainerlab.bsky.social · 20d

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)

Our Hi-C data detects limited TSS-based loops, but is enriched for CTCF-based (architectural) loops

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Sarah Hainer @hainerlab.bsky.social · 20d

Similar to work from the Schubeler lab for BAF, we find that loss of neither BAF nor INO80C impact TAD structures significantly.

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Sarah Hainer @hainerlab.bsky.social · 20d

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.

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Sarah Hainer @hainerlab.bsky.social · 20d

However, there is a reproducible effect on subcompartment structures, where upon KD of either ATPase, we observed a modest increase in the total amount of the genome assigned to inactive subcompartments, especially at locations that these remodelers bind and regulate transcription.

subcompartment analysis of Hi-C data showing impact of remodeler depletion on subcompartments

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Sarah Hainer @hainerlab.bsky.social · 20d

48hr KD of the ATPase subunit for either complex has almost not impact on compartments, assessed by Hi-C:

heatmaps from Hi-C data showing compartment structures

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Sarah Hainer @hainerlab.bsky.social · 20d

New preprint is up, led by former postdoc Braulio Bonilla.
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions

The genome is compacted in the nucleus through a hierarchical chromatin organization, ranging from chromosome territories to compartments, topologically associating domains (TADs), and individual nucl...

www.biorxiv.org

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Sarah Hainer @hainerlab.bsky.social · Aug 29

Oh please add me! Thank you for making this!

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Reposted by Sarah Hainer

Lucas Farnung @lucas.farnunglab.com · Aug 29

🧬 Transcription elongation by RNA polymerase II relies on a web of elongation factors. Our new work shows how IWS1 acts as a modular scaffold to stabilize & stimulate elongation. Fantastic work by Della Syau! www.biorxiv.org/content/10.1...