Sarah Hainer

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...

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.

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

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.

heatmaps from Hi-C data showing compartment structures

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

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...

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...

Oh please add me! Thank you for making this!

🧬 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...

These studies describe a mechanism by which the Chd1 is coupled to transcription elongation and the molecular consequences when this coupling is disrupted and provide insight into a domain in Chd1 for which little is known.

the Rtf1 mutation not being sufficient to break the interaction, and/or represent the complexity and redundancy present in this more complicated system.

So in a murine cell line system (ES cells) what happens? We made the CHCT deletions and an Rtf1 mutation ES cell line, but did not observe the same nucleosome shifts. This may be due to reduced protein levels observed in the Chd1 and Chd2 CHCT deletion cell lines...

Chd1 and Rtf1 are conserved proteins, so we wanted to know if this interaction is conserved in mammalian systems. Y2H using murine constructs demonstrate an interaction between Chd1 and Rtf1 as well as the related remodeler, Chd2, and Rtf1. CHCT deletions and Rtf1 mutations reduce this interaction

Histone PTMs, K4me3 and K36me3 are also shifted 5'

Notably, these precise interaction mutants seem to have a greater defect in nucleosome localization relative to full deletion, which demonstrates the multifunctional aspect of these proteins as well as the need for precision mutations.

As Chd1 is an important nucleosome remodeler, what does this loss of appropriate localization mean to genic nucleosomes? Well, nucleosomes (and overlapping dinucleosomes aka hexasome-nucleosomes) are also shifted 5', and this is exacerbated in Isw1 delete.

By mutating either side of this interaction (deleting the CHCT domain or precise point mutations in Rtf1), we find that while Rtf1 occupancy is unaltered, Chd1 occupancy is shifted 5'

Building off the finding from the Arndt lab in 2003 (10.1093/emboj/cdg179), we narrowed down an interaction between the understudied Chd1 CHCT domain and a N terminal LALA box in Rtf1, a member of the Paf1 elongation complex, which form a direct interaction in budding yeast

A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes Abstract. The nucleosome remodeler Chd1 is required for the re-establishment of nucleosome positioning in the wake of transcription elongation by RNA Polym

Our collaborative paper with the Arndt lab is out today: doi.org/10.1093/nar/... (originally bioRxiv: www.biorxiv.org/content/10.1...). Here we asked the question of how CHD1 localizes to chromatin.

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial.
rdcu.be/exXBX

Oh gosh Anders I am so sorry

Tenure track position alert! Assistant Professor of Molecular Therapeutics in MCB @UCBerkeley. Apply and come be our colleague! 🎉
aprecruit.berkeley.edu/JPF05098

We are hiring! The Dept of Microbiology and Molecular Genetics is looking for faculty at the Assistant or Associate professor level (tenure track). Please consider joining our vibrant microbiology and immunology community at the University of Pittsburgh School of medicine

Assistant/Associate/Full Professor (Botany & Plant Pathology) The Department of Botany and Plant Pathology invites applications for a full-time (1.00 FTE), 9-month, tenure-track or tenured Assistant, Associate, or Full Professor position.Any hiring at the rank o...

The successful candidate will oversee the management and direction of the OSU Herbarium and establish an independent research program by conducting original research in an area of plant systematics, ecology, and/or evolution.

Congrats Marco!