Sarah Hainer
@hainerlab.bsky.social
Assistant Prof @PittBioSci studying transcription dynamics and chromatin biology | passionate about equity in STEM | she/her
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.
September 18, 2025 at 3:00 PM
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.
September 18, 2025 at 3:00 PM
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.
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.
September 18, 2025 at 3:00 PM
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.
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.
September 18, 2025 at 3:00 PM
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.
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)
September 18, 2025 at 3:00 PM
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)
Similar to work from the Schubeler lab for BAF, we find that loss of neither BAF nor INO80C impact TAD structures significantly.
September 18, 2025 at 3:00 PM
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.
September 18, 2025 at 3:00 PM
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.
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.
September 18, 2025 at 3:00 PM
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.
48hr KD of the ATPase subunit for either complex has almost not impact on compartments, assessed by Hi-C:
September 18, 2025 at 3:00 PM
48hr KD of the ATPase subunit for either complex has almost not impact on compartments, assessed by Hi-C:
Oh please add me! Thank you for making this!
August 29, 2025 at 11:21 AM
Oh please add me! Thank you for making this!
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.
August 28, 2025 at 11:07 PM
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.
August 28, 2025 at 11:07 PM
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...
August 28, 2025 at 11:07 PM
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
August 28, 2025 at 11:07 PM
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'
August 28, 2025 at 11:07 PM
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.
August 28, 2025 at 11:07 PM
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.
August 28, 2025 at 11:07 PM
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'
August 28, 2025 at 11:07 PM
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
August 28, 2025 at 11:07 PM
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
Oh gosh Anders I am so sorry
August 21, 2025 at 11:25 AM
Oh gosh Anders I am so sorry