Sarah Hainer
@hainerlab.bsky.social
Assistant Prof @PittBioSci studying transcription dynamics and chromatin biology | passionate about equity in STEM | she/her
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.
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:
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'
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
Happy New Year from us to you!
January 1, 2025 at 3:22 AM
Happy New Year from us to you!
Excited by these findings we made some mutants in mES cells to ask if disrupting this interaction resulted in similar changes to CHD distribution and nucleosome positions. Perhaps due to complexity or resolution, we don't observe these changes.
December 10, 2024 at 12:19 AM
Excited by these findings we made some mutants in mES cells to ask if disrupting this interaction resulted in similar changes to CHD distribution and nucleosome positions. Perhaps due to complexity or resolution, we don't observe these changes.
Is this mechanism for Chd1 distribution conserved in mammals? To test these we asked if murine CHD1 and CHD2 (close homolog) interact with murine RTF1 using yeast two hybrid, and yes, they do! And in fact, this is the conserved LALA box (LLSLA in mammals) and CHD1/2 CHCT
December 10, 2024 at 12:19 AM
Is this mechanism for Chd1 distribution conserved in mammals? To test these we asked if murine CHD1 and CHD2 (close homolog) interact with murine RTF1 using yeast two hybrid, and yes, they do! And in fact, this is the conserved LALA box (LLSLA in mammals) and CHD1/2 CHCT
This also results in a concordant 5' shift in resident histone posttranlational modifications
December 10, 2024 at 12:19 AM
This also results in a concordant 5' shift in resident histone posttranlational modifications
This disrupted interaction and 5' Chd1 shift then leads to a 5' shift of nucleosomes, subnucleosomes, dinucleosomes, and hexasome-nucleosome (OLDN) complexes.
December 10, 2024 at 12:19 AM
This disrupted interaction and 5' Chd1 shift then leads to a 5' shift of nucleosomes, subnucleosomes, dinucleosomes, and hexasome-nucleosome (OLDN) complexes.
Using precise mutants that disrupt this interaction, Sarah found 5' shift in Chd1 localization across genes, with modest effects on RNAPII and Rtf1 occupancy
December 10, 2024 at 12:19 AM
Using precise mutants that disrupt this interaction, Sarah found 5' shift in Chd1 localization across genes, with modest effects on RNAPII and Rtf1 occupancy
Following up from earlier studies from the Arndt lab, Sarah narrowed the interaction between Rtf1 and Chd1 to a region in the N term of Rtf1 we termed the LALA box and the Chd1 CHCT domain. Notably yeast Chd1 chromodomains do not bind K4me3 like mammalian Chd1 chromodomains
December 10, 2024 at 12:19 AM
Following up from earlier studies from the Arndt lab, Sarah narrowed the interaction between Rtf1 and Chd1 to a region in the N term of Rtf1 we termed the LALA box and the Chd1 CHCT domain. Notably yeast Chd1 chromodomains do not bind K4me3 like mammalian Chd1 chromodomains
What an amazing time! Students at #ABRCMS2024 were so impressive! Incredibly proud of all the Pitt Biosci undergrads and grad students
November 18, 2024 at 2:02 AM
What an amazing time! Students at #ABRCMS2024 were so impressive! Incredibly proud of all the Pitt Biosci undergrads and grad students
I could not be more proud of these two amazing women: I told you to watch out for Kya Foxx last year: here she goes giving a talk and winning! And then introducing Bryona Jackson who you should be on the lookout for; just won a poster presentation award. #ABRCMS2024
November 17, 2024 at 3:18 AM
I could not be more proud of these two amazing women: I told you to watch out for Kya Foxx last year: here she goes giving a talk and winning! And then introducing Bryona Jackson who you should be on the lookout for; just won a poster presentation award. #ABRCMS2024
Pitt BIOSC undergrads at #ABRCMS2024
November 15, 2024 at 12:27 AM
Pitt BIOSC undergrads at #ABRCMS2024
Pitt Biosci grad students at #ABRCMS2024! So many amazing posters last night!
November 14, 2024 at 12:25 PM
Pitt Biosci grad students at #ABRCMS2024! So many amazing posters last night!
Kya Foxx checking her talk for Friday at 11:15am (CC-407) #ABRCMS2024 #proudmentor
November 13, 2024 at 7:38 PM
Kya Foxx checking her talk for Friday at 11:15am (CC-407) #ABRCMS2024 #proudmentor