Jon Henninger
@jhenninger.bsky.social
Assistant Professor | Carnegie Mellon University | RNA-directed control of transcription and cell fate | Biomolecular condensates
https://labs.bio.cmu.edu/henninger/
https://labs.bio.cmu.edu/henninger/
Really looking forward to presenting our lab's most recent work on transcriptional control and a surprising non-enzymatic function for RNA polymerase II
🔔Join us next Wednesday for #FragileNucleosome! 2 fantastic talks on chromatin regulation:🔬 @mariamafau.bsky.social on ZIC2's dual role in neural induction 🔬 @jhenninger.bsky.social on how RNA-binding proteins drive transcription
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
November 26, 2025 at 3:55 PM
Really looking forward to presenting our lab's most recent work on transcriptional control and a surprising non-enzymatic function for RNA polymerase II
Reposted by Jon Henninger
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Jon Henninger
We’re excited to share our new work in Soft Matter: doi.org/10.1039/D5SM...
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
Condensation and activator/repressor control of a transcription-regulated biomolecular liquid
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by util...
doi.org
November 21, 2025 at 10:27 AM
We’re excited to share our new work in Soft Matter: doi.org/10.1039/D5SM...
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
Reposted by Jon Henninger
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Jon Henninger
Interested in pursuing a Ph.D. in Biological Sciences?
Join Carnegie Mellon University’s info session on Nov. 12 to learn how our program prepares students to become impactful scientific leaders.
apply-dc-mcs.mcs.cmu.edu/register/?id...
Join Carnegie Mellon University’s info session on Nov. 12 to learn how our program prepares students to become impactful scientific leaders.
apply-dc-mcs.mcs.cmu.edu/register/?id...
PhD Biological Sciences Virtual Info Session
apply-dc-mcs.mcs.cmu.edu
November 5, 2025 at 7:58 PM
Interested in pursuing a Ph.D. in Biological Sciences?
Join Carnegie Mellon University’s info session on Nov. 12 to learn how our program prepares students to become impactful scientific leaders.
apply-dc-mcs.mcs.cmu.edu/register/?id...
Join Carnegie Mellon University’s info session on Nov. 12 to learn how our program prepares students to become impactful scientific leaders.
apply-dc-mcs.mcs.cmu.edu/register/?id...
Reposted by Jon Henninger
(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.
November 4, 2025 at 5:58 PM
(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.
Reposted by Jon Henninger
CMU biologist @jhenninger.bsky.social is uncovering how RNA shapes gene expression and drives disease. His lab is developing tools to visualize transcription and design RNA-based therapies, paving the way for precision treatments for cancers like leukemia.
www.cmu.edu/mcs/news-eve...
www.cmu.edu/mcs/news-eve...
Henninger Explores Targeting RNA in Cancer Prevention, Treatment
Jonathan Henninger, assistant professor of biological sciences at Carnegie Mellon, is finding ways to treat cancer with molecular precision.
www.cmu.edu
October 27, 2025 at 7:30 PM
CMU biologist @jhenninger.bsky.social is uncovering how RNA shapes gene expression and drives disease. His lab is developing tools to visualize transcription and design RNA-based therapies, paving the way for precision treatments for cancers like leukemia.
www.cmu.edu/mcs/news-eve...
www.cmu.edu/mcs/news-eve...
Make an impact in Pittsburgh! We are seeking the next Head of the Dept. of Bio Sciences, with Ferra Executive Search. Nominate or refer now: apply.interfolio.com/174916
#STEMLeadership #HigherEd #LifeSciences #AcademicJobs #jobs #Pittsburgh #CarnegieMellonUniversity #FerraSearch #BiologyChair
#STEMLeadership #HigherEd #LifeSciences #AcademicJobs #jobs #Pittsburgh #CarnegieMellonUniversity #FerraSearch #BiologyChair
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 14, 2025 at 2:17 PM
Make an impact in Pittsburgh! We are seeking the next Head of the Dept. of Bio Sciences, with Ferra Executive Search. Nominate or refer now: apply.interfolio.com/174916
#STEMLeadership #HigherEd #LifeSciences #AcademicJobs #jobs #Pittsburgh #CarnegieMellonUniversity #FerraSearch #BiologyChair
#STEMLeadership #HigherEd #LifeSciences #AcademicJobs #jobs #Pittsburgh #CarnegieMellonUniversity #FerraSearch #BiologyChair
Reposted by Jon Henninger
Happy to share our latest in @natcomputsci.nature.com
led by (amazing) Ryan Krueger + colab w M. Brenner!
We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations.
🧬 doi.org/10.1038/s435...
📰 www.mccormick.northwestern.edu/news/article...
led by (amazing) Ryan Krueger + colab w M. Brenner!
We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations.
🧬 doi.org/10.1038/s435...
📰 www.mccormick.northwestern.edu/news/article...
October 10, 2025 at 6:16 PM
Happy to share our latest in @natcomputsci.nature.com
led by (amazing) Ryan Krueger + colab w M. Brenner!
We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations.
🧬 doi.org/10.1038/s435...
📰 www.mccormick.northwestern.edu/news/article...
led by (amazing) Ryan Krueger + colab w M. Brenner!
We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations.
🧬 doi.org/10.1038/s435...
📰 www.mccormick.northwestern.edu/news/article...
Reposted by Jon Henninger
I am super excited to announce that we have a tenure-track faculty position in biophysics open in the Department of Physics at Carnegie Mellon! 🧪
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
September 26, 2025 at 3:35 PM
I am super excited to announce that we have a tenure-track faculty position in biophysics open in the Department of Physics at Carnegie Mellon! 🧪
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
Reposted by Jon Henninger
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
I am extremely grateful for the support from the Samuel and Emma Winters Foundation! This award directly supports our research on targeting RNA sequences as potential therapies in multiple disorders, including cancer.
🎉 The Department of Medicine is delighted to announce the 2025 Samuel and Emma Winters Foundation awardees! These awards support junior faculty pushing the boundaries of biomedical research in Pittsburgh.
🧵 Meet this year’s awardees:
🧵 Meet this year’s awardees:
September 25, 2025 at 2:55 PM
I am extremely grateful for the support from the Samuel and Emma Winters Foundation! This award directly supports our research on targeting RNA sequences as potential therapies in multiple disorders, including cancer.
Reposted by Jon Henninger
Preprint!
Inspired by condensates that form on specific DNA, we ask:
can we design multicomponent fluids to form distinct condensates on diff. surfaces?
i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization!
arxiv.org/abs/2509.08100
(1/2)
Inspired by condensates that form on specific DNA, we ask:
can we design multicomponent fluids to form distinct condensates on diff. surfaces?
i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization!
arxiv.org/abs/2509.08100
(1/2)
September 22, 2025 at 9:38 PM
Preprint!
Inspired by condensates that form on specific DNA, we ask:
can we design multicomponent fluids to form distinct condensates on diff. surfaces?
i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization!
arxiv.org/abs/2509.08100
(1/2)
Inspired by condensates that form on specific DNA, we ask:
can we design multicomponent fluids to form distinct condensates on diff. surfaces?
i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization!
arxiv.org/abs/2509.08100
(1/2)
Reposted by Jon Henninger
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...
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
September 18, 2025 at 3:00 PM
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...
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...
Reposted by Jon Henninger
The GRFP lives!! (due end of October)
www.nsf.gov/funding/oppo...
www.nsf.gov/funding/oppo...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
September 8, 2025 at 6:23 PM
The GRFP lives!! (due end of October)
www.nsf.gov/funding/oppo...
www.nsf.gov/funding/oppo...
Reposted by Jon Henninger
Reposted by Jon Henninger
New in @pnas.org with @gladfelterlab.bsky.social @sneadlab.bsky.social ! 📢
Cells use condensates (dynamic compartments without membranes) to organize key reactions. Some condensates have core & shell layers… but how do such layers form? 🤔
👉 pnas.org/doi/10.1073/pnas.2504778122 (1/6)
Cells use condensates (dynamic compartments without membranes) to organize key reactions. Some condensates have core & shell layers… but how do such layers form? 🤔
👉 pnas.org/doi/10.1073/pnas.2504778122 (1/6)
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
pnas.org
September 4, 2025 at 2:44 AM
New in @pnas.org with @gladfelterlab.bsky.social @sneadlab.bsky.social ! 📢
Cells use condensates (dynamic compartments without membranes) to organize key reactions. Some condensates have core & shell layers… but how do such layers form? 🤔
👉 pnas.org/doi/10.1073/pnas.2504778122 (1/6)
Cells use condensates (dynamic compartments without membranes) to organize key reactions. Some condensates have core & shell layers… but how do such layers form? 🤔
👉 pnas.org/doi/10.1073/pnas.2504778122 (1/6)
The deadline is coming up for this fantastic meeting on all things RNA in gene regulation. Highly recommend!
www.fusion-conferences.com/conference/1...
www.fusion-conferences.com/conference/1...
2nd Genome Regulation through RNA Conference | Fusion Conferences
Our scientific research conferences support the development of physical, medical and life sciences, providing a powerful platform that encourages discussion and collaboration in luxury locations acros...
www.fusion-conferences.com
September 3, 2025 at 4:23 PM
The deadline is coming up for this fantastic meeting on all things RNA in gene regulation. Highly recommend!
www.fusion-conferences.com/conference/1...
www.fusion-conferences.com/conference/1...
Reposted by Jon Henninger
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!
register here for the entire series: us06web.zoom.us/webinar/regi...
register here for the entire series: us06web.zoom.us/webinar/regi...
September 1, 2025 at 2:59 PM
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!
register here for the entire series: us06web.zoom.us/webinar/regi...
register here for the entire series: us06web.zoom.us/webinar/regi...
Reposted by Jon Henninger
Final version of Bingbing Duan’s main thesis work is out now now in Nature Communications @natureportfolio.nature.com www.nature.com/articles/s41... I’m so pleased with this study that we’ve been working on for so long #epistasis #transcription #geneexpression 1/
Widespread epistasis shapes RNA polymerase II active site function and evolution - Nature Communications
The active site of RNA Polymerase II is highly conserved. Here the authors show that mutations can propagate effects across the enzyme and alter genetic behavior of distal residues, demonstrating plas...
www.nature.com
August 28, 2025 at 1:33 AM
Final version of Bingbing Duan’s main thesis work is out now now in Nature Communications @natureportfolio.nature.com www.nature.com/articles/s41... I’m so pleased with this study that we’ve been working on for so long #epistasis #transcription #geneexpression 1/
Reposted by Jon Henninger
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.
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
doi.org
August 28, 2025 at 11:07 PM
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.
Reposted by Jon Henninger
Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!
tinyurl.com/ydn6e3ac
tinyurl.com/ydn6e3ac
June 30, 2025 at 9:15 PM
Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!
tinyurl.com/ydn6e3ac
tinyurl.com/ydn6e3ac
Reposted by Jon Henninger
Hot off the press for your Friday morning! 🔥 Our new (and highly revised!) preprint is out. It significantly expands on our previous work, unveiling exciting new data on how CBP's intrinsically disordered regions (IDRs) regulate genes.
Link to preprint: tinyurl.com/5npjkyps
#IDRs #condensates #CBP
Link to preprint: tinyurl.com/5npjkyps
#IDRs #condensates #CBP
CBP-IDRs regulate acetylation and gene expression.
Intrinsically disordered regions (IDRs) have emerged as crucial regulators of protein function, allowing proteins to sense and respond to their environment. Creb binding protein (CBP) and EP300 (p300)...
tinyurl.com
June 6, 2025 at 9:53 AM
Hot off the press for your Friday morning! 🔥 Our new (and highly revised!) preprint is out. It significantly expands on our previous work, unveiling exciting new data on how CBP's intrinsically disordered regions (IDRs) regulate genes.
Link to preprint: tinyurl.com/5npjkyps
#IDRs #condensates #CBP
Link to preprint: tinyurl.com/5npjkyps
#IDRs #condensates #CBP
Reposted by Jon Henninger
Reposted by Jon Henninger
Now published! Big congrats to first author @gginell.bsky.social
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
May 23, 2025 at 11:31 AM
Now published! Big congrats to first author @gginell.bsky.social
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...