John Ridenour
@ridenourjb.bsky.social
Assistant Staff Scientist in the Donczew lab at OMRF | broadly interested in how chromatin and other stuff regulate transcription | he/him
Reposted by John Ridenour
Nice work!
#mRNP #Condensation #Stress #Yeast
Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress: Molecular Cell www.cell.com/molecular-ce...
#mRNP #Condensation #Stress #Yeast
Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress: Molecular Cell www.cell.com/molecular-ce...
Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress
Under stress, cells adapt their gene expression programs through changes in transcription
and translation. It is unclear how cells determine which mRNAs are translated or repressed.
Zedan et al. show ...
www.cell.com
December 1, 2025 at 11:50 PM
Nice work!
#mRNP #Condensation #Stress #Yeast
Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress: Molecular Cell www.cell.com/molecular-ce...
#mRNP #Condensation #Stress #Yeast
Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress: Molecular Cell www.cell.com/molecular-ce...
Reposted by John Ridenour
Nice work!
#mRNP #Condensation #Stress #Yeast
Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs: Molecular Cell www.cell.com/molecular-ce...
#mRNP #Condensation #Stress #Yeast
Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs: Molecular Cell www.cell.com/molecular-ce...
Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs
Glauninger, Bard, Wong Hickernell, et al. reveal that stress causes transcriptome-wide
mRNP condensation, largely independent of length and often without stress granule
formation, but newly synthesize...
www.cell.com
December 1, 2025 at 11:51 PM
Nice work!
#mRNP #Condensation #Stress #Yeast
Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs: Molecular Cell www.cell.com/molecular-ce...
#mRNP #Condensation #Stress #Yeast
Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs: Molecular Cell www.cell.com/molecular-ce...
Reposted by John Ridenour
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by John Ridenour
New preprint! A bold aspiration, to target and control genes as chromatin complexes, not as nucleotide strings. How it started: total noise. New resolution: fuzzy blobs coming into focus. Not perfect yet but a huge step. khayneslab.wordpress.com/2025/11/27/r...
Research – bioRxiv – Decoding Gene Responsiveness to Synthetic Chromatin Reader-Actuators with Multi-Modal Epigenomic Profiling
Decoding Gene Responsiveness to Synthetic Chromatin Reader-Actuators with Multi-Modal Epigenomic ProfilingKim SH, Enwerem-Lackland I, Williams NL, Fisher R, Plaisier CL, Haynes KA. (2024) bioRxiv.D…
khayneslab.wordpress.com
November 29, 2025 at 3:06 AM
New preprint! A bold aspiration, to target and control genes as chromatin complexes, not as nucleotide strings. How it started: total noise. New resolution: fuzzy blobs coming into focus. Not perfect yet but a huge step. khayneslab.wordpress.com/2025/11/27/r...
Reposted by John Ridenour
Sign up to present your work in the @fnucleosome.bsky.social seminar series!
Do you have an exciting new chromatin/transcription story that you'd like to share with the #FN community?
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Application to speak in the Fragile Nucleosome series
Thank you for your interest in our seminar series!
We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...
forms.gle
November 24, 2025 at 7:21 PM
Sign up to present your work in the @fnucleosome.bsky.social seminar series!
Reposted by John Ridenour
🌟 G&D SPOTLIGHT 🌟
RESEARCH PAPER: Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate
By Franklin et al., and Sihem Cheloufi
➡️ https://genesdev.cshlp.org/content/39/9-10/652.abstract
#histones #transcription #replication
RESEARCH PAPER: Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate
By Franklin et al., and Sihem Cheloufi
➡️ https://genesdev.cshlp.org/content/39/9-10/652.abstract
#histones #transcription #replication
November 20, 2025 at 4:01 PM
🌟 G&D SPOTLIGHT 🌟
RESEARCH PAPER: Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate
By Franklin et al., and Sihem Cheloufi
➡️ https://genesdev.cshlp.org/content/39/9-10/652.abstract
#histones #transcription #replication
RESEARCH PAPER: Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate
By Franklin et al., and Sihem Cheloufi
➡️ https://genesdev.cshlp.org/content/39/9-10/652.abstract
#histones #transcription #replication
Reposted by John Ridenour
New report shows that NIH grants fueled $95 billion in economic activity and 407,782 jobs in 2024.
That's not to mention the countless lives that biomedical research has saved.
Show me a better investment than that.
www.forbes.com/sites/michae...
That's not to mention the countless lives that biomedical research has saved.
Show me a better investment than that.
www.forbes.com/sites/michae...
NIH Grants Fueled $95 Billion In FY 2024 Economic Activity, Finds New Report
National Institutes of Health grants generated almost $95 billion in economic activity nationwide in FY 2024 according to a new report by United for Medical Research.
www.forbes.com
March 12, 2025 at 8:47 PM
New report shows that NIH grants fueled $95 billion in economic activity and 407,782 jobs in 2024.
That's not to mention the countless lives that biomedical research has saved.
Show me a better investment than that.
www.forbes.com/sites/michae...
That's not to mention the countless lives that biomedical research has saved.
Show me a better investment than that.
www.forbes.com/sites/michae...
Reposted by John Ridenour
Two open positions for a lab manger and a laboratory technician. Applications from displaced federal employees are welcome.
Lab manager position: www.ugajobsearch.com/postings/410...
Lab tech position: www.ugajobsearch.com/postings/391...
Please email zlewis@uga.edu if you have questions
Lab manager position: www.ugajobsearch.com/postings/410...
Lab tech position: www.ugajobsearch.com/postings/391...
Please email zlewis@uga.edu if you have questions
Zachary Lewis on LinkedIn: Laboratory Research Technician
We have open positions for a lab manger and a laboratory technician. Applications from displaced federal employees are welcome.
Lab manager position:…
www.linkedin.com
February 24, 2025 at 1:44 AM
Two open positions for a lab manger and a laboratory technician. Applications from displaced federal employees are welcome.
Lab manager position: www.ugajobsearch.com/postings/410...
Lab tech position: www.ugajobsearch.com/postings/391...
Please email zlewis@uga.edu if you have questions
Lab manager position: www.ugajobsearch.com/postings/410...
Lab tech position: www.ugajobsearch.com/postings/391...
Please email zlewis@uga.edu if you have questions
Reposted by John Ridenour
a short and sweet paper in which we use 3D STED and Micro-C analysis to show dramatic changes in large 3D chromatin structures in quiescence. www.biorxiv.org/content/10.1...
Sir2 is required for the quiescence-specific condensed three-dimensional chromatin structure of rDNA
Quiescence in Saccharomyces cerevisiae is a reversible G0 crucial for long-term survival under nutrient-deprived conditions. During quiescence, the genome is hypoacetylated and chromatin undergoes sig...
www.biorxiv.org
December 13, 2024 at 2:59 PM
a short and sweet paper in which we use 3D STED and Micro-C analysis to show dramatic changes in large 3D chromatin structures in quiescence. www.biorxiv.org/content/10.1...
Reposted by John Ridenour
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
December 12, 2024 at 7:16 PM
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
Reposted by John Ridenour
A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes https://www.biorxiv.org/content/10.1101/2024.12.06.627179v1
December 7, 2024 at 3:17 AM
A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes https://www.biorxiv.org/content/10.1101/2024.12.06.627179v1
Reposted by John Ridenour
Remarkable structural insights from Carl Wu lab: SWR1 complex has a mechanism for sensing open DNA regions to insert H2A.Z-nucleosomes. CryoEM is transforming structural biology:
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
DEFINE_ME
www.cell.com
December 4, 2024 at 8:55 AM
Remarkable structural insights from Carl Wu lab: SWR1 complex has a mechanism for sensing open DNA regions to insert H2A.Z-nucleosomes. CryoEM is transforming structural biology:
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by John Ridenour
Delighted to share my Current Opinions review on nucleosome remodelers in DNA repair, co-authored with Jessica Downs: an uptodate survey of R-loops, 3D organization and remodelers especially jn DSB repair. Enjoy!
article link:
authors.elsevier.com/sd/article/S...
article link:
authors.elsevier.com/sd/article/S...
ScienceDirect.com | Science, health and medical journals, full text articles and books.
authors.elsevier.com
August 13, 2024 at 1:02 AM
Delighted to share my Current Opinions review on nucleosome remodelers in DNA repair, co-authored with Jessica Downs: an uptodate survey of R-loops, 3D organization and remodelers especially jn DSB repair. Enjoy!
article link:
authors.elsevier.com/sd/article/S...
article link:
authors.elsevier.com/sd/article/S...
Reposted by John Ridenour
Reposted by John Ridenour
Our paper on the structure of the complete Rpd3S-nucleosome complex is now out in Nat Comm: rdcu.be/ds6k1 . Congrats to @jonmarkert.bsky.social
and co-corresponding author Seychelle Vos! This is the second HDAC-nucleosome structure from Jon this year. Amazing!
and co-corresponding author Seychelle Vos! This is the second HDAC-nucleosome structure from Jon this year. Amazing!
December 8, 2023 at 12:32 PM
Our paper on the structure of the complete Rpd3S-nucleosome complex is now out in Nat Comm: rdcu.be/ds6k1 . Congrats to @jonmarkert.bsky.social
and co-corresponding author Seychelle Vos! This is the second HDAC-nucleosome structure from Jon this year. Amazing!
and co-corresponding author Seychelle Vos! This is the second HDAC-nucleosome structure from Jon this year. Amazing!
Reposted by John Ridenour
TODAY is your LAST CHANCE to submit an abstract for #Fungal24
#Fungal24 abstracts and early registrations are due today, December 5, 2023 at 8:00 p.m. EST.
community.alliancegenome.org/t/today-is-l...
#Fungal24 abstracts and early registrations are due today, December 5, 2023 at 8:00 p.m. EST.
community.alliancegenome.org/t/today-is-l...
December 5, 2023 at 6:12 PM
TODAY is your LAST CHANCE to submit an abstract for #Fungal24
#Fungal24 abstracts and early registrations are due today, December 5, 2023 at 8:00 p.m. EST.
community.alliancegenome.org/t/today-is-l...
#Fungal24 abstracts and early registrations are due today, December 5, 2023 at 8:00 p.m. EST.
community.alliancegenome.org/t/today-is-l...
Reposted by John Ridenour
This looks very interesting. 🧬🔄🧬
ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes in an acetylation independent manner https://www.biorxiv.org/content/10.1101/2023.10.27.564358v1
ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes in an acetylation independent manner https://www.biorxiv.org/content/10.1101/2023.10.27.564358v1
Transcription initiation involves the coordination of multiple events, starting with activators bind
www.biorxiv.org
October 28, 2023 at 10:43 PM
This looks very interesting. 🧬🔄🧬
Reposted by John Ridenour
Excited to share my postdoc work, REMORA (RNA-encoded molecular recording in adenosines), now officially online in Nature Methods: www.nature.com/articles/s41... (1/7)
October 23, 2023 at 10:14 PM
Excited to share my postdoc work, REMORA (RNA-encoded molecular recording in adenosines), now officially online in Nature Methods: www.nature.com/articles/s41... (1/7)
Reposted by John Ridenour
The Fusarium Workshop is now open for registration at the Fungal Genetics Conference 🥳 Looking forward to co-chairing with Tom
Baldwin and Domingo Martinez-Soto! genetics-gsa.org/fungal-2024/...
Baldwin and Domingo Martinez-Soto! genetics-gsa.org/fungal-2024/...
October 24, 2023 at 8:12 PM
The Fusarium Workshop is now open for registration at the Fungal Genetics Conference 🥳 Looking forward to co-chairing with Tom
Baldwin and Domingo Martinez-Soto! genetics-gsa.org/fungal-2024/...
Baldwin and Domingo Martinez-Soto! genetics-gsa.org/fungal-2024/...
Reposted by John Ridenour
The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitiv...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
October 21, 2023 at 9:37 PM
The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by John Ridenour
Registration has started for the Fungal Genetics Conference 2024! Looking forward to organizing the session ‘Chromatin and Chromosome Biology‘ with Mareike Möller, many thanks to the organizers Michael Freitag and Natalia Requena for this opportunity! genetics-gsa.org/fungal-2024/...
Invited Speakers - 32nd Fungal Genetics Conference
Visit our website to learn more.
genetics-gsa.org
October 20, 2023 at 2:27 PM
Registration has started for the Fungal Genetics Conference 2024! Looking forward to organizing the session ‘Chromatin and Chromosome Biology‘ with Mareike Möller, many thanks to the organizers Michael Freitag and Natalia Requena for this opportunity! genetics-gsa.org/fungal-2024/...
Reposted by John Ridenour
📣 New preprint! Pol II forms clusters, some of which are giant: Pol II clusters at fly histone genes could fill a yeast nucleus!👇How do these structures regulate transcription? This is what
Feiyue Lu, a joint postdoc w Ruth Lehmann, looked into 1/6 biorxiv.org/content/10.1...
Feiyue Lu, a joint postdoc w Ruth Lehmann, looked into 1/6 biorxiv.org/content/10.1...
October 20, 2023 at 7:10 PM
📣 New preprint! Pol II forms clusters, some of which are giant: Pol II clusters at fly histone genes could fill a yeast nucleus!👇How do these structures regulate transcription? This is what
Feiyue Lu, a joint postdoc w Ruth Lehmann, looked into 1/6 biorxiv.org/content/10.1...
Feiyue Lu, a joint postdoc w Ruth Lehmann, looked into 1/6 biorxiv.org/content/10.1...
Reposted by John Ridenour
ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions https://www.biorxiv.org/content/10.1101/2023.10.15.562421v1
ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions https://www.biorxiv.org/content/10.1101/2023.10.15.562421v1
Defining the in vivo DNA binding specificity of transcription factors (TFs) has relied nearly exclus
www.biorxiv.org
October 19, 2023 at 3:33 AM
ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions https://www.biorxiv.org/content/10.1101/2023.10.15.562421v1
Reposted by John Ridenour
#RNABiology recent highlight, a thoroughly revised and streamlined RiboSeq method from @nickingolia.bsky.social
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. doi.org/10.1038/s415...
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. doi.org/10.1038/s415...
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells - Nature Methods
A comprehensive redevelopment of the ribosome profiling workflow involves improved nuclease treatment and sequencing library preparation, enabling richer and more accurate translatome profiling with l...
doi.org
October 17, 2023 at 12:39 PM
#RNABiology recent highlight, a thoroughly revised and streamlined RiboSeq method from @nickingolia.bsky.social
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. doi.org/10.1038/s415...
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. doi.org/10.1038/s415...
Reposted by John Ridenour
A clever approach because it combines Oxfordn nanopore sequencing with barcoded molecular probes to achieve highly multiplexed and sensitive detection of various biomolecules in a single sample.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins an...
This study establishes a method for multiplexed detection of up to 40 different biomarkers in a single assay by combining nanopore sequencing with analyte-selective barcoded probes, including cardiac ...
www.nature.com
October 14, 2023 at 10:45 AM
A clever approach because it combines Oxfordn nanopore sequencing with barcoded molecular probes to achieve highly multiplexed and sensitive detection of various biomolecules in a single sample.
www.nature.com/articles/s41...
www.nature.com/articles/s41...