John Ridenour

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4

Preprint: www.biorxiv.org/content/10.6...

Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore

Mapping single-cell diploid chromatin fiber architectures using DAF-seq - Nature Biotechnology Single-molecule chromatin fiber sequencing exposes single-cell-level heterogeneity in the chromatin architecture of individual regulatory elements.

A Nature study uses #PacBio long-read sequencing to map chromatin architecture in single cells with DAF-seq, extending Fiber-seq and showing multiomic HiFi reads capture chromatin features and sequence, revealing haplotype-specific regulatory variation across cells.

Details: go.nature.com/4pODNVl

Took us a bit, but proud of this published version. We now examine the genetic interaction of phosphorylation with oligomerization and where bulk and phospho-Swi6 localize. Wonder if chromatin affinity tuning to enable Suv39 H3K9me3 spreading is a conserved mechanism ?

doi.org/10.1093/nar/...

SET1/MLL complexes control transcription independently of H3K4me3 Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...

An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!

www.biorxiv.org/content/10.6...

DNA bendability inside the nucleosome regulates INO80’s nucleosome positioning Shukla et al. find that the INO80 chromatin remodeler positions nucleosomes at specific genomic positions, including the 5′ end of genes. INO80 recognizes DNA shape rather than a unique DNA sequence. Nucleosome movement is blocked when INO80 encounters inflexible DNA inside the nucleosome, mediated by the DNA-rigidity-sensitive binding of its Arp5 subunit.

DNA bendability inside the nucleosome regulates INO80’s nucleosome positioning

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 ...

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...

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...

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...

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

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…

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...

Sign up to present your work in the @fnucleosome.bsky.social seminar series!

🌟 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

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.

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...

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:…

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

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...

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...

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

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

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...

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...

On my reading list, a incredible work again by the Xu lab #cryoEM

www.science.org/doi/10.1126/...

Structure of Rpd3S-nucleosome complex.

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!

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...

This looks very interesting. 🧬🔄🧬

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)

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/...

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

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...

Invited Speakers - 32nd Fungal Genetics Conference Visit our website to learn more.

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/...

Nucleus showing Pol II cluster at the histone locus

📣 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...

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

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