Josh T Cuperus

Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at ...

What an amazing assay.

DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...

This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.

i'm glad it's posted now, but damn that's a gut-punch for any 2nd year students planning to apply this cycle

NSF Graduate Research Fellowship Program (GRFP)

Continuing efforts to hurt the research pipeline, the very late NSF GFRP solicitation no longer allows 2nd year PhD students to apply. Lots of these students chose not to apply last year because they were told they would have a better change once in their thesis lab www.nsf.gov/funding/oppo...

The GRFP announcement from NSF cuts out an entire cohort of 2nd year students from consideration, without warning. This is so deeply unfair that it warrants a formal protest from the scientific community. If someone wants to work with me to craft an open letter and solicit signatures, LMK.

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/

Dosa: A method to covalently barcode proteins for high throughput biochemistry Deep mutational scanning couples a proteins activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like g...

www.biorxiv.org/content/10.1...

Dosa: A method to covalently barcode proteins for high throughput biochemistry Deep mutational scanning couples a proteins activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like g...

#microsky

www.biorxiv.org/content/10.1...

Carrington lab reunion, Oregon State edition

Push rDNA outside natural range and you get effects:
• Replication defects in yeast: academic.oup.com/genetics/art...
• Growth defects in yeast: academic.oup.com/genetics/art...
• Developmental issues in C. elegans: academic.oup.com/genetics/art...

Thanks to all collaborators!
3/3

Don’t trust short-read rDNA quantification:
📄 pmc.ncbi.nlm.nih.gov/articles/pmi...
📄 doi.org/10.1038/s415...

In C. elegans, natural variation = no phenotype (~100-400 copies!)
📄 doi.org/10.1101/2025... (now in press at PLOS gen)

2/3

Here ends our foray into rDNA variation in model organisms—w/ Christine Queitsch, Bonnie Brewer, and many others. Especially Ashley Hall and Elizabeth Morton.

tl;dr: In natural ranges of rDNA copy number, phenotypes are rare (yeast + C. elegans).
But outside those ranges? Some things happen.
1/3

Proposed cut to NSF Biology budget is 70%.

70%. Seventy.

Call your senators & reps nonstop. Give them numbers on NSF impact for state/district. tableau.external.nsf.gov/views/NSFbyN... explain this will decimate the economy if their districts, especially if it has a major research univ. 🧪

Considerations in the analysis of plant chromatin accessibility data - PubMed Transcriptional control is exerted primarily through the binding of transcription factor proteins to regulatory elements in DNA. By virtue of eukaryotic DNA being complexed with histones, transcriptio...

pubmed.ncbi.nlm.nih.gov/32113082/

Love/hate this

YouTube video by CNN Fareed’s Take: Trump is gutting what made American science great

important historical perspective on the value of federal funding of basic research at universities: "These are the building blocks of America's extraordinary strength, created over the last 100 years, and they are now being dismantled in 100 days" 🧪

www.youtube.com/watch?v=0Qk4...

Trump’s war on science is an attack against anyone who has ever loved someone with cancer.

The American people do not want us to slash cancer research in order to give more tax breaks for billionaires.

The regulatory potential of transposable elements in maize - Nature Plants Long-read chromatin assay reveals (1) a novel class of accessible chromatin regions, (2) accessibility within individual LTR retrotransposons and (3) the relationship between diffuse accessibility, ge...

www.nature.com/articles/s41...

Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans The genes for ribosomal RNA (rRNA) are encoded by ribosomal DNA (rDNA), whose structure is notable for being present in arrays of tens to thousands of tandemly repeated copies in eukaryotic genomes. T...

www.biorxiv.org/content/10.1... new paper out!

The regulatory potential of transposable elements in maize bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Thrilled to present our collaboration w/ Stergachis lab members “The regulatory potential of transposable elements in maize”. Single-molecule Fiber-seq - accurate and sensitive accessibility in maize. New open chromatin regions in LTRs and much more! www.biorxiv.org/content/10.1...