Charles Danko

Charles Danko

@charlesdanko.bsky.social

I study how genome sequence controls gene expression at Cornell.

1.3K followers526 following40 posts

Charles Danko reposted

Cohen Lab @Cornell
@cohenlab.bsky.social

Very proud of this tour de force from two former students, Stephanie Tanis and Leah Simon, with help from a huge team, including @charlesdanko.bsky.social highlighting a novel-overlooked intervention point for male contraception www.pnas.org/doi/10.1073/...

pnas.orgMeiotic prophase I disruption as a strategy for nonhormonal male contraception using small-molecule inhibitor JQ1 | PNASDeveloping safe, reversible, and nonhormonal male contraceptives has been hindered by the lack of defined biological windows that can be transientl...

Charles Danko reposted

Michael Guertin
@guertin.bsky.social

Our latest work indicates that termination of paused RNA polymerase is its most likely fate, while attempting to reconcile disparate estimates of relative rates and pause residency times from previous studies: www.biorxiv.org/content/10.1...

biorxiv.orgGenome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminateWe present a simple model for analyzing and interpreting data from kinetic experiments that measure engaged RNA polymerase occupancy. The framework represents the densities of nascent transcripts with...
Charles Danko
@charlesdanko.bsky.social

The admin plans to pick off universities 1-by-1. Instead, we have to come together. Universities need to stand together, fight in court, and take our case to the public by explaining the importance of what we do.

Chris Pickett@chrispickett5.bsky.social

This is a simply shameful statement from Columbia. Rolling over in the face of bad faith, unconstitutional attacks by a bully only encourages the bully. When the Trump admin comes for other universities, and they will, I sincerely hope they do the opposite of Columbia.

Charles Danko reposted

Jacob Schreiber
@jmschreiber91.bsky.social

Accurate de novo transcription unit annotation from run-on and sequencing data @charlesdanko.bsky.social www.biorxiv.org/content/10.1...

biorxiv.orgAccurate de novo transcription unit annotation from run-on and sequencing dataFunctional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure th...
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Charles Danko
@charlesdanko.bsky.social

Universities need to band together, hire excellent public relations teams, advertising firms, lobbyists. We need to run advertisements that tell the audience how they benefit. Adds need to run everywhere, including and especially, Fox News.

Charles Danko
@charlesdanko.bsky.social

This will be a long and expensive fight. There are lots of sympathetic people out there. But to win, we need to engage with folks who know how to tell our stories to a general audience. We need to work together to make the case for science clear to absolutely everyone in the US.

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Charles Danko
@charlesdanko.bsky.social

Most importantly, we need to explain to the public why they benefit from what we do and how it impacts their lives. Make sure that absolutely everyone in the US knows about the economic impact, cures for children's diseases and all of the other benefits to society.

Charles Danko
@charlesdanko.bsky.social

Frankly, Universities suck at the types of public outreach we need right now. We haven't built it because we haven't had to. The case for supporting science is just *so* strong from pretty much every perspective that it has enjoyed bipartisan support for decades.

Charles Danko reposted

Andrea Bernardini
@bernardini-andrea.bsky.social

We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon! Q-rich activation domains: flexible ‘rulers’ for transcription start site selection? www.cell.com/trends/genet...

cell.comQ-rich activation domains: flexible ‘rulers’ for transcription start site selection?Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term ‘ruler’ TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.

Charles Danko reposted

Andrea Bernardini
@bernardini-andrea.bsky.social

Brief thread on our opinion article "Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?". Transcription people are surely aware of the important reports on the DNA sequence determinants of start site (TSS) selection in the human genome that came out this year. 1/15

Andrea Bernardini@bernardini-andrea.bsky.social

We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon! Q-rich activation domains: flexible ‘rulers’ for transcription start site selection? www.cell.com/trends/genet...

cell.comQ-rich activation domains: flexible ‘rulers’ for transcription start site selection?Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term ‘ruler’ TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.
Charles Danko
@charlesdanko.bsky.social

Latest from our lab: Training sequence-to-function models using matched genome sequence and functional data improves performance in variant interpretation tasks. Congrats to Adam He and Nathan Palamuttam on getting this out. www.biorxiv.org/content/10.1...

biorxiv.orgTraining deep learning models on personalized genomic sequences improves variant effect predictionSequence-to-function models have broad applications in interpreting the molecular impact of genetic variation, yet have been criticized for poor performance in this task. Here we show that training mo...
Charles Danko
@charlesdanko.bsky.social

Important thread.

John Greally@greally.bsky.social

Time to roll out an updated version of something I post periodically, why the @NIH needs to change its modular budget and budget cap. The Modular Budget was introduced in 1998 by the@NIH. If you stayed under the ceiling of $250,000, you didn't have to break down your costs.

Charles Danko reposted

John Greally
@greally.bsky.social

Replying to @greally.bsky.social

Let's say is clearly: $474K is what the modular budget cap would be if it kept pace with inflation over 25 years.    If you're sticking to $250K these days, how much is that equivalent to in 1998 dollars? About $132,000.

Charles Danko
@charlesdanko.bsky.social

This looks very interesting. 🧬🔄🧬

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social

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

biorxiv.orgATAC 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

Charles Danko reposted

Shaun Mahony
@shaunmahony.bsky.social

New faculty position in Gene Regulation at Penn State! Come join the fantastic collaborative environment in the Center for Eukaryotic Gene Regulation ( www.cegr.psu.edu )! Review of applications starts Nov. 1st 🧪🧬🔄🖥️ psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

psu.wd1.myworkdayjobs.comFaculty Position in Gene Regulation at Penn StateAPPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...
Charles Danko
@charlesdanko.bsky.social

CC gene regulation community. 🔄🧬🔄 bsky.app/profile/char...

Charles Danko@charlesdanko.bsky.social

cBAF genomic targeting relies on the IDR. Looks like a very nice paper that begins to work out some of the amino acids involved. www.cell.com/cell/fulltex...

cell.comA disordered region controls cBAF activity via condensation and partner recruitmentIntrinsically disordered regions (IDRs), together with the ARID DNA-binding domain of ARID1A/B subunits, dictate cBAF chromatin remodeler complex condensate formation, chromatin localization, and prot...
Charles Danko
@charlesdanko.bsky.social

cBAF genomic targeting relies on the IDR. Looks like a very nice paper that begins to work out some of the amino acids involved. www.cell.com/cell/fulltex...

cell.comA disordered region controls cBAF activity via condensation and partner recruitmentIntrinsically disordered regions (IDRs), together with the ARID DNA-binding domain of ARID1A/B subunits, dictate cBAF chromatin remodeler complex condensate formation, chromatin localization, and prot...
Charles Danko
@charlesdanko.bsky.social

What's the over/ under on this pushing back the Oct 5 NIH deadline?!

The Washington Post@washingtonpost.com

Breaking news: The U.S. government started notifying federal workers on Thursday that a shutdown appears imminent, as the Biden administration embarks on the formal, methodical process of preparing much of Washington to come to a halt.

washingtonpost.comU.S. government starts notifying federal employees a shutdown may be imminentThe message will serve to acknowledge the growing risk that millions of employees may stop receiving pay, unless lawmakers can avert a government shutdown.

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