Jon Markert

YouTube video by Fragile Nucleosome Jon Markert

Check out @jonmarkert.bsky.social's recent talk for the @fnucleosome.bsky.social series, covering his recent breakthrough paper (www.science.org/stoken/autho...) on co-transcriptional histone mark deposition of H3K36me3: www.youtube.com/watch?v=ByJr...


🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...

Excited to see everyone tonight at Whitehead Institute for the 2nd GEARS seminar, featuring three talks from Harleen Saini, Vikram Agarwal, and Ava Carter!

I’m excited to share my first paper in the Farnung lab, in which we report four cryo-EM structures of the human DNA replication machinery engaging with and progressing into a nucleosome.

Our work on DNA replication is out! Led by @felixsteinruecke.bsky.social, we monitor the replisome progressing into nucleosomes!

Take a look at our new collaboration project with the Phil Cole lab, we demonstrate how SIRT6 can recognize and remove a variety of different Histone acylations!

Are you interested in hearing this SETD2 story in more detail? I’ll be presenting it at @fnucleosome.bsky.social this week! Please see the poster for more details

🥁We are just 3 days away from our next #FragileNucleosome seminar! We are delighted to host, 2 amazing ECR researchers @rachelhoffman.bsky.social & @jonmarkert.bsky.social this Wed!
PS1: Don't forget that US has switched to PDT
PS2: The recurring registration link:
us06web.zoom.us/webinar/regi...

DIC and cryo-ET images of G1 and G0 fission yeast cells.

Zhi Yang Tan & @shujuncai.bsky.social's comparative study of G0 (quiescent) and interphase fission yeast cells is out in @jcellsci.bsky.social doi.org/10.1242/jcs.263654. This study combines multiple cell-biological analyses with in situ cryo-ET. Raw data: www.ebi.ac.uk/empiar/EMPIAR-10339

TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network CDK7 kinase activity is found to control RNAPII transcription through a cohort of TFs that drive cell cycle and proliferation.

For our latest paper, we worked with SYROS Pharmaceuticals, the groups of Dylan Taatjes and Robin Dowell at CU Boulder, and @abhaykot.bsky.social. Junjie Feng in my lab determined the #cryoEM structure of the CDK7 inhibitor SY5609 bound to its target...
www.science.org/doi/10.1126/...

Very excited to bring GEARs back with @jonmarkert.bsky.social and @ara-latifkar.bsky.social. We look forward to seeing you in Goldenson 122, Harvard Medical School for our first seminar on 02/27, 6PM.

Farnung Lab

Excited about mechanistic biology and processes in the cell's nucleus? Join our lab as a post-doctoral researcher! We have a state-of-the-art cryo-EM facility (new microscopes coming!), a brand-new lab space, and a vibrant community at HMS!
DM/email me or check farnunglab.com for more info.

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription During transcription, RNA polymerase II traverses through chromatin, and posttranslational modifications including histone methylations mark regions of active transcription. Histone protein H3 lysine ...

Our story on the mechanism of co-transcriptional histone mark deposition is now officially out: www.science.org/doi/10.1126/...

The structural basis for RNA slicing by human Argonaute2 Mohamed et al. report the cryoelectron microscopy structure of human AGO2 with fully paired guide RNA. Their analysis reveals the structural basis for the slicing activity that drives RNAi, showing that the slicing-competent conformation is achieved by domain movements and RNA-protein contacts distinct from those of conformational intermediates and prokaryotic homologs.

Our collaborative AGO2 work with @bartellab.bsky.social is published! Abdallah and Peter used cryo-EM and biochemistry to determine the structure of AGO2 in a slicing competent conformation with a fully paired RNA. Read more about it here: tinyurl.com/AGO2-slicing

Another highlight from our story: @jonmarkert.bsky.social uncovered how SPT6 binds the exposed H2A–H2B dimer during nucleosomal traversal by Pol II. AlphaFold helped tremendously in validating this interaction. tinyurl.com/setd2 Also check out our H2A–H2B screen: www.biorxiv.org/content/10.1...

Pol2 stimulates
SETD2 methylation
Of histone H3

#ChromatinHaiku #H3K36
www.science.org/doi/10.1126/...

Pam taught me so much (how to make nucleosomes, how to use AKTAs…), I’m so incredibly grateful to have worked with her! The entire chromatin field is impacted by her, a very bittersweet day for the Luger lab! I wish her the best!!

Online today @science.org Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription
by @jonmarkert.bsky.social @lucas.farnunglab.com et al. at @harvardcellbio.bsky.social #cryoEM
#chromatin #transcription #cryoEM #Pol_II🧪🧬❄️🔬
www.science.org/doi/10.1126/...

Thanks Emma! Wishing you the best in your work at Scripps!

Thank you CJ! Hope all is well in Madison!

Thanks so much Alessandro!

This would not have been possible without the support from my advisor @lucas.farnunglab.com, the cryo-EM facility at HMS @hc2em.bsky.social, and funding from the Fred Goldberg fellowship @harvardcellbio.bsky.social. We are excited to see this story finally come out, take a look!

With 8 composite cryo-EM maps (totaling 47 EMDB entries) and several biochemical assays, we demonstrate the mechanistic basis for the positioning of H3K36me3 within actively transcribed regions. Surprisingly, SETD2 must be relieved of auto inhibition by the transcription machinery!

Circular Engineered Sortase for Interrogating Histone H3 in Chromatin Reversible modification of the histone H3 N-terminal tail is critical in regulating the chromatin structure, gene expression, and cell states, while its dysregulation contributes to disease pathogenesis. Understanding the crosstalk between H3 tail modifications in nucleosomes constitutes a central challenge in epigenetics. Here, we describe an engineered sortase transpeptidase, cW11, that displays highly favorable properties for introducing scarless H3 tails onto nucleosomes. This approach significantly accelerates the production of both symmetrically and asymmetrically modified nucleosomes. We demonstrate the utility of asymmetrically modified nucleosomes produced in this way in dissecting the impact of multiple modifications on eraser enzyme processing and molecular recognition by a reader protein. Moreover, we show that cW11 sortase is very effective at cutting and tagging histone H3 tails from endogenous histones, facilitating multiplex “cut-and-paste” middle-down proteomics with tandem mass tags. This cut-and-paste proteomics approach permits the quantitative analysis of histone H3 modification crosstalk after treatment with different histone deacetylase inhibitors. We propose that these chemoenzymatic tail isolation and modification strategies made possible with cW11 sortase will broadly power epigenetic discovery and therapeutic development.

A great collaboration with Phil Cole (Harvard) engineering Sortase to facilitate its transpeptidase activity on histone H3 has been published in JACS. This work developed multiplexed "cut-and-paste" middle-down proteomics with tandem mass tags for quantification.
pubs.acs.org/doi/full/10....

Congrats to all! The 350 truncation is interesting, phosphorylated is worse at ATP hydrolysis but better at exchange!

Thank you Karolin!

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!