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Reposted by Jon Markert

Harvard Med Cell Biology @harvardcellbio.bsky.social · 20d

New work from the Moazed lab reveals the requirements for establishment & epigenetic stability of mammalian heterochromatin! www.cell.com/molecular-ce...

Requirements for establishment and epigenetic stability of mammalian heterochromatin

Tatarakis et al. study how H3K9me3 heterochromatin is formed and inherited in mammalian cells. Using a synthetic heterochromatin assembly system and genetic screens, they uncover requirements for init...

www.cell.com

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Lucas Farnung @lucas.farnunglab.com · Aug 29

🧬 Transcription elongation by RNA polymerase II relies on a web of elongation factors. Our new work shows how IWS1 acts as a modular scaffold to stabilize & stimulate elongation. Fantastic work by Della Syau! www.biorxiv.org/content/10.1...

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Lucas Farnung @lucas.farnunglab.com · May 30

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...

Jon Markert

YouTube video by Fragile Nucleosome

www.youtube.com

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Lucas Farnung @lucas.farnunglab.com · May 6

🧬🎉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...

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GEARs @gearseminar.bsky.social · May 1

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

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Felix Steinruecke @felixsteinruecke.bsky.social · Apr 6

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.

Lucas Farnung @lucas.farnunglab.com · Apr 6

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

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Jon Markert @jonmarkert.bsky.social · Apr 6

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

Lucas Farnung @lucas.farnunglab.com · Apr 6

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

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Jon Markert @jonmarkert.bsky.social · Mar 28

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!

Lucas Farnung @lucas.farnunglab.com · Mar 28

🚨New paper🚨Our new study with the lab of Phil Cole uncovers how SIRT6 dynamically adapts structurally and enzymatically to target diverse histone acylations (e.g., H3K27ac) within nucleosomes. @jonmarkert.bsky.social
doi.org/10.1016/j.jb... #Chromatin #SIRT6 #CryoEM

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Jon Markert @jonmarkert.bsky.social · Mar 10

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

Lucas Farnung @lucas.farnunglab.com · Dec 12

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

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FragileNucleosome @fnucleosome.bsky.social · Mar 10

🥁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...

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Mitosis Lab @mitosislab.bsky.social · Mar 4

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

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

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Basil Greber @bjgreber.bsky.social · Feb 28

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/...

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.

www.science.org

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Reposted by Jon Markert

Xiaoli Sky Wu @xiaoliwu.bsky.social · Feb 14

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.

GEARs @gearseminar.bsky.social · Feb 14

After a long break, GEARs is back! We will feature three speakers on Feb 27th, 6PM in Goldenson 122. Please register via docs.google.com/forms/d/e/1F... so we can get enough food and drinks. You can nominate speaker sor volunteer for our future seminars through docs.google.com/forms/d/e/1F....

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Lucas Farnung @lucas.farnunglab.com · Jan 31

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.

Farnung Lab

farnunglab.com

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Lucas Farnung @lucas.farnunglab.com · Jan 30

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

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 ...

www.science.org

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Seychelle Vos @voslab.org · Jan 1

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

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.

tinyurl.com

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Lucas Farnung @lucas.farnunglab.com · Dec 18

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...

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Reposted by Jon Markert

Chromatin Haiku @chromatinhaiku.bsky.social · Dec 13

Pol2 stimulates
SETD2 methylation
Of histone H3

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

Fig. 1. Biochemical reconstitution of H3K36me3 deposition by SETD2 during transcription.
(A) Schematic of RNA extension-coupled histone mark deposition assay in the presence of all NTPs. (B) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2. SETD2 concentration is 3.5 μM. (C) Schematic of RNA extension-coupled histone mark deposition assay with pause sites (bp −31, bp −15, and bp +27). (D) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2 on partially transcribed downstream nucleosome. SETD2 concentration is 3.5 μM. (E) Denaturing gel of RNA products and Western blot analysis reveals transcription stimulates H3K36me3 deposition by SETD2 on transferred upstream nucleosome (bp +115). SETD2 concentration is 700 nM. RNA extension gel and Western blot from (E) is the same as in fig. S13F.

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Jon Markert @jonmarkert.bsky.social · Dec 13

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!!

Karolin Luger @nucleosomepolice.bsky.social · Dec 12

Saying goodbye to our lab manager of 25 years. we owe her EVERYTHING, she will be missed. To make sure she doesnt forget about #nucleosomes, we presented her with nucleosome art by the gifted Montana Fowler. also fun to hang out with current and many former lab members!

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Di Jiang @dijiang319.bsky.social · Dec 13

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/...

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Jon Markert @jonmarkert.bsky.social · Dec 13

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

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Jon Markert @jonmarkert.bsky.social · Dec 13

Thank you CJ! Hope all is well in Madison!

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Jon Markert @jonmarkert.bsky.social · Dec 12

Thanks so much Alessandro!

Jon Markert @jonmarkert.bsky.social · Dec 12

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!

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Jon Markert @jonmarkert.bsky.social · Dec 12

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!

Lucas Farnung @lucas.farnunglab.com · Dec 12

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

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