Jens Schmidt

Evolution of error correction through a need for speed Kinetic proofreading is a class of error-correcting mechanisms in biology that expend energy to avoid mistakes during replication, transcription, and translation. Proofreading is typically assumed to ...

@science.org Evolution of error correction through a need for speed | Science #evolution 🧬🔬 www.science.org/doi/10.1126/...

This work was made possible by the relentless efforts of Mariia Mikhova and the B cell and CSR magicians in Dr. Kefei Yu’s lab, who made all cell lines used in this study. 12/12

Altogether, we propose a model in which the specific binding of AID to switch region RNAs and the formation of the large RNA hub by nascent switch region transcripts, specifically recruits AID to the IgH locus to facilitate class switch recombination. 11/n

Finally, we combined the RNA and protein imaging modalities to analyze AID binding to the IgH locus. AID binding events are rare and last 40 seconds on average, which should allow a single AID to deaminate a substantial number of cytosines. 10/n

This change in AID dynamics is completely dependent on the presence of switch region transcripts, which is consistent with AID binding to the switch region RNA. 9/n

Next, we analyze AID trafficking in the nucleus at the single-molecule level. Our experiments demonstrate that the rate of AID diffusion is reduced over the course of CSR and dynamic properties of slowly diffusing AID molecules matches those of mobile switch region transcripts. 8/n

Surprisingly, we found that the Sa switch region is rapidly transcribed (~2.5 kb/min), which suggests that R-loop formation is very transient and does not impact transcription or maybe does not occur at all!!? 7/n

The switch regions are highly repetitive and have a G-rich on the non-template strand, i.e. textbook examples of R-loop forming sequences. To test whether R-loop formation impedes or stalls transcription across the switch regions, we inserted PP7 and MS2 arrays flanking the Sa switch region. 6/n

We also identified mobile switch region transcripts that diffused through the nucleus of the B cells and were able to re-associate with the actively transcribed IgH locus. 5/n

To analyze switch regions transcription in real time we introduced PP7 and MS2 stem loop arrays in various locations in the IgH locus and detected bright transcriptional signals which reflect 10s of nascent switch region transcripts associated with the IgH locus forming a large RNA hub. 4/n

DNA break induction requires switch region transcription and the recruitment of the cytidine deaminase AID. How switch region transcription leads to the almost exclusive recruitment of AID to the IgH locus was unclear. 3/n

CSR is a large scale intrachromosomal deletion that leads to the expression of different antibody isotypes (IgG, IgA, etc.). This deletion requires specific induction of DNA breaks in highly repetitive switch regions that precede the antibody isotype coding regions. 2/n

New pre-print from the lab! Lead by Mariia Mikhova and in collaboration with Kefei Yu’s lab @msumgi.bsky.social we dug into the molecular mechanism of class switch recombination in B cells using simultaneous RNA and protein single-molecule imaging. 1/n
www.biorxiv.org/content/10.6...

Tom Cech to Davos: RNA research is 'still a big deal' The Nobel laureate and CU Boulder professor, recently ranked #1 globally for RNA research, will speak at the World Economic Forum annual meeting in Davos,

www.colorado.edu/today/2026/0...

The other two teams left standing in the AFC are beatable for the Broncos. However, your Seahawks look pretty scary!

Well you did but not in that play 🤣🤣

Better hope it’s just a hold and not a fumble out of the end zone.

Nuclear actin and DNA replication stress regulate telomere maintenance by telomerase - Nature Communications Telomerase recruitment to telomeres is a tightly regulated process which is stimulated by replication stress. Here, the authors identify that nuclear filamentous actin is important for interaction bet...

New @natcomms.nature.com paper today from Tracy Bryan's lab @cmri.bsky.social: "Nuclear actin and DNA replication stress regulate telomere maintenance by telomerase".

Happy our lab could play a small part.

Congrats Tracy, Ash Harman, Noa Lamm and the whole team.

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

The ERCC6L2-MRI-KU complex coordinates NHEJ at staggered DNA double-strand breaks ERCC6L2 disease is a recessive bone marrow failure (BMF) syndrome caused by mutations in the SNF2-like putative DNA helicase ERCC6L2. While implicated in DNA replication, double strand break (DSB) rep...

New lab preprint! ERCC6L2 disease is a recessive bone marrow failure syndrome caused by mutations in the putative DNA helicase ERCC6L2. Using mouse genetics, biochemistry and AF3 we uncover ERCC6L2-MRI as a KU-regulatory complex stimulating NHEJ at staggered DSBs: www.biorxiv.org/content/10.1...

We conclude that Ku70/80 was upregulated in higher primates to suppress Alu elements from altering mRNA splicing. When Ku is depleted a number of essential genes involved in ribosome biogenesis and mRNA processing are miss-spliced and lost due to NMD, leading to cell death. 6/6

Upon closer inspection, we demonstrate that Ku depletion activates cryptic splice acceptor sites within antisense Alu elements, which are located immediately upstream of a stem loop that Shan Zha’s group recently demonstrated to be bound by Ku70/80. 5/n

Using a Halo-PROTAC ligand we can degrade Halo-Ku70 and Halo-Ku80 and cells rapidly die! At an early timepoint before a substantial amount of cell death occurs, we observed dramatic changes in RNA splicing. Strikingly, antisense Alu elements were significantly enriched in miss-spliced introns. 4/n

Giovanni and Kathy had previously demonstrated that the number of Alu repeats substantially increased in the genomes of higher primates at the exact evolutionary junction at which Ku expression shot through the roof. Could there be a connection between Alu element expansion and Ku expression? 3/n

Ku70/80 is typically thought of as a NHEJ factor that repairs DSBs. However, Ku is essential in human cells, but not in mouse cells. Ku expression is also dramatically increased in higher primates, compared to primitive primates and other mammals. So, what is Ku’s essential function? 2/n

Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements Alu elements are short repeats that occupy approximately 10% of the human genome. Saturation of primate genomes with Alu sequences occurred at the prosimian/new-world monkey evolutionary juncture. Alu...

New Print Alert! A fun collab with Kathy Meek at MSU. Led by talented bioinformatician Giovanni Pascarella we demonstrate that Ku70/80 binds intronic antisense Alu elements to inhibit cryptic splice sites. For details see the thread below! 1/n

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

Using a Halo-PROTAC ligand we can rapidly degrade Ku70 and Ku80 and cells rapidly die! At an early timepoint before a substantial amount of cell death occurs, we observed dramatic changes in RNA splicing. Strikingly, antisense Alu elements were dramatically enriched in miss-spliced introns. 4/n

Kathy Meek had previously demonstrated that at the Alu elements content substantially expanded in the genomes of higher primates at the exact evolutionary junction at which Ku expression increased. Could there be a connection between Alu element expansion and Ku expression? 3/n

Ku70/80 is a NHEJ factor that repairs DNA double strand breaks. However, Ku is essential in human cells but not in mouse cells. Ku expression is also dramatically increased in higher primates, compared to primitive primates and other mammals. So, what is Ku’s essential function? 2/n

There is no way they will be able to reschedule before January.

Human RPA is an essential telomerase processivity factor for maintaining telomeres Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical ...

Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...