Reyes-Lamothe lab

Do you work on DNA or RNA protein complexes? 🧬

Come to Machines on Genes this June in Crete! ☀️

Super early discount is ending this Sunday so register now! 😃

Xiaofeng combined 2D live-cell single-particle tracking with 3D simulations to specifically measure the bacterial nucleoid accessibility and viscosity! Our preprint describes how these nucleoid properties respond to cellular processes! Code is available too.
www.biorxiv.org/content/10.6...

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

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

To kickstart this new Bluesky account: We're hiring!
The Bertolin Lab @dundee.ac.uk is looking for a postdoc to work on DNA-end homeostasis & genome stability, funded by Wellcome Trust Award. Exciting science, fantastic environment, founding role in the lab.
Details in the flyer — get in touch! 👇

Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries Eukaryotic gene expression is orchestrated by RNA polymerases (RNAPI, II, and III) and associated factors, yet their real-time dynamics remain obscure. Using single-molecule tracking in living yeast, ...

🧬🔬🎥 @science.org Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries | Science www.science.org/doi/10.1126/...

We are excited to share that our latest work from the lab aimed at understanding how the tRNA nuclease SLFN11 is activated in response to DNA damage and replication stress has just been published in @natcellbio.nature.com!

Open access link: www.nature.com/articles/s41...

(1/9)

We’re looking for a postdoc to join the Hendrickson lab!
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...

IFI16 senses and protects stalled replication forks Replication stress is a key driver of DNA damage and genome instability. Here, we report that replication stress induces an inflammatory response in t…

New paper in collaboration with @unterholznerlab.bsky.social @cejkalab.bsky.social IFI16 protects stalled replication forks.

www.sciencedirect.com/science/arti...

Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change The ability to generate genomic diversity expands opportunities for understanding and engineering biology. Here, we demonstrate on-demand generation of diversity in bacterial genome configurations and...

After 4 years of joint effort of my Lab and Dr. Llorente Team we took for first time SCRaMbLE to a bacterial system! This allowed us to massively reordered the main chromosome of Vibrio natriegens!

biorxiv.org/content/10.6...
Here's a 🧵

Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication The formation of RNA-DNA hybrid (RDH) primers by primase is an essential step in the recruitment of DNA polymerase during replication initiation and for the synthesis of each Okazaki fragment on the l...

Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication www.biorxiv.org/content/10.6...

OPPORTUNITY: McGill Plant Science is looking for an expert in plant pathology, plant breeding, or horticulture in the context of the Canada Impact+ Research Chairs Program (senior established researcher).
Contact: www.mcgill.ca/plant/contact
Program: lnkd.in/eavfNu7e

Please re-post.

A toxin/antitoxin system targeting the replication sliding-clamp induces competence in Streptococcus pneumoniae Author summary The environment in which bacteria live puts them under a great deal of stress, forcing them to adapt constantly, either temporarily or permanently. Streptococcus pneumoniae, a pathogeni...

Delighted to share a new paper from our lab, a study led by Mathieu Bergé looking at how an endogenous toxin targets replication to induce competence in the pneumococcus. dx.plos.org/10.1371/jour...

Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading - Nature Communications DNA damage can lead to cell death. Here, the authors show that a simple cut on either strand of DNA can inactivate bacterial chromosome replication. Surprisingly, only a core set of recombination prot...

A cool genetic system to study site-pecific replication fork collapse and repair from the brilliant @winterhalterlab.bsky.social

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

My PhD students Aoi Otsuka @masaashimazoe.bsky.social et al. published @csf-jscb.bsky.social 🎉 Single-nucleosome imaging in an oncogene-inducible human carcinogenesis model shows biphasic chromatin dynamics (1–3 d same; 5–7 d ↑; back by week 4). Congrats! 👉
doi.org/10.1247/csf....

Proud of contributing to this work on archaeal chromosome segregation! Congrats, Rachel and Steve!
www.nature.com/articles/s41...

AMPK modulates a DEAH box RNA-helicase to attenuate TOR signaling and establish developmental quiescence in Caenorhabditis elegans Caenorhabditis elegans adapts to starvation and other stressors by transiting through the quiescent developmental stage dauer, but the underlying mechanisms remain unclear. This study shows that TOR a...

In a new paper, Rashid & Roy characterize a novel RNA-binding helicase, HZL-1. The protein regulates reproductive developmental quiescence in C. elegans through inhibition of key mRNAs, and sits on the axis between conserved AMPK & TOR metabolic signaling pathways.
journals.plos.org/plosbiology/...

Nucleoplasmic Lamin A/C controls replication fork restart upon stress by modulating local H3K9me3 and ADP-ribosylation levels Nature Communications - Replication fork plasticity upon genotoxic stress is modulated by nuclear architectural components by elusive mechanisms. Here the authors implicate Lamin A/C – best...

Thrilled to share our latest work - now available in full in Nature Communications - led in my lab by @vcherdy.bsky.social, with key collaborative contributions from @nitikataneja.bsky.social .

rdcu.be/eVrxX

McGill’s Arts Building on campus, featuring its stone façade and green dome, with the McGill flag raised and autumn foliage surrounding the building.

McGill is recruiting top-tier researchers working abroad through the federally funded Canada Impact+ Research Chairs program, addressing global and national challenges. The first round is due in early 2026.

Learn more and submit your candidacy: https://mcgill.ca/x/5Zh

a model for TIMELESS positions at the active fork: one complex sits at the leading edge of the fork, while the other one is on the lagging strand ssDNA/RPA, between the Okazaki fragments

Ever wondered how TIMELESS/TIPIN can sit at the leading edge of the replication fork regulating its speed, but also bind polymerases and ssDNA/RPA in replication stress? We have an idea how it might work! Check out our new preprint, any feedback is highly appreciated!
www.biorxiv.org/content/10.6...

replicationists & recombinatics take note 👇

cells deal with transcription-replication collisions (TRCs) much more professionally and efficiently than the best bridge engineers. OK, they've had more time to practice...

thx, zeynep for pointing this out 🙏 #MicroSky

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation Abstract. Conjugative plasmids are a major driving force for the dissemination of antimicrobial resistance. During conjugation, plasmid DNA is transferred

academic.oup.com/nar/article/... Collaboration with Y. Yamaichi. Killing donor bacteria in conjugation mixes using water enables transcriptomic profiling of early plasmid genes ! Superb tool for studying zygotic induction of these early genes, which include anti-SOS and anti-RM factors. #microsky

How DNA secondary structures drive replication fork instability DNA secondary structures, such as hairpins, cruciforms, triplexes, G-quadruplexes and iMotifs, are common, dynamic features that replication forks rou…

Our @costerlab.bsky.social review is out!

It’s a great read on the impact of DNA secondary structures on eukaryotic replication fork progression - a totally unbiased opinion, of course!

www.sciencedirect.com/science/arti...

@adityasethi.bsky.social @billiedelpino.bsky.social

Comparative analysis of the Caulobacter SOS response under mitomycin-C damage. Top left: Schematic summarizing the RNA-sequencing experiment. Caulobacter cells were treated with 0.25 μg/ml mitomycin-C for 20 and 40 min (Created in BioRender). Samples were collected for transcriptomic analysis before (0 min, control), and at 20 and 40 min post damage induction. Top right: Venn diagram representing the genes that meet the listed criteria: 1. Genes induced in wild type cells under MMC damage at 40 min (white circle). 2. Genes induced in ΔlexA in the absence of damage (blue circle). 3. Genes not induced in ΔrecA background under MMC damage at 40 min (gray circle). Genes fulfilling all three criteria are in the gray circle. Number of genes in each category is indicated. Bottom left: Bar graph indicating whether promoters of the shortlisted genes exhibit binding by the LexA protein as assessed from ChIP-seq analysis [10]. Bottom right: LexA ChIP-seq profile for genes belonging to the SOS response. Normalized reads (in rpm) are represented for 500 bp upstream and downstream of the gene CDS.

The bacterial #SOSresponse unfolds in a defined temporal order, but how does this arise? @adityakamat.bsky.social @anjbadri.bsky.social &co show that intrinsic #promoter strength, modulated by #SigmaFactor usage, governs timing of SOS gene activation in Caulobacter @plosbiology.org 🧪 plos.io/4oAKf0Q

Cohesin drives chromatin scanning during the RAD51-mediated homology search Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...

Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation | PNAS Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...

Our preprint is now published in PNAS! This came together thanks to a great collaboration with Antoine Hocher and a strong team effort from the Le Lab. Thank you to the reviewers and to everyone who helped improve it. I hope ParB aficionados will enjoy it.

www.pnas.org/doi/10.1073/...

Cool work from Heath Murray's lab where they use Cas9 nickase to study how ssDNA breaks are repaired in Bacillus subtilis #MicroSky www.nature.com/articles/s41...

Congrats to Viri, who successfully defended her PhD thesis yesterday. Well done Dr. Lopez Jauregui! 🎉🎉💯

We are recruiting a postdoctoral fellow to study mechanisms of DNA replication stress using single-molecule imaging tools. If you are excited about microscopy, replisome dynamics, and genome stability, we’d love to hear from you.

Application deadline: 24 December

www.crick.ac.uk/careers-stud...

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes ...

‘Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli‘ by Drs. Nico Yehya, Christopher Bohrer, and collaborators, is now available on bioRxiv. Check it out! doi: doi.org/10.1101/2025...

Thanks Nitin