Benjamin Pardo LAB
@pardolab.bsky.social
Ph.D in Biology. Particular interest in the molecular mechanisms of DNA replication and repair. Signaling of the DNA damage response.
CNRS, University of Montpellier, France.
https://www.igh.cnrs.fr/en/project/index/0/134/igh
CNRS, University of Montpellier, France.
https://www.igh.cnrs.fr/en/project/index/0/134/igh
Reposted by Benjamin Pardo LAB
Check out our web tool to see interactive networks of DSB repair genes, browse your gene of interest for its contribution to DSB repair profiles and analyze functional relationships based on similarities in repair patterns
Enjoy!!!
repairome.bioinfo.cnio.es
Enjoy!!!
repairome.bioinfo.cnio.es
REPAIRome
repairome.bioinfo.cnio.es
October 4, 2025 at 7:27 AM
Check out our web tool to see interactive networks of DSB repair genes, browse your gene of interest for its contribution to DSB repair profiles and analyze functional relationships based on similarities in repair patterns
Enjoy!!!
repairome.bioinfo.cnio.es
Enjoy!!!
repairome.bioinfo.cnio.es
Reposted by Benjamin Pardo LAB
New paper! Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones - Genome Biology
Background The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using ...
genomebiology.biomedcentral.com
May 12, 2025 at 10:35 AM
New paper! Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
Reposted by Benjamin Pardo LAB
New preprint from the Lab at @cabimer.bsky.social. We present PLAMseq, using TurboID to do like ChIPseq and proximity proteomics in the same protocol with extra powers like mapping protein interactions in the genome.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.
Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively, for a prote...
www.biorxiv.org
April 28, 2025 at 7:55 AM
New preprint from the Lab at @cabimer.bsky.social. We present PLAMseq, using TurboID to do like ChIPseq and proximity proteomics in the same protocol with extra powers like mapping protein interactions in the genome.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Benjamin Pardo LAB
New preprint from the lab:
ATM controls fork processing and restart, and the PPM1D phosphatase is needed to properly balance this action of ATM.
Congratulations to @yitingcao.bsky.social @yingzhengwang.bsky.social and Jumana Badar.
www.biorxiv.org/content/10.1...
ATM controls fork processing and restart, and the PPM1D phosphatase is needed to properly balance this action of ATM.
Congratulations to @yitingcao.bsky.social @yingzhengwang.bsky.social and Jumana Badar.
www.biorxiv.org/content/10.1...
An ATM-PPM1D Circuit Controls the Processing and Restart of DNA Replication Forks
In response to DNA replication stress, DNA damage signaling kinases inhibit origin firing and promote the remodeling and stabilization of replication forks, leading to a systemic reduction in DNA synt...
www.biorxiv.org
May 16, 2025 at 1:02 PM
New preprint from the lab:
ATM controls fork processing and restart, and the PPM1D phosphatase is needed to properly balance this action of ATM.
Congratulations to @yitingcao.bsky.social @yingzhengwang.bsky.social and Jumana Badar.
www.biorxiv.org/content/10.1...
ATM controls fork processing and restart, and the PPM1D phosphatase is needed to properly balance this action of ATM.
Congratulations to @yitingcao.bsky.social @yingzhengwang.bsky.social and Jumana Badar.
www.biorxiv.org/content/10.1...
Reposted by Benjamin Pardo LAB
Built a peer review system that doesn’t take forever.
Spoiler: scientists love it.
Huge thanks to the amazing team at The Company of Biologists for making Fast & Fair happen.
Read the preprint: bit.ly/4iZ30st
#biologists100 @biologists.bsky.social @biologyopen.bsky.social
Spoiler: scientists love it.
Huge thanks to the amazing team at The Company of Biologists for making Fast & Fair happen.
Read the preprint: bit.ly/4iZ30st
#biologists100 @biologists.bsky.social @biologyopen.bsky.social
Fast & Fair peer review: a pilot study demonstrating feasibility of rapid, high-quality peer review in a biology journal
Traditional peer review is slow, often delayed by the time-consuming process of identifying reviewers and lengthy review turnaround times. This study tests the feasibility of the Fast & Fair peer revi...
bit.ly
March 26, 2025 at 11:52 AM
Built a peer review system that doesn’t take forever.
Spoiler: scientists love it.
Huge thanks to the amazing team at The Company of Biologists for making Fast & Fair happen.
Read the preprint: bit.ly/4iZ30st
#biologists100 @biologists.bsky.social @biologyopen.bsky.social
Spoiler: scientists love it.
Huge thanks to the amazing team at The Company of Biologists for making Fast & Fair happen.
Read the preprint: bit.ly/4iZ30st
#biologists100 @biologists.bsky.social @biologyopen.bsky.social
Reposted by Benjamin Pardo LAB
Postdoc position available in my group at CABIMER (Sevilla, Spain). Please, spread the word!
Contact: nestor.garcia@cabimer.es
Contact: nestor.garcia@cabimer.es
March 19, 2025 at 5:44 PM
Postdoc position available in my group at CABIMER (Sevilla, Spain). Please, spread the word!
Contact: nestor.garcia@cabimer.es
Contact: nestor.garcia@cabimer.es
Reposted by Benjamin Pardo LAB
Exciting seminar series from Genome integrity italian Network (GiiN), chaired by myself and Raffaella Di Micco! Short talks (2x30’), at convenient time for EU/USA attendees. Big shots and raising stars in an expanding field. See flyers + link to receive email alerts. Please repost to your network!👇
March 17, 2025 at 9:58 PM
Exciting seminar series from Genome integrity italian Network (GiiN), chaired by myself and Raffaella Di Micco! Short talks (2x30’), at convenient time for EU/USA attendees. Big shots and raising stars in an expanding field. See flyers + link to receive email alerts. Please repost to your network!👇
Reposted by Benjamin Pardo LAB
Science under attack: a growing list of statements from journals
@jama.com
jamanetwork.com/journals/jam...
@plos.org
theplosblog.plos.org/2025/02/plos...
@science.org
www.science.org/doi/10.1126/...
@nature.com
www.nature.com/articles/d41...
@embopress.org
www.embopress.org/doi/full/10....
@jama.com
jamanetwork.com/journals/jam...
@plos.org
theplosblog.plos.org/2025/02/plos...
@science.org
www.science.org/doi/10.1126/...
@nature.com
www.nature.com/articles/d41...
@embopress.org
www.embopress.org/doi/full/10....
March 19, 2025 at 12:01 PM
Science under attack: a growing list of statements from journals
@jama.com
jamanetwork.com/journals/jam...
@plos.org
theplosblog.plos.org/2025/02/plos...
@science.org
www.science.org/doi/10.1126/...
@nature.com
www.nature.com/articles/d41...
@embopress.org
www.embopress.org/doi/full/10....
@jama.com
jamanetwork.com/journals/jam...
@plos.org
theplosblog.plos.org/2025/02/plos...
@science.org
www.science.org/doi/10.1126/...
@nature.com
www.nature.com/articles/d41...
@embopress.org
www.embopress.org/doi/full/10....
Reposted by Benjamin Pardo LAB
Vous avez raté le rassemblement #StandUpForScience Vendredi soir sur la place de la comédie à #Montpellier ? Retrouvez le texte de la prises de parole de notre président Patrick Lemaire ici 👇
March 9, 2025 at 5:23 PM
Vous avez raté le rassemblement #StandUpForScience Vendredi soir sur la place de la comédie à #Montpellier ? Retrouvez le texte de la prises de parole de notre président Patrick Lemaire ici 👇
Reposted by Benjamin Pardo LAB
Review: Hyrien et al. discuss the nature of the initiation sites of DNA replication, amalgamating findings from various advanced DNA replication mapping techniques in order to build a more cohesive model of DNA replication initiation.
Learn more here:
➡️ tinyurl.com/gd352227
Learn more here:
➡️ tinyurl.com/gd352227
March 6, 2025 at 10:43 PM
Review: Hyrien et al. discuss the nature of the initiation sites of DNA replication, amalgamating findings from various advanced DNA replication mapping techniques in order to build a more cohesive model of DNA replication initiation.
Learn more here:
➡️ tinyurl.com/gd352227
Learn more here:
➡️ tinyurl.com/gd352227
Reposted by Benjamin Pardo LAB
How do replisomes walk on DNA? And what happens when they run into a G-quadruplex? @sahilbatra.bsky.social and @benallwein.bsky.social provide unexpected insight in our latest paper with Richard Hite @mskcancercenter.bsky.social @science.org www.science.org/doi/10.1126/.... Congrats to all authors!
G-quadruplex–stalled eukaryotic replisome structure reveals helical inchworm DNA translocation
DNA G-quadruplexes (G4s) are non–B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork ...
www.science.org
March 6, 2025 at 9:30 PM
How do replisomes walk on DNA? And what happens when they run into a G-quadruplex? @sahilbatra.bsky.social and @benallwein.bsky.social provide unexpected insight in our latest paper with Richard Hite @mskcancercenter.bsky.social @science.org www.science.org/doi/10.1126/.... Congrats to all authors!
Reposted by Benjamin Pardo LAB
'In 2024, a budget cut of €900m shocked the scientific community. More recently, additional amendments to this budget proposed further cuts of €630m, along with an extra €534m reduction to the France 2030 program. These cuts threaten not only basic research but also higher education'
The importance of delivering Recherche d'Avenir – research for the future
In recent years, several European countries, including France, have reduced their investment in scientific research, with biomedical research taking a significant hit. The primary casualty is basic re...
journals.biologists.com
February 26, 2025 at 6:16 PM
'In 2024, a budget cut of €900m shocked the scientific community. More recently, additional amendments to this budget proposed further cuts of €630m, along with an extra €534m reduction to the France 2030 program. These cuts threaten not only basic research but also higher education'
Reposted by Benjamin Pardo LAB
SAVE THE DATE! The next EMBO | EMBL Symposium on 'DNA replication and genome maintenance: from basic biology to disease' will be held October 20-23, 2026.
Organized by Helle Ulrich (IMB), Johannes Walter (Harvard) and Anja Groth (Danish Cancer Institute).
www.embl.org/about/info/c...
Organized by Helle Ulrich (IMB), Johannes Walter (Harvard) and Anja Groth (Danish Cancer Institute).
www.embl.org/about/info/c...
DNA replication and genome maintenance: from basic biology to disease
www.embl.org
February 26, 2025 at 3:22 PM
SAVE THE DATE! The next EMBO | EMBL Symposium on 'DNA replication and genome maintenance: from basic biology to disease' will be held October 20-23, 2026.
Organized by Helle Ulrich (IMB), Johannes Walter (Harvard) and Anja Groth (Danish Cancer Institute).
www.embl.org/about/info/c...
Organized by Helle Ulrich (IMB), Johannes Walter (Harvard) and Anja Groth (Danish Cancer Institute).
www.embl.org/about/info/c...
Reposted by Benjamin Pardo LAB
🔴⚠CNIO-CaixaResearch Frontiers Meetings: Machines acting on DNA and RNA, a molecular mechanistic perspective.
📆May 28-30th
👥 @oscarllorca.bsky.social, @rfleiro.bsky.social and @nogaleslab.bsky.social.
🔗https://www.cnio.es/eventos/machines-acting-on-dna-and-rna-a-molecular-mechanistic-perspective/
📆May 28-30th
👥 @oscarllorca.bsky.social, @rfleiro.bsky.social and @nogaleslab.bsky.social.
🔗https://www.cnio.es/eventos/machines-acting-on-dna-and-rna-a-molecular-mechanistic-perspective/
February 5, 2025 at 4:03 PM
🔴⚠CNIO-CaixaResearch Frontiers Meetings: Machines acting on DNA and RNA, a molecular mechanistic perspective.
📆May 28-30th
👥 @oscarllorca.bsky.social, @rfleiro.bsky.social and @nogaleslab.bsky.social.
🔗https://www.cnio.es/eventos/machines-acting-on-dna-and-rna-a-molecular-mechanistic-perspective/
📆May 28-30th
👥 @oscarllorca.bsky.social, @rfleiro.bsky.social and @nogaleslab.bsky.social.
🔗https://www.cnio.es/eventos/machines-acting-on-dna-and-rna-a-molecular-mechanistic-perspective/
Reposted by Benjamin Pardo LAB
New from
@MorieLAB.bsky.social!
Neutral Lipids restrict DNA mobility!!
1. This has important implications for DNA repair in vivo,
2. also in vitro when you measure DNA breaks using the comet assay, beware!
3. And, we provide a fast new protocol overcoming this issue 😍
doi.org/10.1111/boc....
@MorieLAB.bsky.social!
Neutral Lipids restrict DNA mobility!!
1. This has important implications for DNA repair in vivo,
2. also in vitro when you measure DNA breaks using the comet assay, beware!
3. And, we provide a fast new protocol overcoming this issue 😍
doi.org/10.1111/boc....
Neutral lipids restrict the mobility of broken DNA molecules during comet assays
This study reveals that neutral lipids (NL), naturally present in cells, become trapped within genomic DNA as a consequence of the standard execution of the comet assay, a technique used to measure D...
doi.org
January 25, 2025 at 11:05 AM
New from
@MorieLAB.bsky.social!
Neutral Lipids restrict DNA mobility!!
1. This has important implications for DNA repair in vivo,
2. also in vitro when you measure DNA breaks using the comet assay, beware!
3. And, we provide a fast new protocol overcoming this issue 😍
doi.org/10.1111/boc....
@MorieLAB.bsky.social!
Neutral Lipids restrict DNA mobility!!
1. This has important implications for DNA repair in vivo,
2. also in vitro when you measure DNA breaks using the comet assay, beware!
3. And, we provide a fast new protocol overcoming this issue 😍
doi.org/10.1111/boc....
Reposted by Benjamin Pardo LAB
The Shu complex –a conserved homologous recombination factor– interact with ORC and MCM replication initiation factors to facilitate error-free bypass of replicative DNA damage
Kara Bernstein, Katrin Paeschke and coworkers
www.embopress.org/doi/full/10....
Kara Bernstein, Katrin Paeschke and coworkers
www.embopress.org/doi/full/10....
January 22, 2025 at 2:26 PM
The Shu complex –a conserved homologous recombination factor– interact with ORC and MCM replication initiation factors to facilitate error-free bypass of replicative DNA damage
Kara Bernstein, Katrin Paeschke and coworkers
www.embopress.org/doi/full/10....
Kara Bernstein, Katrin Paeschke and coworkers
www.embopress.org/doi/full/10....
Reposted by Benjamin Pardo LAB
In this new paper we find that Tel1 kinase (yeast ATM) targets D/E-S/T motifs… more prevalent than S/T-Q!
Mec1 (yeast ATR) can’t target D/E-S/T, so we think D/E-S/T targeting allows Tel1 functional specialization.
A mutation in Tel1 makes it only target S/T-Q… and cells become CPT sensitive.
Mec1 (yeast ATR) can’t target D/E-S/T, so we think D/E-S/T targeting allows Tel1 functional specialization.
A mutation in Tel1 makes it only target S/T-Q… and cells become CPT sensitive.
Profiling Tel1 Signaling Reveals a Non-Canonical Motif Targeting DNA Repair and Telomere Control Machineries
The stability of the genome relies on Phosphatidyl Inositol 3-Kinase-related Kinases (PIKKs) that sense DNA damage and trigger elaborate downstream si…
www.sciencedirect.com
January 21, 2025 at 3:36 PM
In this new paper we find that Tel1 kinase (yeast ATM) targets D/E-S/T motifs… more prevalent than S/T-Q!
Mec1 (yeast ATR) can’t target D/E-S/T, so we think D/E-S/T targeting allows Tel1 functional specialization.
A mutation in Tel1 makes it only target S/T-Q… and cells become CPT sensitive.
Mec1 (yeast ATR) can’t target D/E-S/T, so we think D/E-S/T targeting allows Tel1 functional specialization.
A mutation in Tel1 makes it only target S/T-Q… and cells become CPT sensitive.
Reposted by Benjamin Pardo LAB
We hope you all had fantastic holidays and are ready for 2025! The GIIN webinars will restart next Tuesday, January 14th, with exciting talks from @labthoma.bsky.social and @stesantaguida.bsky.social ! Follow the zoom link to join: uniroma1.zoom.us/j/95149984403
January 8, 2025 at 10:08 AM
We hope you all had fantastic holidays and are ready for 2025! The GIIN webinars will restart next Tuesday, January 14th, with exciting talks from @labthoma.bsky.social and @stesantaguida.bsky.social ! Follow the zoom link to join: uniroma1.zoom.us/j/95149984403
HU traps Top1 on stalled replication forks! Important to consider when inducing replication stress with HU. In addiction to HU-induced oxidative stress!
Nice work by Ismail Hassan Ismail lab in Canada!
www.cell.com/cell-reports...
Nice work by Ismail Hassan Ismail lab in Canada!
www.cell.com/cell-reports...
PNKP safeguards stalled replication forks from nuclease-dependent degradation during replication stress
Mashayekhi et al. demonstrate that polynucleotide kinase-phosphatase (PNKP) protects stalled replication forks from excessive degradation by preventing the accumulation of DNA ends with incompatible termini. Loss of PNKP leads to nascent DNA degradation via EXO1 exonuclease activity, independently of the BRCA2 pathway.
www.cell.com
January 5, 2025 at 2:57 PM
HU traps Top1 on stalled replication forks! Important to consider when inducing replication stress with HU. In addiction to HU-induced oxidative stress!
Nice work by Ismail Hassan Ismail lab in Canada!
www.cell.com/cell-reports...
Nice work by Ismail Hassan Ismail lab in Canada!
www.cell.com/cell-reports...