QCD challenges from pp to AA collisions: 4th edition

This paper is a write-up of the ideas that were presented, developed and discussed at the fourth International Workshop on QCD Challenges from pp to AA, which took place in February 2023 in Padua, Italy. The goal of the workshop was to focus on some of the open questions in the field of high-energy heavy-ion physics and to stimulate the formulation of concrete suggestions for making progresses on both the experimental and theoretical sides. The paper gives a brief introduction to each topic and then summarizes the primary results

The Plague (1992). From Albert Camus to Luis Puenzo

La peste muestra cómo se afecta la vida en una ciudad tras ser declarada una epidemia de peste. Pero va mucho más allá y refleja como el desastre y la desgracia pueden hacer aflorar los mejores sentimientos y actitudes de las personas para luchar y lograr sobreponerse ante lo que consideran injusto. El protagonista, el doctor Rieux, se queda en la ciudad porque marcharse sería desertar, siente la necesidad decombatir para acabar con el mal, que tiene la forma de la temible peste bubónica. Esta enfermedad da al traste con las vidas e ilusiones de cientos de inocentes. El miedo inunda las calles, y, además del doctor Rieux, hay otras personas dispuestas a ayudar y conseguir terminar con el horror. El esfuerzo común logra que la peste acabe desapareciendo ante el júbilo de todos. Pero queda planteada la duda sobre si no es posible que la amenaza siga vigente y algún día regrese.The Plague shows how a city s life is disrupted after an epidemic of plague has been declared. However, the film goes much further than this and reflects how disaster and misfortune can release people s better feelings and attitudes to struggle against adversity and survive asituation they consider unjust. The main character, Dr. Rieux, remains in the city because to flee would be to desert, and he truly feels the need to fight against such appalling circumstances brought about by the bubonic plague, a plague able to banish the hopes and cull the lives of hundreds of innocent people. Fear stalks the streets but as well as Dr. Rieux there are others willing to stay and combat the horror. The commonefforts finally manage to vanquish the evil, to the delight of all. Nevertheless, the doubt remains as to whether the threat remains and mightspring up again some time

Función de Dot1 en el checkpoint de recombinación meiótica y en la tolerancia al daño en el DNA

[ES] Las modificaciones post-traduccionales de las histonas repercuten en numerosas funciones biológicas, regulando procesos esenciales como la transcripción, la replicación, la reparación del DNA, la recombinación o el control del ciclo celular. En la presente tesis doctoral se ha estudiado la influencia de la metilación de la lisina 79 de la histona H3 (H3K79me), mediada en exclusiva por la singular enzima Dot1, en mecanismos celulares implicados en el mantenimiento de la integridad genómica. Así, hemos dilucidado las bases moleculares de la función de Dot1 en el checkpoint de recombinación meiótica en Saccharomyces cerevisiae, un mecanismo de vigilancia que asegura la correcta distribución del material genético a los gametos. La metilación de H3K79me es necesaria para la apropiada localización y activación de proteínas adaptadoras y efectoras del checkpoint, que consiguen disparar este mecanismo de supervivencia celular. Además, hemos expandido nuestra investigación a la meiosis en mamíferos analizando la distribución de DOT1L y de la metilación de H3K79me en espermatocitos de ratón. Los patrones diferenciales de localización de las distintas formas de H3K79me, apuntan a funciones específicas para cada marca epigenética durante la espermatogénesis. Por otro lado, puesto que Dot1 también actúa durante el ciclo mitótico, hemos determinado la relevancia funcional de la metilación de H3K79 en la tolerancia al daño por alquilación en el DNA mediado por síntesis a través de lesión (TLS) en la levadura de gemación. En conclusión, las modificaciones epigenéticas catalizadas por la proteína conservada evolutivamente Dot1 participan en múltiples procesos cruciales para la estabilidad del genoma tanto durante el ciclo de división meiótico, como mitótico

Impact of histone H4K16 acetylation on the meiotic recombination checkpoint in Saccharomyces cerevisiae

In meiotic cells, the pachytene checkpoint or meiotic recombination checkpoint is a surveillance mechanism that monitors critical processes, such as recombination and chromosome synapsis, which are essential for proper distribution of chromosomes to the meiotic progeny. Failures in these processes lead to the formation of aneuploid gametes. Meiotic recombination occurs in the context of chromatin; in fact, the histone methyltransferase Dot1 and the histone deacetylase Sir2 are known regulators of the pachytene checkpoint in Saccharomyces cerevisiae. We report here that Sas2-mediated acetylation of histone H4 at lysine 16 (H4K16ac), one of the Sir2 targets, modulates meiotic checkpoint activity in response to synaptonemal complex defects. We show that, like sir2, the H4-K16Q mutation, mimicking constitutive acetylation of H4K16, eliminates the delay in meiotic cell cycle progression imposed by the checkpoint in the synapsis-defective zip1 mutant. We also demonstrate that, like in dot1, zip1-induced phosphorylation of the Hop1 checkpoint adaptor at threonine 318 and the ensuing Mek1 activation are impaired in H4-K16 mutants. However, in contrast to sir2 and dot1, the H4-K16R and H4-K16Q mutations have only a minor effect in checkpoint activation and localization of the nucleolar Pch2 checkpoint factor in ndt80-prophase-arrested cells. We also provide evidence for a cross-talk between Dot1-dependent H3K79 methylation and H4K16ac and show that Sir2 excludes H4K16ac from the rDNA region on meiotic chromosomes. Our results reveal that proper levels of H4K16ac orchestrate this meiotic quality control mechanism and that Sir2 impinges on additional targets to fully activate the checkpoint.SC was partially supported by a postdoctoral JAE-Doc contract and DO by a predoctoral JAE-Predoc contract from the Consejo Superior de Investigaciones Científicas (CSIC) of Spain. This work was funded by grants BFU2012-35748 and BFU2015-65417-R, from the Ministry of Economy and Competitiveness of Spain (MINECO), and grant CSI084U16 from Junta de Castilla y León (Spain), to PSS.Peer Reviewe

Dynamics of DOT1L localization and H3K79 methylation during meiotic prophase I in mouse spermatocytes

PMCID: PMC3969405During meiotic prophase I, interactions between maternal and paternal chromosomes, under checkpoint surveillance, establish connections between homologs that promote their accurate distribution to meiotic progeny. In human, faulty meiosis causes aneuploidy resulting in miscarriages and genetic diseases. Meiotic processes occur in the context of chromatin; therefore, histone post-translational modifications are expected to play important roles. Here, we report the cytological distribution of the evolutionarily conserved DOT1L methyltransferase and the different H3K79 methylation states resulting from its activity (mono-, di- and tri-methylation; H3K79me1, me2 and me3, respectively) during meiotic prophase I in mouse spermatocytes. In the wild type, whereas low amounts of H3K79me1 are rather uniformly present throughout prophase I, levels of DOT1L, H3K79me2 and H3K79me3 exhibit a notable increase from pachynema onwards, but with differential subnuclear distribution patterns. The heterochromatic centromeric regions and the sex body are enriched for H3K79me3. In contrast, H3K79me2 is present all over the chromatin, but is largely excluded from the sex body despite the accumulation of DOT1L. In meiosis-defective mouse mutants, the increase of DOT1L and H3K79me is blocked at the same stage where meiosis is arrested. H3K79me patterns, combined with the cytological analysis of the H3.3, γH2AX, macroH2A and H2A.Z histone variants, are consistent with a differential role for these epigenetic marks in male mouse meiotic prophase I. We propose that H3K79me2 is related to transcriptional reactivation on autosomes during pachynema, whereas H3K79me3 may contribute to the maintenance of repressive chromatin at centromeric regions and the sex body. © 2013 Springer-Verlag.DO was supported by a predoctoral fellowship (JAE-Predoc) from the CSIC (Spain) and an EMBO short-term fellowship. Research was supported by NIH grant R01 GM105421 (to Maria Jasin and SK) and grants from MINECO (BFU2012-35748), Junta de Castilla y León (CSI025A11-2), and Fundación Ramón Areces to PSS.Peer Reviewe

Dot1-dependent histone H3K79 methylation promotes activation of the Mek1 meiotic checkpoint effector kinase by regulating the Hop1 adaptor

This is an open-access article distributed under the terms of the Creative Commons Attribution License.During meiosis, accurate chromosome segregation relies on the proper interaction between homologous chromosomes, including synapsis and recombination. The meiotic recombination checkpoint is a quality control mechanism that monitors those crucial events. In response to defects in synapsis and/or recombination, this checkpoint blocks or delays progression of meiosis, preventing the formation of aberrant gametes. Meiotic recombination occurs in the context of chromatin and histone modifications, which play crucial roles in the maintenance of genomic integrity. Here, we unveil the role of Dot1-dependent histone H3 methylation at lysine 79 (H3K79me) in this meiotic surveillance mechanism. We demonstrate that the meiotic checkpoint function of Dot1 relies on H3K79me because, like the dot1 deletion, H3-K79A or H3-K79R mutations suppress the checkpoint-imposed meiotic delay of a synapsis-defective zip1 mutant. Moreover, by genetically manipulating Dot1 catalytic activity, we find that the status of H3K79me modulates the meiotic checkpoint response. We also define the phosphorylation events involving activation of the meiotic checkpoint effector Mek1 kinase. Dot1 is required for Mek1 autophosphorylation, but not for its Mec1/Tel1-dependent phosphorylation. Dot1-dependent H3K79me also promotes Hop1 activation and its proper distribution along zip1 meiotic chromosomes, at least in part, by regulating Pch2 localization. Furthermore, HOP1 overexpression bypasses the Dot1 requirement for checkpoint activation. We propose that chromatin remodeling resulting from unrepaired meiotic DSBs and/or faulty interhomolog interactions allows Dot1-mediated H3K79-me to exclude Pch2 from the chromosomes, thus driving localization of Hop1 along chromosome axes and enabling Mek1 full activation to trigger downstream responses, such as meiotic arrest. © 2013 Ontoso et al.This work was supported by grants from MICINN (SAF2010-22357, CONSOLIDER-Ingenio 2010 CDS2007-0015) to RF; from the Dutch Cancer Society (KWF2009-4511) to FvL; and from the Ministry of Science and Innovation of Spain (BFU2009-07159), Junta de Castilla y León (CSI025A11-2), and Fundación Ramón Areces to PAS-S. DO was supported by a predoctoral fellowship (JAE-predoc) from the CSIC (Spain).Peer Reviewe

Functional analysis of chromatin modifications during meiosis

Comunicación presentada al International Workshop: "The enemy within: endogenous DNA damage as a source of cancer and ageing" celebrado en Baeza del 17 al 19 de Noviembre de 2011 y a la "8ª Reunión de la Red Española de Levaduras" celebrada en El Escorial del 14 al 16 de diciembre de 2011.Peer Reviewe

Regulation of tolerance to DNA alkylating damage by Dot1 and Rad53 in Saccharomyces cerevisiae

12 páginas, 8 figuras, 2 tablas.-- El pdf del artículo es la versión de autor.To maintain genomic integrity cells have to respond properly to a variety of exogenous and endogenous factors that produce genome injuries and interfere with DNA replication. DNA integrity checkpoints coordinate this response by slowing cell cycle progression to provide time for the cell to repair the damage, stabilizing replication forks and stimulating DNA repair to restore the original DNA sequence and structure. In addition, there are also mechanisms of damage tolerance, such as translesion synthesis (TLS), which are important for survival after DNA damage. TLS allows replication to continue without removing the damage, but results in a higher frequency of mutagenesis. Here, we investigate the functional contribution of the Dot1 histone methyltransferase and the Rad53 checkpoint kinase to TLS regulation in Saccharomyces cerevisiae. We demonstrate that the Dot1-dependent status of H3K79 methylation modulates the resistance to the alkylating agent MMS, which depends on PCNA ubiquitylation at lysine 164. Strikingkly, either the absence of DOT1, which prevents full activation of Rad53, or the expression of an HA-tagged version of RAD53, which produces low amounts of the kinase, confer increased MMS resistance. However, the dot1Δ rad53-HA double mutant is hypersensitive to MMS and shows barely detectable amounts of activated kinase. Furthermore, moderate overexpression of RAD53 partially suppresses the MMS resistance of dot1Δ. In addition, we show that MMS-treated dot1Δ and rad53-HA cells display increased number of chromosome-associated Rev1 foci. We propose that threshold levels of Rad53 activity exquisitely modulate the tolerance to alkylating damage at least by controlling the abundance of the key TLS factor Rev1 bound to chromatin.DO and AGS were supported by predoctoral fellowships from CSIC and MEC (Spain), respectively. Research in our labs is supported by grants from Ministry of Science and Innovation of Spain (BFU2009-06938 to AB and BFU2009-07159 to PSS) and a grant from Fundación Ramón Areces to PSS.Peer reviewe

The Pch2 AAA+ ATPase promotes phosphorylation of the Hop1 meiotic checkpoint adaptor in response to synaptonemal complex defects

Meiotic cells possess surveillance mechanisms that monitor critical events such as recombination and chromosome synapsis. Meiotic defects resulting from the absence of the synaptonemal complex component Zip1 activate a meiosis-specific checkpoint network resulting in delayed or arrested meiotic progression. Pch2 is an evolutionarily conserved AAA+ ATPase required for the checkpoint-induced meiotic block in the zip1 mutant, where Pch2 is only detectable at the ribosomal DNA array (nucleolus). We describe here that high levels of the Hop1 protein, a checkpoint adaptor that localizes to chromosome axes, suppress the checkpoint defect of a zip1 pch2 mutant restoring Mek1 activity and meiotic cell cycle delay. We demonstrate that the critical role of Pch2 in this synapsis checkpoint is to sustain Mec1-dependent phosphorylation of Hop1 at threonine 318. We also show that the ATPase activity of Pch2 is essential for its checkpoint function and that ATP binding to Pch2 is required for its localization. Previous work has shown that Pch2 negatively regulates Hop1 chromosome abundance during unchallenged meiosis. Based on our results, we propose that, under checkpoint-inducing conditions, Pch2 also possesses a positive action on Hop1 promoting its phosphorylation and its proper distribution on unsynapsed chromosome axes.Ministry of Economy and Competitiveness (MINECO) of Spain [BFU2012-35748 and BFU2015-65417-R]; Predoctoral contract from the University of Salamanca (Spain) (to E.H.); Predoctoral fellowship (JAE-predoc) (to D.O.) and a postdoctoral fellowship (JAE-doc) (to S.C.) from the CSIC (Spain). Funding for open access charge: Ministry of Economy and Competitiveness (MINECO) of Spain [BFU2012-35748 and BFU2015-65417-R].Peer Reviewe

Meiotic checkpoint control of chromosome dynamics by the nucleolar Pch2 AAA+ ATPase

Resumen del trabajo presentado a la 10ª Reunión de la Red Española de Levaduras, celebrada en El Escorial (Madrid) del 16 al 18 de diciembre de 2015.Meiotic cells possess surveillance mechanisms or checkpoints that monitor critical meiotic events, such as recombination and chromosome synapsis. Defects in these processes, such as those resulting from the absence of the Zip1 protein (an structural component of the synaptonemal complex), activate a meiosis-specific checkpoint network resulting in a delay or arrest of meiotic progression. We are studying this meiotic checkpoint at different levels. Pch2 is an evolutionarily conserved AAA+ ATPase initially discovered as a checkpoint protein required for the zip1-induced meiotic arrest in budding yeast. Pch2 impacts multiple aspects of meiotic chromosome metabolism, including negative regulation of Hop1 chromosomal localization. Hop1 is a structural component of chromosome axis required to transmit the checkpoint signal. It has been suggested that Pch2 promotes the turnover of the Hop1 protein; thus, the pch2 single mutant exhibits more abundant Hop1 localization along synapsed chromosomes. Interestingly, in the zip1 mutant, when the checkpoint is induced, Pch2 is only detectable at the rDNA region (nucleolus). A special chromatin environment determined by the chromosomal distribution of Dot1-dependent histone H3K79 methylation and by the action of the Sir2 histone deacetylase contributes to Pch2’s nucleolar confinement. To gain insight into the molecular mechanisms underlying the function of Pch2 in the synapsis checkpoint triggered by the absence of Zip1, we carried out a genetic screen for high-copy suppressors of meiotic progression in zip1 pch2 and, unexpectedly, we identified HOP1. Analysis of Mek1 activation (the meiotic counterpart of the Rad53 checkpoint effector kinase) revealed that Pch2 is required for checkpoint-induced Mek1 autophosphorylation, but not for the Mec1/Tel1 priming phosphorylation. HOP1 overexpression restored full Mek1 activation in zip1 pch2, thus explaining the re-establishment of the meiotic block. Surprisingly, we observed that, in contrast with the pch2 single mutant, Hop1 localization on the axes was no more abundant in zip1 pch2 compared with zip1. Moreover, Mec1/Tel1-dependent phosphorylation of Hop1 at T318 is strongly reduced in zip1 pch2 compared to zip1. Unlike wild-type HOP1, overexpression of a hop1-T318A mutant does not restore checkpoint function in zip1 pch2. Taken together, these observations imply that Pch2 activity is required for proper accumulation of phosphorylated Hop1-T318 on unsynapsed chromosome axes, and argue that Pch2 regulates Hop1 in different and even opposite manners in a wild type (checkpoint off) versus a zip1 (checkpoint on) situation.Peer Reviewe