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2020

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence.

Author(s) : Sati S, Bonev B, Szabo Q, Jost D, Bensadoun P, Serra F, Loubiere V, Papadopoulos G, Rivera-Mulia J, Fritsch L, Bouret P, Castillo D, Gelpi J, Orozco M, Vaillant C, Pellestor F, Bantignies F, Marti-Renom M, Gilbert D, Lemaitre J, Cavalli G,
Journal : Mol Cell
2020
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced senescence (OIS). We identify senescence-associated heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to the formation of senescence-associated heterochromatin foci (SAHFs) in OIS but not in RS. ThisOIS-specific configuration brings active genes located in genomic regions adjacent to SAHDs in close spatial proximity and favors their expression. We also identify DNMT1 as a factor that induces SAHFs by promoting HMGA2 expression. Upon DNMT1 depletion, OIS cells transition to a 3D genome conformation akin to that of cells in replicative senescence. These data show how multi-omics and imaging canidentify critical features of RS and OIS and discover determinants of acute senescence and SAHF formation.

[Circular RNA, actors and biomarkers of cancers]

Author(s) : Ladet J, Mortreux F,
Journal : Med Sci (Paris)
2020

A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities

Author(s) : Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M,
Journal : Molecular & Cellular Proteomics
2020
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pM to 17 µM. After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.

A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities

Author(s) : Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M,
Journal : Molecular & Cellular Proteomics
2020
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pM to 17 µM. After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.

A Role for Caenorhabditis elegans COMPASS in Germline Chromatin Organization.

Author(s) : Herbette M, Robert V, Bailly A, Gely L, Feil R, Llères D, Palladino F,
Journal : Cells
2020
Deposition of histone H3 lysine 4 (H3K4) methylation at promoters is catalyzed bythe SET1/COMPASS complex and is associated with context-dependent effects on geneexpression and local changes in chromatin organization. The role of SET1/COMPASS inshaping chromosome architecture has not been investigated. Here we usedCaenorhabditis elegans to address this question through a live imaging approach andgenetic analysis. Using quantitative FRET (Förster resonance energy transfer)-basedfluorescence lifetime imaging microscopy (FLIM) on germ cells expressing histoneseGFP-H2B and mCherry-H2B, we find that SET1/COMPASS influences meiotic chromosomeorganization, with marked effects on the close proximity between nucleosomes. Wefurther show that inactivation of set-2, encoding the C. elegans SET1 homologue, orCFP-1, encoding the chromatin targeting subunit of COMPASS, enhances germlinechromosome organization defects and sterility of condensin-II depleted animals.set-2 loss also aggravates germline defects resulting from conditional inactivationof topoisomerase II, another structural component of chromosomes. Expressionprofiling of set-2 mutant germlines revealed only minor transcriptional changes,suggesting that the observed effects are at least partly independent oftranscription. Altogether, our results are consistent with a role for SET1/COMPASSin shaping meiotic chromosomes in C. elegans, together with the non-histone proteinscondensin-II and topoisomerase. Given the high degree of conservation, our findingsexpand the range of functions attributed to COMPASS and suggest a broader role ingenome organization in different species.

Aurora B and condensin are dispensable for chromosome arm and telomere separation during meiosis II.

Author(s) : Berthezene J, Reyes C, Li T, Coulon S, Bernard P, Gachet Y, Tournier S,
Journal : Mol Biol Cell
2020
In mitosis, while the importance of kinetochore (KT)-microtubule (MT) attachment hasbeen known for many years, increasing evidence suggests that telomere dysfunctionsalso perturb chromosome segregation by contributing to the formation of chromatinbridges at anaphase. Recent evidence suggests that Aurora B kinase ensures properchromosome segregation during mitosis not only by controlling KT-MT attachment butalso by regulating telomere and chromosome arm separation. However, whether and howAurora B governs telomere separation during meiosis has remained unknown. Here, weshow that fission yeast Aurora B localizes at telomeres during meiosis I andpromotes telomere separation independently of the meiotic cohesin Rec8. In meiosisII, Aurora B controls KT-MT attachment but appears dispensable for telomere andchromosome arm separation. Likewise, condensin activity is nonessential in meiosisII for telomere and chromosome arm separation. Thus, in meiosis, the requirementsfor Aurora B are distinct at centromeres and telomeres, illustrating the criticaldifferences in the control of chromosome segregation between mitosis and meiosis II.

Caenorhabditis elegans SET1/COMPASS Maintains Germline Identity by Preventing Transcriptional Deregulation Across Generations.

Author(s) : Robert V, Knutson A, Rechtsteiner A, Garvis S, Yvert G, Strome S, Palladino F,
Journal : Front Cell Dev Biol
2020
Chromatin regulators contribute to the maintenance of the germline transcriptionalprogram. In the absence of SET-2, the Caenorhabditis elegans homolog of theSET1/COMPASS H3 Lys4 (H3K4) methyltransferase, animals show transgenerational lossof germline identity, leading to sterility. To identify transcriptional signaturesassociated with progressive loss of fertility, we performed expression profiling ofset-2 mutant germlines across generations. We identify a subset of genes whosemisexpression is first observed in early generations, a step we refer to as priming;their misexpression then further progresses in late generations, as animals reachsterility. Analysis of misregulated genes shows that down-regulation of germlinegenes, expression of somatic transcriptional programs, and desilencing of theX-chromosome are concurrent events leading to loss of germline identity in bothearly and late generations. Upregulation of transcription factor LIN-15B, the C/EBPhomolog CEBP-1, and TGF-β pathway components strongly contribute to loss offertility, and RNAi inactivation of cebp-1 and TGF-β/Smad signaling delays the onsetof sterility, showing they individually contribute to maintenance of germ cellidentity. Our approach therefore identifies genes and pathways whose misexpressionactively contributes to the loss of germ cell fate. More generally, our data showshow loss of a chromatin regulator in one generation leads to transcriptional changesthat are amplified over subsequent generations, ultimately leading to loss ofappropriate cell fate.

Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans.

Author(s) : Triqueneaux G, Burny C, Symmons O, Janczarski S, Gruffat H, Yvert G,
Journal : Commun Biol
2020
Variability in gene expression across a population of homogeneous cells is known toinfluence various biological processes. In model organisms, natural genetic variantswere found that modify expression dispersion (variability at a fixed mean) but veryfew studies have detected such effects in humans. Here, we analyzed single-cellexpression of four proteins (CD23, CD55, CD63 and CD86) across cell lines derivedfrom individuals of the Yoruba population. Using data from over 30 million cells, wefound substantial inter-individual variation of dispersion. We demonstrate, via denovo cell line generation and subcloning experiments, that this variation exceedsthe variation associated with cellular immortalization. We detected a geneticassociation between the expression dispersion of CD63 and the rs971 SNP. Our resultsshow that human DNA variants can have inherently-probabilistic effects on geneexpression. Such subtle genetic effects may participate to phenotypic variation anddisease outcome.

Chromosome dynamics during interphase: a biophysical perspective.

Author(s) : Tortora M, Salari H, Jost D,
Journal : Curr Opin Genet Dev
2020
The dynamic nature of chromosome organization plays a central role in the regulation of many crucial processes, such as DNA transcription and replication.However, the molecular bases of the link between genomic function, structure anddynamics remain elusive. In this review, we focus on how biophysical modelling can be instrumentally used to rationalize experimental studies of chromosome dynamics, and to probe the impact of putative mechanisms on genome folding kinetics during interphase. We introduce the general connection between chromatin internal organization and dynamics, and outline the potential effects of passiveinteractions mediated by architectural proteins and of active, energy-dependent processes on chromatin motion. Finally, we discuss current ambiguities emerging from in vivo observations, in particular related to ATP depletion and transcriptional activation, and highlight future perspectives.

Cohesin regulates homology search during recombinational DNA repair

Author(s) : Piazza A, Bordelet H, Dumont A, Thierry A, Savocco J, Girard F, Koszul R,
Journal : Biorxiv
2020
Homologous recombination (HR) is a ubiquitous DNA double-strand break (DSB) repair mechanism that promotes cell survival. It entails a potentially genome-wide homology search step, carried out along a conserved RecA/Rad51-ssDNA nucleoprotein filament (NPF) assembled on each DSB ends. This search is subdued to NPF-dsDNA collision probability, dictated in part by chromatin conformation. In contrast to the extensive knowledge about chromatin composition and mobility changes elicited by the DNA damage checkpoint (DDC), whether, how, and to which extent a DSB impacts spatial chromatin organization, and whether this organization in turns influences the homology search process, remains ill-defined. Here we characterize two layers of spatial chromatin reorganization following DSB formation in S. cerevisiae. While cohesin folds chromosomes into cohesive arrays of 10-20 kb long chromatin loops as cells arrest in G2/M, the DSB-flanking regions locally interact in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin and HR proteins. This local structure blocks cohesin progression, constraining the extending NPF at loop base. Functionally this organization promotes side-specific cis DSB-dsDNA interactions that scales with loop expansion span, and provides a kinetic advantage for identification of intra- over inter-chromosomal homologies. We propose that cohesins regulate homology search by promoting cis dsDNA over-sampling, both upon loop expansion-coupled unidimensional dsDNA scanning, NPF trapping, and chromosome individualization, largely independent of their role in sister chromatid cohesion.

Developmental variability channels mouse molar evolution.

Author(s) : Hayden L, Lochovska K, Semon M, Renaud S, Delignette-Muller M, Vilcot M, Peterkova R, Hovorakova M, Pantalacci S,
Journal : Elife
2020
Do developmental systems preferentially produce certain types of variation that orient phenotypic evolution along preferred directions? At different scales, from the intra-population to the interspecific, the murine first upper molar shows repeated anterior elongation. Using a novel quantitative approach to compare thedevelopment of two mouse strains with short or long molars, we identified temporal, spatial and functional differences in tooth signaling center activity,that arise from differential tuning of the activation-inhibition mechanisms underlying tooth patterning. By tracing their fate, we could explain why only the upper first molar reacts via elongation of its anterior part. Despite a lack of genetic variation, individuals of the elongated strain varied in tooth length and the temporal dynamics of their signaling centers, highlighting the intrinsic instability of the upper molar developmental system. Collectively, these resultsreveal the variational properties of murine molar development that drive morphological evolution along a line of least resistance.

Diversification and hybrid incompatibility in auto-pseudogamous species of Mesorhabditis nematodes.

Author(s) : Launay C, Félix M, Dieng J, Delattre M,
Journal : BMC Evol Biol
2020
BACKGROUND: Pseudogamy is a reproductive system in which females rely on the spermof males to activate their oocytes, generally parasitizing males of other species,but do not use the sperm DNA. The nematode Mesorhabditis belari uses a specific formof pseudogamy, where females produce their own males as a source of sperm. Malesdevelop from rare eggs with true fertilization, while females arise by gynogenesis.Males thus do not contribute their genome to the female offspring. Here, we exploredthe diversity of reproductive mode within the Mesorhabditis genus and addressedspecies barriers in pseudogamous species. RESULTS: To this end, we established acollection of over 60 Mesorhabditis strains from soil and rotting vegetal matter. Wefound that males from pseudogamous species displayed a reduced size of their body,male tail and sperm cells compared to males of sexual Mesorhabditis species, asexpected for males that face little competition. Using rDNA sequences and crosses,we could define 11 auto-pseudogamous biological species, with closely relatedspecies pairs and a possible single origin of pseudogamy in the Mesorhabditis genus.Most crosses between males and females of different species did not even producefemale progeny. This surprising species barrier in pseudogamous egg activation waspre or postcopulatory depending on the species pair. In the latter case, when hybridembryos were produced, most arrested before the first embryonic cell division.Hybrid incompatibility between auto-pseudogamous species was due to defectiveinteraction between sperm and oocyte as well as defective reconstitution of zygoticcentrosomes. CONCLUSIONS: We established a collection of sexual and pseudo-sexualspecies which offer an ideal framework to explore the origin and consequences oftransition to asexuality. Our results demonstrate that speciation occurs in thepseudogamous state. Whereas genomic conflicts are responsible for hybridincompatibility in sexual species, we here reveal that centrosomes constitute keyorganelles in the establishment of species barrier.

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.

Author(s) : Hennion M, Arbona J, Lacroix L, Cruaud C, Theulot B, Tallec B, Proux F, Wu X, Novikova E, Engelen S, Lemainque A, Audit B, Hyrien O,
Journal : Genome Biol
2020
Genome replication mapping methods profile cell populations, masking cell-to-cellheterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to mapreplication of single DNA molecules at 200-nucleotide resolution. By quantifyingBrdU incorporation along pulse-chased replication intermediates from Saccharomycescerevisiae, we orient 58,651 replication tracks reproducing population-basedreplication directionality profiles and map 4964 and 4485 individual initiation andtermination events, respectively. Although most events cluster at known origins andfork merging zones, 9% and 18% of initiation and termination events, respectively,occur at many locations previously missed. Thus, FORK-seq reveals the full extent ofcell-to-cell heterogeneity in DNA replication.

Genome organization via loop extrusion, insights from polymer physics models.

Author(s) : Ghosh S, Jost D,
Journal : Brief Funct Genomics
2020
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination withcutting-edge polymer physics models, have provided access to precise informationon 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteinsplay an important role in the local structuration of chromatin, putatively via aloop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.

Gradient in cytoplasmic pressure in germline cells controls overlying epithelial cell morphogenesis

Author(s) : Lamiré L, Milani P, Runel G, Kiss A, Arias L, Vergier B, de Bossoreille S, Das P, Cluet D, Boudaoud A, Grammont M,
Journal : PLoS Biol
2020

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software.

Author(s) : Decamps C, Prive F, Bacher R, Jost D, Waguet A, Houseman E, Lurie E, Lutsik P, Milosavljevic A, Scherer M, Blum M, Richard M,
Journal : BMC Bioinformatics
2020
BACKGROUND: Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, definedas the proportion of the various cell-types in a tumor, can be inferred from DNAmethylation of surgical specimens. However, confounding factors known to associate with methylation values, such as age and sex, complicate accurate inference of cell-type proportions. While reference-free algorithms have been developed to infer cell-type proportions from DNA methylation, a comparative evaluation of the performance of these methods is still lacking. RESULTS: Here we use simulations to evaluate several computational pipelines based on the software packages MeDeCom, EDec, and RefFreeEWAS. We identify that accounting for confounders, feature selection, and the choice of the number of estimated cell types are critical steps for inferring cell-type proportions. We find that removal of methylation probes which are correlated with confounder variables reduces the error of inference by 30-35%, and that selection of cell-type informative probes has similar effect. We show that Cattell's rule based on the scree plot is a powerful tool to determine the number of cell-types. Once the pre-processing steps are achieved, the three deconvolution methods provide comparable results. We observe that all the algorithms' performance improves when inter-sample variation of cell-type proportions is large or when the number of available samples is large. We find that under specific circumstances the methods are sensitive to the initialization method, suggesting that averaging different solutions or optimizing initialization is an avenue for future research. CONCLUSION: Based on the lessons learned, to facilitate pipeline validation and catalyze further pipeline improvement by the community, we develop a benchmark pipeline for inference of cell-type proportions and implement it in the R package medepir.

Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory.

Author(s) : Loppin B, Berger F,
Journal : Annual Review of Genetics
2020
Nucleosome dynamics and properties are central to all forms of genomic activities.Among the core histones, H3 variants play a pivotal role in modulating nucleosomestructure and function. Here, we focus on the impact of H3 variants on variousfacets of development. The deposition of the replicative H3 variant following DNAreplication is essential for the transmission of the epigenomic information encodedin posttranscriptional modifications. Through this process, replicative H3 maintainscell fate while, in contrast, the replacement H3.3 variant opposes celldifferentiation during early embryogenesis. In later steps of development, H3.3 andspecialized H3 variants are emerging as new, important regulators of terminal celldifferentiation, including neurons and gametes. The specific pathways that regulatethe dynamics of the deposition of H3.3 are paramount during reprogramming eventsthat drive zygotic activation and the initiation of a new cycle of development.

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

Author(s) : Ameur L, Marie P, Thenoz M, Giraud G, Combe E, Claude J, Lemaire S, Fontrodona N, Polveche H, Bastien M, Gessain A, Wattel E, Bourgeois C, Auboeuf D, Mortreux F,
Journal : Nat Commun
2020

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer.

Author(s) : Richard M, Decamps C, Chuffart F, Brambilla E, Rousseaux S, Khochbin S, Jost D,
Journal : PLoS Comput Biol
2020
The hopes of precision medicine rely on our capacity to measure various high-throughput genomic information of a patient and to integrate them for personalized diagnosis and adapted treatment. Reaching these ambitious objectives will require the development of efficient tools for the detection of molecular defects at the individual level. Here, we propose a novel method, PenDA, to perform Personalized Differential Analysis at the scale of a single sample. PenDA is based on the local ordering of gene expressions within individual cases and infers the deregulation status of genes in a sample of interest compared to a reference dataset. Based on realistic simulations of RNA-seq data of tumors, we showed that PenDA outcompetes existing approaches with very high specificity andsensitivity and is robust to normalization effects. Applying the method to lung cancer cohorts, we observed that deregulated genes in tumors exhibit a cancer-type-specific commitment towards up- or down-regulation. Based on the individual information of deregulation given by PenDA, we were able to define two new molecular histologies for lung adenocarcinoma cancers strongly correlated tosurvival. In particular, we identified 37 biomarkers whose up-regulation lead tobad prognosis and that we validated on two independent cohorts. PenDA provides arobust, generic tool to extract personalized deregulation patterns that can thenbe used for the discovery of therapeutic targets and for personalized diagnosis.An open-access, user-friendly R package is available at https://github.com/bcm-uga/penda.

Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces

Author(s) : Auboeuf D,
Journal : Life (Basel)
2020

Rdh54/Tid1 Inhibits Rad51-Rad54-Mediated D-loop Formation and Limits D-loop Length

Author(s) : Shah S, Hartono S, Piazza A, Som V, Wright W, Chedin F, Heyer W,
Journal : Elife
2020
Displacement loops (D-loops) are critical intermediates formed during homologous recombination. Rdh54 (a.k.a. Tid1), a Rad54 paralog in Saccharomyces cerevisiae, is well-known for its role with Dmc1 recombinase during meiotic recombination. Yet contrary to Dmc1, Rdh54/Tid1 is also present in somatic cells where its function is less understood. While Rdh54/Tid1 enhances the Rad51 DNA strand invasion activity in vitro, it is unclear how it interplays with Rad54. Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner. Using a novel D-loop Mapping Assay, we further demonstrate that Rdh54/Tid1 uniquely restricts the length of Rad51-Rad54-mediated D-loops. The alterations in D-loop properties appear to be important for cell survival and mating-type switch in haploid yeast. We propose that Rdh54/Tid1 and Rad54 compete for potential binding sites within the Rad51 filament, where Rdh54/Tid1 acts as a physical roadblock to Rad54 translocation, limiting D-loop formation and D-loop length.

Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors.

Author(s) : Sun Y, Zhu J, Xie L, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci E, Weng Z, Li X,
Journal : Nat Cell Biol
2020
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5'-proximal short ORFs (uORFs) of piRNA precursors. The MOV10L1/Armitage RNA helicase then facilitates the translocation of ribosomes into the uORF downstream regions (UDRs). The ribosome-bound UDRs are targeted by piRNA processing machinery, with the processed ribosome-protected regions becoming piRNAs. The dual modes of interaction between ribosomes and piRNA precursors underlie the distinct piRNA biogenesis requirements at uORFs and UDRs. Ribosomes also mediatepiRNA processing in roosters and green lizards, implying that this mechanism is evolutionarily conserved in amniotes. Our results uncover a function for ribosomes on non-coding regions of RNAs and reveal the mechanisms underlying howpiRNAs are defined.

RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans.

Author(s) : Cassart C, Yague-Sanz C, Bauer F, Ponsard P, Stubbe F, Migeot V, Wery M, Morillon A, Palladino F, Robert V, Hermand D,
Journal : Sci Adv
2020
Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered aCdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance ofCTD S2P in metazoan development is unknown. We show that cdk-12 lesions or afull-length CTD S2A substitution results in an identical phenotype in Caenorhabditiselegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvaearrest development, mimicking the diapause induced when hatching occurs in theabsence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, onlya subset of growth-related genes is not properly expressed. These genes correspondto SL2 trans-spliced mRNAs located in position 2 and over within operons. We showthat CDK-12 is required for maximal occupancy of cleavage stimulatory factornecessary for SL2 trans-splicing. We propose that CTD S2P functions as agene-specific signaling mark ensuring the nutritional control of the C. elegansdevelopmental program.

Saccharomyces Cerevisiae Mus81-Mms4 Prevents Accelerated Senescence in Telomerase-Deficient Cells

Author(s) : Scwartz E, Hung S, Meyer D, Piazza A, Yan K, Fu B, Heyer W,
Journal : PLoS Genetics
2020
Alternative lengthening of telomeres (ALT) in human cells is a conserved process that is often activated in telomerase-deficient human cancers. This process exploits components of the recombination machinery to extend telomere ends, thus allowing for increased proliferative potential. Human MUS81 (Mus81 in Saccharomyces cerevisiae) is the catalytic subunit of structure-selective endonucleases involved in recombination and has been implicated in the ALT mechanism. However, it is unclear whether MUS81 activity at the telomere is specific to ALT cells or if it is required for more general aspects of telomere stability. In this study, we use S. cerevisiae to evaluate the contribution of the conserved Mus81-Mms4 endonuclease in telomerase-deficient yeast cells that maintain their telomeres by mechanisms akin to human ALT. Similar to human cells, we find that yeast Mus81 readily localizes to telomeres and its activity is important for viability after initial loss of telomerase. Interestingly, our analysis reveals that yeast Mus81 is not required for the survival of cells undergoing recombination-mediated telomere lengthening, i.e. for ALT itself. Rather we infer from genetic analysis that Mus81-Mms4 facilitates telomere replication during times of telomere instability. Furthermore, combining mus81 mutants with mutants of a yeast telomere replication factor, Rrm3, reveals that the two proteins function in parallel to promote normal growth during times of telomere stress. Combined with previous reports, our data can be interpreted in a consistent model in which both yeast and human MUS81-dependent nucleases participate in the recovery of stalled replication forks within telomeric DNA. Furthermore, this process becomes crucial under conditions of additional replication stress, such as telomere replication in telomerase-deficient cells.

The Enigma of Centriole Loss in the 1182-4 Cell Line.

Author(s) : Debec A, Loppin B, Zheng C, Liu X, Megraw T,
Journal : Cells
2020
The Drosophila melanogaster cell line 1182-4, which constitutively lacks centrioles,was established many years ago from haploid embryos laid by females homozygous forthe maternal haploid (mh) mutation. This was the first clear example of animal cellsregularly dividing in the absence of this organelle. However, the cause of theacentriolar nature of the 1182-4 cell line remained unclear and could not be clearlyassigned to a particular genetic event. Here, we detail historically thelongstanding mystery of the lack of centrioles in this Drosophila cell line. Recentadvances, such as the characterization of the mh gene and the genomic analysis of1182-4 cells, allow now a better understanding of the physiology of these cells. Bycombining these new data, we propose three reasonable hypotheses of the genesis ofthis remarkable phenotype.

The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition.

Author(s) : Torres-Campana D, Kimura S, Orsi G, Horard B, Benoit G, Loppin B,
Journal : PLoS Genet
2020
Following fertilization of a mature oocyte, the formation of a diploid zygote involves a series of coordinated cellular events that ends with the first embryonic mitosis. In animals, this complex developmental transition is almost entirely controlled by maternal gene products. How such a crucial transcriptional program is established during oogenesis remains poorly understood. Here, we haveperformed an shRNA-based genetic screen in Drosophila to identify genes requiredto form a diploid zygote. We found that the Lid/KDM5 histone demethylase and itspartner, the Sin3A-HDAC1 deacetylase complex, are necessary for sperm nuclear decompaction and karyogamy. Surprisingly, transcriptomic analyses revealed that these histone modifiers are required for the massive transcriptional activation of deadhead (dhd), which encodes a maternal thioredoxin involved in sperm chromatin remodeling. Unexpectedly, while lid knock-down tends to slightly favorthe accumulation of its target, H3K4me3, on the genome, this mark was lost at the dhd locus. We propose that Lid/KDM5 and Sin3A cooperate to establish a local chromatin environment facilitating the unusually high expression of dhd, a key effector of the oocyte-to-zygote transition.

ZRANB2 and SYF2-mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin

Author(s) : Tanaka I, Chakraborty A, Saulnier O, Benoit-Pilven C, Vacher S, Labiod D, Lam E, Bi?che I, Delattre O, Pouzoulet F, Auboeuf D, Vagner S, Dutertre M,
Journal : Nucleic Acids Res
2020