Directory
2024
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Space-Scale Hybrid Continuous-Discrete Sliding Frank-Wolfe Method
- Journal : IEEE Signal Processing Letters
- 2024
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Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.
- Journal : Nat Commun
- 2024
- Although our understanding of the involvement of heterochromatin architecturalfactors in shaping nuclear organization is improving, there is still ongoingdebate regarding the role of active genes in this process. In this study, weutilize publicly-available Micro-C data from mouse embryonic stem cells toinvestigate the relationship between gene transcription and 3D gene folding. Ouranalysis uncovers a nonmonotonic - globally positive - correlation betweenintragenic contact density and Pol II occupancy, independent of cohesin-basedloop extrusion. Through the development of a biophysical model integrating therole of transcription dynamics within a polymer model of chromosome organization,we demonstrate that Pol II-mediated attractive interactions with limited valencybetween transcribed regions yield quantitative predictions consistent withchromosome-conformation-capture and live-imaging experiments. Our work providescompelling evidence that transcriptional activity shapes the 4D genome throughPol II-mediated micro-compartmentalization.
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Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae.
- Journal : Mol Cell
- 2024
- Homology search is a central step of DNA double-strand break (DSB) repair byhomologous recombination (HR). How it operates in cells remains elusive. Wedeveloped a Hi-C-based methodology to map single-stranded DNA (ssDNA) contactsgenome-wide in S. cerevisiae, which revealed two main homology search phases.Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) isconfined in cis by cohesin-mediated chromatin loop folding. Progressive growth ofstiff NPFs enables exploration of distant genomic sites. Long-range resectiondrives this transition from local to genome-wide search by increasing theprobability of assembling extensive NPFs. DSB end-tethering promotes coordinatedsearch by opposite NPFs. Finally, an autonomous genetic element on chromosome IIIengages the NPF, which stimulates homology search in its vicinity. This workreveals the mechanism of the progressive expansion of homology search thatis orchestrated by chromatin organizers, long-range resection,end-tethering, and specialized genetic elements and that exploits the stiff NPFstructure conferred by Rad51 oligomerization.
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A new type of non-Mendelian segregation.
- Journal : Nat Ecol Evol
- 2024
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Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae
- Journal : Molecular Cell
- 2024
- Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembling extensive NPFs. DSB end-tethering promotes coordinated search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search that is orchestrated by chromatin organizers, long-range resection, end-tethering, and specialized genetic elements and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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The C. elegans SET1 histone methyltransferase SET-2 is not required for transgenerational memory of silencing.
- Journal : MicroPubl Biol
- 2024
- The SET-2 /SET1 histone H3K4 methyltransferase and RNAi pathway components arerequired to maintain fertility across generations in C. elegans . SET-2 preservesthe germline transcriptional program transgenerationally, and RNAi pathways relyon small RNAs to establish and maintain transgenerational gene silencing. Weinvestigated whether the functionality of RNAi-induced transgenerationalsilencing and the composition of pools of endogenous small RNA are affected bythe absence of SET-2 . Our results suggest that defects in RNAi pathways are notresponsible for the transcriptional misregulation observed in the absence ofSET-2 .
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AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility
- Journal : Journal of Chemical Information and Modeling
- 2024
- Predicting whether two proteins physically interact is one of the holy grails of computational biology, galvanized by rapid advancements in deep learning. AlphaFold2, although not developed with this goal, is promising in this respect. Here, I test the prediction capability of AlphaFold2 on a very challenging data set, where proteins are structurally compatible, even when they do not interact. AlphaFold2 achieves high discrimination between interacting and non-interacting proteins, and the cases of misclassifications can either be rescued by revisiting the input sequences or can suggest false positives and negatives in the data set. AlphaFold2 is thus not impaired by the compatibility between protein structures and has the potential to be applied on a large scale.
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Dynamics of Protein–RNA Interfaces Using All-Atom Molecular Dynamics Simulations
- Journal : The Journal of Physical Chemistry B
- 2024
- Facing the current challenges posed by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein–RNA interactions. To understand these interactions, many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein–RNA complexes provides structural, mechanical, and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein–RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein–RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and, for the RNA part, the change in the puckering. Second, we extensively analyzed the interfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue–residue contacts with respect to the experimental structure.
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Ultrastructure Expansion Microscopy applied to C. elegans embryos.
- Journal : MicroPubl Biol
- 2024
- Visualization of organelles using expansion microscopy has been previouslyapplied to Caenorhadbitis elegans adult gonads or worms. However, its applicationto embryos has remained a challenge due to the protective eggshell barrier. Here,by combining freeze-cracking and ultrastructure expansion microscopy (U-ExM), wedemonstrate a four-time isotropic expansion of C. elegans embryos. As an examplestructure, we chose the nuclear pore and demonstrate that we achieve sufficientresolution to distinguish them individually. Our work provides proof of principlefor U-ExM in C. elegans embryos, which will be applicable for imaging a widerange of cellular structures in this model system.
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Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation.
- Journal : Genome Res
- 2024
- mRNA translation and decay are tightly interconnected processes both in thecontext of mRNA quality-control pathways and for the degradation of functionalmRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions,and the recruitment of specific proteins to ribosomes is an important determinantof mRNA turnover. However, the extent to which translation-dependent mRNA decay(TDD) and translation-independent mRNA decay (TID) pathways participate in thedegradation of mRNAs has not been studied yet. Here we describe a comprehensiveanalysis of basal and signal-induced TDD and TID in mouse primary CD4(+) T cells.Our results indicate that most cellular transcripts are decayed to some extent ina translation-dependent manner. Our analysis further identifies the length ofuntranslated regions, the density of ribosomes, and GC3 content as importantdeterminants of TDD magnitude. Consistently, all transcripts that undergo changesin ribosome density within their coding sequence upon T cell activation display acorresponding change in their TDD level. Moreover, we reveal a dynamic modulationin the relationship between GC3 content and TDD upon T cell activation, with areversal in the impact of GC3- and AU3-rich codons. Altogether, our data show astrong and dynamic interconnection between mRNA translation and decay inmammalian primary cells.
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Stable structures or PABP1 loading protects cellular and viral RNAs against ISG20-mediated decay.
- Journal : Life Sci Alliance
- 2024
- ISG20 is an IFN-induced 3'-5' RNA exonuclease that acts as a broad antiviralfactor. At present, the features that expose RNA to ISG20 remain unclear,although recent studies have pointed to the modulatory role of epitranscriptomicmodifications in the susceptibility of target RNAs to ISG20. These findings raisethe question as to how cellular RNAs, on which these modifications are abundant,cope with ISG20. To obtain an unbiased perspective on this topic, we used RNA-seqand biochemical assays to identify elements that regulate the behavior of RNAsagainst ISG20. RNA-seq analyses not only indicate a general preservation of thecell transcriptome, but they also highlight a small, but detectable, decrease inthe levels of histone mRNAs. Contrarily to all other cellular ones, histone mRNAsare non-polyadenylated and possess a short stem-loop at their 3' end, promptingus to examine the relationship between these features and ISG20 degradation. Theresults we have obtained indicate that poly(A)-binding protein loading on the RNA3' tail provides a primal protection against ISG20, easily explaining the overallprotection of cellular mRNAs observed by RNA-seq. Terminal stem-loop RNAstructures have been associated with ISG20 protection before. Here, were-examined this question and found that the balance between resistance andsusceptibility to ISG20 depends on their thermodynamic stability. These resultsshed new light on the complex interplay that regulates the susceptibility ofdifferent classes of viruses against ISG20.
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Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair.
- Journal : NAR Cancer
- 2024
- Amino acid bioavailability impacts mRNA translation in a codon-dependent manner.Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease theintracellular concentration of aspartate and glutamate in melanoma cells. Thiscoincides with the accumulation of ribosomes on codons corresponding to theseamino acids and triggers the translation-dependent degradation of mRNAs encodingaspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNAreplication and repair. Consequently, cells that survive MAPKi degrade aspartateand glutamate likely to generate energy, which simultaneously decreases theirrequirement for amino acids due to the downregulation of aspartate- andglutamate-rich proteins involved in cell proliferation. Concomitantly, thedownregulation of aspartate- and glutamate-rich proteins involved in DNA repairincreases DNA damage loads. Thus, DNA repair defects, and therefore mutations,are at least in part a secondary effect of the metabolic adaptation of cellsexposed to MAPKi.
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SIN-3 transcriptional coregulator maintains mitochondrial homeostasis and polyamine flux
- Journal : iScience
- 2024
- Summary Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays a role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals revealed a mitochondria stress signature and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.
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Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability
- Journal : Elife
- 2024
- Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
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RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin.
- Journal : Cell Rep
- 2024
- Condensin shapes mitotic chromosomes by folding chromatin into loops, but whetherit does so by DNA-loop extrusion remains speculative. Although loop-extrudingcohesin is stalled by transcription, the impact of transcription on condensin,which is enriched at highly expressed genes in many species, remains unclear.Using degrons of Rpb1 or the torpedo nuclease Dhp1(XRN2) to either deplete ordisplace RNAPII on chromatin in fission yeast metaphase cells, we show thatRNAPII does not load condensin on DNA. Instead, RNAPII retains condensin in cisand hinders its ability to fold mitotic chromatin and to support chromosomesegregation, consistent with the stalling of a loop extruder. Transcriptiontermination by Dhp1 limits such a hindrance. Our results shed light on theintegrated functioning of condensin, and we argue that a tight control oftranscription underlies mitotic chromosome assembly by loop-extruding condensin.
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Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota.
- Journal : Nat Commun
- 2024
- The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitorcells through contact-dependent translocation of toxic effector proteins. InProteobacteria, the T6SS is anchored to the cell envelope through amegadalton-sized membrane complex (MC). However, the genomes of Bacteroidota withT6SSs appear to lack genes encoding homologs of canonical MC components. Here, weidentify five genes in Bacteroides fragilis (tssNQOPR) that are essential forT6SS function and encode a Bacteroidota-specific MC. We purify this complex,reveal its dimensions using electron microscopy, and identify a protein-proteininteraction network underlying the assembly of the MC including the stoichiometryof the five TssNQOPR components. Protein TssN mediates the connection between theBacteroidota MC and the conserved baseplate. Although MC gene content andorganization varies across the phylum Bacteroidota, no MC homologs are detectedoutside of T6SS loci, suggesting ancient co-option and functional convergencewith the non-homologous MC of Pseudomonadota.
Link to PubMed entry