DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis

International audienceProfiling of DNA and histone modifications has recently allowed the establishment of reference epigenomes from several model organisms. This identified a major chromatin state for active genes that contains monoubiquitinated H2B (H2Bub), a mark linked to transcription elongation. However, assessment of dynamic chromatin changes during the reprogramming of gene expression in response to extrinsic or developmental signals has been more difficult. Here we used the major developmental switch that Arabidopsis thaliana plants undergo upon their initial perception of light, known as photomorphogenesis, as a paradigm to assess spatial and temporal dynamics of monoubiquitinated H2B (H2Bub) and its impact on transcriptional responses. The process involves rapid and extensive transcriptional reprogramming and represents a developmental window well suited to studying cell division-independent chromatin changes. Genome-wide H2Bub distribution was determined together with transcriptome profiles at three time points during early photomorphogenesis. This revealed de novo marking of 177 genes upon the first hour of illumination, illustrating the dynamic nature of H2Bub enrichment in a genomic context. Gene upregulation was associated with H2Bub enrichment, while H2Bub levels generally remained stable during gene downregulation. We further report that H2Bub influences the modulation of gene expression, as both gene up-and downregulation were globally weaker in hub1 mutant plants that lack H2Bub. H2Bub-dependent regulation notably impacted genes with fast and transient light induction, and several circadian clock components whose mRNA levels are tightly regulated by sharp oscillations. Based on these findings, we propose that H2B monoubiquitination is part of a transcription-coupled, chromatin-based mechanism to rapidly modulate gene expression

The conserved factor DE-ETIOLATED 1 cooperates with CUL4–DDB1DDB2 to maintain genome integrity upon UV stress

In plants, the conserved ubiquitin ligase component DET1 is implicated in photomorphogenesis. Independent from this, DET1 is also found to directly function in UV protection in Arabidopsis, teaming up with a key nucleotide excision repair ubiquitin ligase

Light signaling controls nuclear architecture reorganization during seedling establishment

The spatial organization of chromatin can be subject to extensive remodeling in plant somatic cells in response to developmental and environmental signals. However, the mechanisms controlling these dynamic changes and their functional impact on nuclear activity are poorly understood. Here, we determined that light perception triggers a switch between two different nuclear architectural schemes during Arabidopsis postembryonic development. Whereas progressive nucleus expansion and heterochromatin rearrangements in cotyledon cells are achieved similarly under light and dark conditions during germination, the later steps that lead to mature nuclear phenotypes are intimately associated with the photomorphogenic transition in an organ-specific manner. The light signaling integrators DE-ETIOLATED 1 and CONSTITUTIVE PHOTOMORPHOGENIC 1 maintain heterochromatin in a decondensed state in etiolated cotyledons. In contrast, under light conditions cryptochrome-mediated photoperception releases nuclear expansion and heterochromatin compaction within conspicuous chromocenters. For all tested loci, chromatin condensation during photomorphogenesis does not detectably rely on DNA methylation-based processes. Notwithstanding, the efficiency of transcriptional gene silencing may be impacted during the transition, as based on the reactivation of transposable element-driven reporter genes. Finally, we report that global engagement of RNA polymerase II in transcription is highly increased under light conditions, suggesting that cotyledon photomorphogenesis involves a transition from globally quiescent to more active transcriptional states. Given these findings, we propose that light-triggered changes in nuclear architecture underlie interplays between heterochromatin reorganization and transcriptional reprogramming associated with the establishment of photosynthesis

Regulated expression of glutamyl-tRNA synthetase is directed by a mobile genetic element in the cyanobacterium Tolypothrix sp. PCC 7601

International audienceThe genome of Tolypothrix sp. PCC 7601 carries two copies of a novel insertion sequence, ISTosp1. One of the two copies is located upstream of the gene encoding glutamyl-tRNA synthetase, an enzyme playing a key role in protein and pigment synthesis. The tnpA gene of the IS element and gltX were co-transcribed and their expression was transiently upregulated upon retrieval of the ammonium source irrespective of whether nitrate or no nitrogen source were available. The second copy is also transcribed and shows a similar regulatory pattern. Structural elements of the promoter (-10 and -35 sequences) directing the expression of the tnpA-gltX operon have been localized within the IS. Regulatory sequences involving the NtcA transcription factor in the control of tnpA-gltX expression were found both within and in sequences upstream of the insertion element. The expression of gltX in a closely related cyanobacterium, Nostoc sp. PCC 7120, which lacks the insertion upstream of gltX, decreased upon ammonium retrieval, a regulatory pattern that markedly differs from that observed in Tolypothrix sp. PCC 7601. ISTosp1 constitutes a good example of how cells can make use of a transposable element to evolve an original regulatory mechanism

Measurements of inclusive J/ψ\psi production at midrapidity and forward rapidity in Pb−-Pb collisions at sNN\sqrt{s_{\mathrm{NN}}} = 5.02 TeV

International audienceThe measurements of the inclusive J/$\psi$ yield at midrapidity ($\left | y \right | < 0.9$) and forward rapidity (2.5 $< y <$ 4) in Pb$-$Pb collisions at $\sqrt{s_{\mathrm{NN}}}=5.02$ TeV with the ALICE detector at the LHC are reported. The inclusive J/$\psi$ production yields and nuclear modification factors, $R_{\rm AA}$, are measured as a function of the collision centrality, J/$\psi$ transverse momentum ($p_{\rm T}$), and rapidity. The J/$\psi$ average transverse momentum and squared transverse momentum ($\langle p_{\mathrm{T}}\rangle$ and $\langle p_{\mathrm{T}}^{\mathrm{2}}\rangle$) are evaluated as a function of the centrality at midrapidity. Compared to the previous ALICE publications, here the entire Pb$-$Pb collisions dataset collected during the LHC Run 2 is used, which improves the precision of the measurements and extends the $p_{\rm T}$ coverage. The $p_{\rm T}$-integrated $R_{\rm AA}$ shows a hint of an increasing trend towards unity from semicentral to central collisions at midrapidity, while it is flat at forward rapidity. The $p_{\rm T}$-differential $R_{\rm AA}$ shows a strong suppression at high $p_{\rm T}$ with less suppression at low $p_{\rm T}$ where it reaches a larger value at midrapidity compared to forward rapidity. The ratio of the $p_{\rm T}$-integrated yields of J/$\psi$ to those of D$^{0}$ mesons is reported for the first time for the central and semicentral event classes at midrapidity. Model calculations implementing charmonium production via the coalescence of charm quarks and antiquarks during the fireball evolution (transport models) or in a statistical approach with thermal weights are in good agreement with the data at low $p_{\rm T}$. At higher $p_{\rm T}$, the data are well described by transport models and a model based on energy loss in the strongly-interacting medium produced in nuclear collisions at the LHC

Search for jet quenching effects in high-multiplicity pp collisions at s\sqrt{s} = 13 TeV via di-jet acoplanarity

International audienceThe ALICE Collaboration reports a search for jet quenching effects in high-multiplicity (HM) proton$-$proton collisions at $\sqrt{s}$ = 13 TeV, using the semi-inclusive azimuthal-difference distribution $\Delta\varphi$ of charged-particle jets recoiling from a high transverse momentum (high-$p_{\mathrm{T,trig}}$) trigger hadron. Jet quenching may broaden the $\Delta\varphi$ distribution measured in HM events compared to that in minimum bias (MB) events. The measurement employs a $p_{\mathrm{T,trig}}$-differential observable for data-driven suppression of the contribution of multiple partonic interactions, which is the dominant background. While azimuthal broadening is indeed observed in HM compared to MB events, similar broadening for HM events is observed for simulations based on the PYTHIA 8 Monte Carlo generator, which does not incorporate jet quenching. We elucidate the origin of the broadening by comparing biases induced by HM selection in the data and simulations, and discuss its implications for the study of jet quenching in small collision systems

System size dependence of hadronic rescattering effect at LHC energies

International audienceThe first measurements of $\mathrm{K^{*}(892)^{0}}$ resonance production as a function of charged-particle multiplicity in Xe$-$Xe collisions at $\sqrt{s_{\mathrm{NN}}}=$ 5.44 TeV and pp collisions at $\sqrt{s}=$ 5.02 TeV using the ALICE detector are presented. The resonance is reconstructed at midrapidity ($|y|< 0.5$) using the hadronic decay channel $\mathrm{K^{*0}} \rightarrow \mathrm{K^{\pm} \pi^{\mp}}$. Measurements of transverse-momentum integrated yield, mean transverse-momentum, nuclear modification factor of $\mathrm{K^{*0}}$, and yield ratios of resonance to stable hadron ($\mathrm{K^{*0}}$/K) are compared across different collision systems (pp, p$-$Pb, Xe$-$Xe, and Pb$-$Pb) at similar collision energies to investigate how the production of $\mathrm{K^{*0}}$ resonances depends on the size of the system formed in these collisions. The hadronic rescattering effect is found to be independent of the size of colliding systems and mainly driven by the produced charged-particle multiplicity, which is a proxy of the volume of produced matter at the chemical freeze-out. In addition, the production yields of $\mathrm{K^{*0}}$ in Xe$-$Xe collisions are utilized to constrain the dependence of the kinetic freeze-out temperature on the system size using HRG-PCE model