Comparison between a complete preconditioning programme and conventional conduct on behaviour, health and performance of young bulls from small cow-calf herds

Bovine respiratory diseases (BRDs) have major socioeconomic impacts in the beef sector. Antimicrobials have been traditionally used to prevent the development of BRDs upon arrival in fattening units. Currently, from a "One Health and One Welfare" perspective, alternative solutions are being investigated. Preconditioning programmes that aim at reducing stress and reinforcing immune functions have been proposed to decrease BRDs incidence. In this study, we assessed the effect of a preconditioning protocol set up in nine commercial beef herds on young bulls' behaviour, health, and performance. Preconditioned bulls (PREC) were weaned indoors 50 days before departure, and progressively fed a concentrate diet supplemented with vitamins and trace elements. They also received an anthelmintic treatment, and two doses of a trivalent vaccine against respiratory pathogens at 4-week intervals. In contrast, controls (CTRL) were kept on pasture with their dams with no vaccination or particular diets. All calves were transported together to a single sorting facility to be sorted by experimental groups, origins, and BW, forming new groups before dispatch to four fattening units. At arrival, CTRL were treated with anthelmintic drugs and received one injection of the same BRDs vaccine. No intervention was performed on PREC bulls. BRD-scores were 0.73 in PREC versus 0.07 in CTRL (P = 0.01) during the preconditioning period and 0.96 in PREC versus 0.54 in CTRL (P = 0.41) after 15 days in the fattening units. Morbidity estimates were 18% in PREC versus 1% in CTRL (P < 0.001) during the preconditioning period and 32% in PREC versus 19% (P = 0.07) in CTRL after 15 days in the fattening units. Poor housing conditions during preconditioning and a different aetiology could partly explain these results. At arrival to fattening, the average daily gain (ADG) was 1 605 g for PREC versus 1 140 g (P = 0.012) for CTRL. After fattening for 180 days, differences in BW, ADG, carcass weight and conformation were inconclusive. In Europe, preconditioning programmes including vaccination must be set up coherently with good husbandry practices and with a global adaptation of batch management of the beef sector otherwise, they may be less effective than expected.

Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition

In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.

[Hepatopulmonary syndrome]

The hepatopulmonary syndrome (HPS) is one of the lung diseases associated with cirrhosis and portal hypertension. It should be discussed for any dyspnea in cirrhotic patients. HPS is a pulmonary vascular disease characterized by intrapulmonary vascular dilatations (IPVD). The pathogenesis is complex and seems to rely on communications between the portal and pulmonary circulations. The diagnosis is based on a triad of liver disease and portal hypertension, evidence of IPVDs, and impaired gas exchange (alveolar-arterial oxygen difference [A-aO2]≥15mmHg). HPS impairs prognosis (23% survival at 5years) and patients' quality of life. Liver transplantation (LT) allows regression of IPDVD in almost 100% of cases, normalization of gas exchange and improves survival with a 5-year post-LT survival between 76 and 87%. It is the only curative treatment, indicated in patients with severe HPS, defined by an arterial partial pressure of oxygen (PaO2) below 60mmHg. When LT is not indicated or feasible, long-term oxygen therapy may be proposed as a palliative treatment. A better understanding of the pathophysiological mechanisms is needed to improve the therapeutic possibilities in a near future.

Transcription-coupled nucleosome assembly

Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.

Uncoupling the TFIIH Core and Kinase Modules Leads To Unregulated RNA Polymerase II CTD Serine 5 Phosphorylation

TFIIH is an essential transcription initiation factor for RNA polymerase II (RNApII). This multi-subunit complex comprises two modules that are physically linked by the subunit Tfb3 (MAT1 in metazoans). The TFIIH Core Module, with two DNA-dependent ATPases and several additional subunits, promotes DNA unwinding. The TFIIH Kinase Module phosphorylates Serine 5 of the C-terminal domain (CTD) of RNApII subunit Rpb1, a modification that coordinates exchange of initiation and early elongation factors. While it is not obvious why these two disparate activities are bundled into one factor, the connection may provide temporal coordination during early initiation. Here we show that Tfb3 can be split into two parts to uncouple the TFIIH modules. The resulting cells grow slower than normal, but are viable. Chromatin immunoprecipitation of the split TFIIH shows that the Core Module, but not the Kinase, is properly recruited to promoters. Instead of the normal promoter-proximal peak, high CTD Serine 5 phosphorylation is seen throughout transcribed regions. Therefore, coupling the TFIIH modules is necessary to localize and limit CTD kinase activity to early stages of transcription. These results are consistent with the idea that the two TFIIH modules began as independent functional entities that became connected by Tfb3 during early eukaryotic evolution.

When the +1 nucleosome gets in the way, TFIIH fails but does not fall

In this issue of Molecular Cell, Abril-Garrido et al.¹ used cryo-EM to uncover that the +1 nucleosome inhibits transcription by interfering with the function of the TFIIH translocase via mechanisms that depend on its position relative to the transcription start site.

[Dysfunction of endothelial BMP-9 signaling in pulmonary vascular disease]

The signaling pathway of the bone morphogenetic protein (BMP)-9 binding to the endothelial receptor BMP receptor type II (BMPR-II), activin receptor-like kinase-1 (ALK1) and the coreceptor endoglin is essential to maintain the pulmonary vascular integrity. Dysregulation of this pathway is implicated in numerous vascular diseases, such as pulmonary arterial hypertension (PAH), hereditary hemorrhagic telangiectasia (HHT) and hepatopulmonary syndrome (HPS). This article aims to provide a comprehensive review of the implication of the BMP-9/BMPR-II/ALK1/endoglin pathway in the pathophysiology of these diseases.

Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation

Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.

The Histone Variant H2A.Z C-Terminal Domain Has Locus-Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

The incorporation of histone variant H2A.Z into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, such as gene transcription. In Saccharomyces cerevisiae, the diverging H2A.Z C terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C terminus genome-wide, we used derivatives in which the C terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide (ZA-rII'), with the intent of regenerating the H2A.Z-dependent regulation globally. The distribution of these H2A.Z derivatives indicates that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency versus nucleosome positioning varies enormously depending on the locus analyzed. Specifically, the role of H2A.Z in global transcription regulation relies on its C-terminal region. Remarkably, however, this mostly involves genes without a H2A.Z nucleosome in the promoter. Lastly, we demonstrate that the main chaperone complex which deposits H2A.Z to gene regulatory region (SWR1-C) is necessary to localize all H2A.Z derivatives at their specific loci, indicating that the differential association of these derivatives is not due to impaired interaction with SWR1-C. IMPORTANCE We provide evidence that the Saccharomyces cerevisiae C-terminal region of histone variant H2A.Z can mediate its special function in performing gene regulation by interacting with effector proteins and chaperones. These functional interactions allow H2A.Z not only to incorporate to very specific gene regulatory regions, but also to facilitate the gene expression process. To achieve this, we used a chimeric protein which lacks the native H2A.Z C-terminal region but contains an acidic activating region, a module that is known to interact with components of chromatin-remodeling entities and/or transcription modulators. We reasoned that because this activating region can fulfill the role of the H2A.Z C-terminal region, at least in part, the role of the latter would be to interact with these activating region targets.

In situ study of the evolution of NiFe nanocatalysts in reductive and oxidative environments upon thermal treatments

The conversion of biomass as a sustainable path to access valuable chemicals and fuels is very attractive for the chemical industry, but catalytic conversions still often rely on the use of noble metals. Sustainability constraints require developing alternative catalysts from abundant and low-cost metals. In this context, NiFe nanoparticles are interesting candidates. In their reduced and supported form, they have been reported to be more active and selective than monometallic Ni in the hydrogenation of the polar functions of organic molecules, and the two metals are very abundant. However, unlike noble metals, Ni and Fe are easily oxidized in ambient conditions, and understanding their transformation in both oxidative and reductive atmospheres is an important though seldom investigated issue to be addressed before their application in catalysis. Three types of NiFe nanoparticles were prepared by an organometallic approach to ensure the formation of ultrasmall nanoparticles (<3.5 nm) with a narrow size distribution, controlled composition and chemical order, while working in mild conditions: Ni2Fe1 and Ni1Fe1, both with a Ni rich core and Fe rich surface, and an alloy with a Ni1Fe9 composition. Supported systems were obtained by the impregnation of silica with a colloidal solution of the preformed nanoparticles. Using advanced characterization techniques, such as wide-angle X-ray scattering (WAXS) and X-ray absorption spectroscopy (XAS) in in situ conditions, this study reports on the evolution of the chemical order and of the oxidation state of the metals upon exposure to air, hydrogen, and/or increasing temperature, all factors that may affect their degree of reduction and subsequent performance in catalysis. We show that if oxidation readily occurs upon exposure to air, the metals can revert to their initial state upon heating in the presence of H₂ but with a change in structure and chemical ordering.

From structure to molecular condensates: emerging mechanisms for Mediator function

Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.

The histone chaperone FACT: a guardian of chromatin structure integrity

The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.

Hexaphyrin-cyclodextrin hybrids: Getting larger, getting confused

The diversity of hexaphyrin-cyclodextrin hybrids (HCD), previously formed from the covalent assembly of regular hexaphyrin and [Formula: see text]-cyclodextrin subunits, has been increased following two main directions: enlarging the confined space provided by the cyclodextrin and tuning the N-core of the hexaphyrin aiming at bimetallic complexes. The larger [Formula: see text]-cyclodextrin unit was selectively functionalized with aldehyde linkers on its primary rim which were further reacted with 2 eq. of pentafluorophenyl tripyrrane in acidic conditions, followed by DDQ oxidation. Doubly-linked HCD hybrids were obtained with structural variations in the hexaphyrin macrocycles depending on the MSA concentration (2 vs. 200 mM) producing either regular ([26] rectangular/[28] Möbius) or doubly N-confused dioxo ([26] rectangular) scaffolds. For the latter, two isomers were isolated featuring mirror transoid skeletons and long-side meso-linking patterns, giving rise to planar chirality at the origin of intense and opposite electronic circular dichroism (ECD) spectra. Zn(II) complexation was then investigated leading to two main findings. (i) The regular [28] Möbius HCD afforded a mixture of monometallic Möbius Zn(II) complexes in the presence of acac ligand. ECD spectroscopy indicated a chirality transfer from the [Formula: see text]-cyclodextrin favoring a [Formula: see text] Möbius twist, but opposite to that arising from the narrower [Formula: see text]-cyclodextrin congener ([Formula: see text] twist favored). (ii) Owing to N3O coordination boxes, dissymmetric bimetallic Zn(II) complexes were readily formed with the doubly N-confused dioxo HCDs through a positive cooperative process. Both metal centers bind a DMAP ligand in axial positions, which is of interest for the

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

Correlation between surface chemistry and magnetism in iron nanoparticles

To shed light on the factors governing the stability and surface properties of iron nanoparticles, a series of iron nanoparticles has been produced by hydrogenation of two different iron amido complexes: the bis[bis(trimethylsilyl)amido] Fe(ii), [Fe(N(SiMe₃)₂)₂]₂, and the bis(diphenylamido) Fe(ii), [Fe(NPh₂)₂]. Nanostructured materials of bcc structure, or nanoparticles displaying average sizes below 3 nm and a polytetrahedral structure, have been obtained. Depending on the synthesis conditions, the magnetization of the nanoparticles was either significantly lower than that of bulk iron, or much higher as for clusters elaborated under high vacuum conditions. Unexpectedly, hydrogenation of aromatic groups of the ligands of the [Fe(NPh₂)₂] precursor has been observed in some cases. Confrontation of the experimental results with DFT calculations made on polytetrahedral Fe₉₁ model clusters bearing hydrides, amido and/or amine ligands at their surface, has shown that amido ligands can play a key role in the stabilisation of the nanoparticles in solution while the hydride surface coverage governs their surface magnetic properties. This study indicates that magnetic measurements give valuable indicators of the surface properties of iron nanoparticles in this size range, and beyond, of their potential reactivity.

The deubiquitylase Ubp15 couples transcription to mRNA export

Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

Genomic DNA is framed by additional layers of information, referred to as the epigenome. Epigenomic marks such as DNA methylation, histone modifications, and histone variants are concentrated on specific genomic sites, where they can both instruct and reflect gene expression. How this information is maintained, notably in the face of transcription, is not completely understood. Specifically, the extent to which modified histones themselves are retained through RNA polymerase II passage is unclear. Here, we show that several histone modifications are mislocalized when the transcription-coupled histone chaperones FACT or Spt6 are disrupted in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates nucleosome loss, which is partially compensated for by the increased activity of non-transcription-coupled histone chaperones. The random incorporation of transcription-evicted modified histones scrambles epigenomic information. Our work highlights the importance of local recycling of modified histones by FACT and Spt6 during transcription in the maintenance of the epigenomic landscape.

Dietary supplementation of Scutellaria baicalensis extract during early lactation decreases milk somatic cells and increases whole lactation milk yield in dairy cattle

Systemic inflammation is common in early lactation dairy cows and is associated with decreased milk production. The Scutellaria baicalensis plant contains flavonoids with anti-inflammatory and anti-oxidative properties, which may counteract the inflammatory state in early lactation dairy cows. The objective of this experiment was to determine whether Scutellaria baicalensis extract (SBE), a source of bioactive flavonoids, would alter the adaptation to lactation. Multiparous Holstein cows (n = 122) were used in a randomized block design to determine the effect of short-term and long-term postpartum administration of SBE on 305-d milk yield, 120-d milk component yield, and early lactation milk markers of inflammation and metabolic function. Treatments were 1) control, 2) short term (5-d) administration of the SBE (SBE5), and 3) long term (60-d) administration of the SBE (SBE60). Treatments were included in a treatment pellet that was identical to a control pellet in ingredient source and composition except for the extract (10 g/d SBE providing 3.3 g/d of the flavonoid baicalin), both provided via an automated milking system beginning on d 1 of lactation. Milk samples were collected on d 1, 3, and once during d 5–12 of lactation, followed by weekly sampling until 120 days in milk (DIM). Milk samples collected in the first 2 wk were used for biomarker analysis (haptoglobin, β-hydroxybutyrate [BHB], and glucose-6-phosphate [G6P]), and all samples were used for composition analysis. Cows were body condition scored every 2 wk prepartum and postpartum. Milk production, programmed pellet allocation, and actual provision of both pelleted feeds were recorded daily. Treatment effects were evaluated by contrasts between control and SBE5 and control and SBE60 for both the treatment (TP; wk 1–9) and carryover periods (CP; wk 10–37). Total pellet offered was greater for SBE60 in both the TP (P < 0.01) and CP (P = 0.02) but was not different for SBE5 during either period (P ≥ 0.13). No treatment effects were observed for body condition score (BCS), milk haptoglobin, BHB, or G6P. SBE5 did not alter milk yield or milk components. SBE60 increased whole-lactation milk yield by 1,419 kg (13%; P = 0.03). SBE60 increased milk lactose and fat yields (P ≤ 0.04) and tended to increase milk protein yield (P = 0.09) during TP, and each increased during CP (P ≤ 0.04). Somatic cell count decreased by 10% in SBE60 during TP (P = 0.02) but not CP (P = 0.13). Mastitis incidence tended to differ by treatment, being lesser for both SBE5 and SBE60 vs. control (14 and 15% vs. 33%). SBE supplementation did not impact time to pregnancy or hazard of leaving the herd. In conclusion, despite no detected treatment effects on BCS or milk biomarkers of inflammation and metabolic status, supplementation of postpartum dairy cows with Scutellaria baicalensis extract for 60 d was effective at increasing whole lactation milk yield.

RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

In Saccharomyces cerevisiae, transcription termination at protein-coding genes is coupled to the cleavage of the nascent transcript, whereas most non-coding RNA transcription relies on a cleavage-independent termination pathway involving Nrd1, Nab3, and Sen1 (NNS). Termination involves RNA polymerase II CTD phosphorylation, but a systematic analysis of the contribution of individual residues would improve our understanding of the role of the CTD in this process. Here we investigated the effect of mutating phosphorylation sites in the CTD on termination. We observed widespread termination defects at protein-coding genes in mutants for Ser2 or Thr4 but rare defects in Tyr1 mutants for this genes class. Instead, mutating Tyr1 led to widespread termination defects at non-coding genes terminating via NNS. Finally, we showed that Tyr1 is important for pausing in the 5' end of genes and that slowing down transcription suppresses termination defects. Our work highlights the importance of Tyr1-mediated pausing in NNS-dependent termination.

Insights into the origin of carbonaceous chondrite organics from their triple oxygen isotope composition

Dust grains of organic matter were the main reservoir of C and N in the forming Solar System and are thus considered to be an essential ingredient for the emergence of life. However, the physical environment and the chemical mechanisms at the origin of these organic grains are still highly debated. In this study, we report high-precision triple oxygen isotope composition for insoluble organic matter isolated from three emblematic carbonaceous chondrites, Orgueil, Murchison, and Cold Bokkeveld. These results suggest that the O isotope composition of carbonaceous chondrite insoluble organic matter falls on a slope 1 correlation line in the triple oxygen isotope diagram. The lack of detectable mass-dependent O isotopic fractionation, indicated by the slope 1 line, suggests that the bulk of carbonaceous chondrite organics did not form on asteroidal parent bodies during low-temperature hydrothermal events. On the other hand, these O isotope data, together with the H and N isotope characteristics of insoluble organic matter, may indicate that parent bodies of different carbonaceous chondrite types largely accreted organics formed locally in the protosolar nebula, possibly by photochemical dissociation of C-rich precursors.

Investigation of the Geochemical Preservation of ca. 3.0 Ga Permineralized and Encapsulated Microfossils by Nanoscale Secondary Ion Mass Spectrometry

Observations of Archean organic-walled microfossils suggest that their fossilization took place through both encapsulation and permineralization. In this study, we investigated microfossils from the ca. 3.0 Ga Farrel Quartzite (Pilbara, Western Australia) using transmitted light microscopy, scanning electron microscopy, Raman microspectrometry, and nanoscale secondary ion mass spectrometry (NanoSIMS) ion microprobe analyses. In contrast to previous studies, we demonstrated that permineralized microfossils were not characterized by the micrometric spatial relationships between Si and C-N as observed in thin sections. Permineralized microfossils are composed of carbonaceous globules that did not survive the acid treatment, whereas encapsulated microfossils were characterized due to their resistance to the acid maceration procedure. We also investigated the microscale relationship between the ¹²C¹⁴N^- and ¹²C₂^- ion emission as a proxy of the N/C atomic ratio in both permineralized and encapsulated microfossils. After considering any potential matrix and microtopography effects, we demonstrate that the encapsulated microfossils exhibit the highest level of geochemical preservation. This finding shows that the chemical heterogeneity of the microfossils, observed at a spatial resolution of a few hundreds of micrometers, can be related to fossilization processes. Key Words: Carbonaceous matter-Farrel Quartzite-Fossilization-NanoSIMS-Nitrogen-Permineralization. Astrobiology 17, 1192-1202.

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes

Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, thereby preventing the emergence of cryptic transcripts from spurious promoter sequences. How these transcripts are regulated and processed remains poorly characterized. Notably, very little is known about the termination of cryptic transcripts. Here, we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae. We found polyadenylated cryptic transcripts running both sense and antisense relative to genes in this mutant. Cryptic promoters were enriched for TATA boxes, suggesting that the underlying DNA sequence defines the location of cryptic promoters. While intragenic sense cryptic transcripts terminate at the terminator of the genes that host them, we found that antisense cryptic transcripts preferentially terminate near the 3΄-end of the upstream gene. This finding led us to demonstrate that most terminators in yeast are bidirectional, leading to termination and polyadenylation of transcripts coming from both directions. We propose that S. cerevisiae has evolved this mechanism in order to prevent/attenuate spurious transcription from invading neighbouring genes, a feature that is particularly critical for organisms with small compact genomes.

TC-PTP regulates the IL-7 transcriptional response during murine early T cell development

Cytokines play a critical role in directing the discrete and gradual transcriptional changes that define T cell development. The interleukin-7 receptor (IL-7R), via its activation of the JAK-STAT pathway, promotes gene programs that change dynamically as cells progress through T cell differentiation. The molecular mechanism(s) directing differential gene expression downstream of the IL-7R are not fully elucidated. Here, we have identified T cell protein tyrosine phosphatase (TC-PTP), also known as PTPN2, as a negative regulator of IL-7R-STAT signaling in T cell progenitors, contributing to both the quantitative and qualitative nature of STAT-gene targeting. Novel genetic strategies used to modulate TC-PTP expression demonstrate that depletion of TC-PTP expression heightens the phosphorylation of STAT family members, causing aberrant expression of an interferon-response gene profile. Such molecular re-programming results in deregulation of early development checkpoints culminating in inefficient differentiation of CD4⁺CD8⁺ double positive cells. TC-PTP is therefore shown to be required to safeguard the dynamic transcriptome necessary for efficient T cell differentiation.

Bidirectional terminators: an underestimated aspect of gene regulation

Recent experimental and computational work revealed that transcriptional terminators in Saccharomyces cerevisiae can terminate transcription coming from both directions. This mechanism helps budding yeast cope with the pervasive nature of transcription by limiting aberrant transcription from invading neighboring genes.

Erratum: Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy

This corrects the article DOI: 10.1038/ncomms11977.

Organic molecular heterogeneities can withstand diagenesis

Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.

Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo

Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head, and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked, allowing detection of transient Mediator forms. We found that although all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM. Interestingly, our data show that CKM regulates Mediator-UAS interaction rather than Mediator-promoter association. In addition, although Tail is required for Mediator recruitment to UAS, Tailless Mediator nevertheless interacts with core promoters. Collectively, our data suggest that the essential function of Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles.

Threshold Levels of Gfi1 Maintain E2A Activity for B Cell Commitment via Repression of Id1

A regulatory circuit that controls myeloid versus B lymphoid cell fate in hematopoietic progenitors has been proposed, in which a network of the transcription factors Egr1/2, Nab, Gfi1 and PU.1 forms the core element. Here we show that a direct link between Gfi1, the transcription factor E2A and its inhibitor Id1 is a critical element of this regulatory circuit. Our data suggest that a certain threshold of Gfi1 is required to gauge E2A activity by adjusting levels of Id1 in multipotent progenitors, which are the first bipotential myeloid/lymphoid-restricted progeny of hematopoietic stem cells. If Gfi1 levels are high, Id1 is repressed enabling E2A to activate a specific set of B lineage genes by binding to regulatory elements for example the IL7 receptor gene. If Gfi1 levels fall below a threshold, Id1 expression increases and renders E2A unable to function, which prevents hematopoietic progenitors from engaging along the B lymphoid lineage.

Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy

The significant degradation that fossilized biomolecules may experience during burial makes it challenging to assess the biogenicity of organic microstructures in ancient rocks. Here we investigate the molecular signatures of 1.88 Ga Gunflint organic microfossils as a function of their diagenetic history. Synchrotron-based XANES data collected in situ on individual microfossils, at the submicrometre scale, are compared with data collected on modern microorganisms. Despite diagenetic temperatures of ∼150–170 °C deduced from Raman data, the molecular signatures of some Gunflint organic microfossils have been exceptionally well preserved. Remarkably, amide groups derived from protein compounds can still be detected. We also demonstrate that an additional increase of diagenetic temperature of only 50 °C and the nanoscale association with carbonate minerals have significantly altered the molecular signatures of Gunflint organic microfossils from other localities. Altogether, the present study provides key insights for eventually decoding the earliest fossil record.

Thermal diagenesis is generally seen as detrimental to the preservation of organic biosignatures. Using synchrotron-based XANES data, Alleon et al. find preservation of the molecular signatures of organic microfossils from the 1.88 Ga Gunflint cherts.

The Raman-Derived Carbonization Continuum: A Tool to Select the Best Preserved Molecular Structures in Archean Kerogens

The search for indisputable traces of life in Archean cherts is of prime importance. However, their great age and metamorphic history pose constraints on the study of molecular biomarkers. We propose a quantitative criterion to document the thermal maturity of organic matter in rocks in general, and Archean rocks in particular. This is definitively required to select the best candidates for seeking non-altered sample remnants of life. Analysis of chemical (Raman spectroscopy, (13)C NMR, elemental analysis) and structural (HRTEM) features of Archean and non-Archean carbonaceous matter (CM) that was submitted to metamorphic grades lower than, or equal to, that of greenschist facies showed that these features had all undergone carbonization but not graphitization. Raman-derived quantitative parameters from the present study and from literature spectra, namely, R1 ratio and FWHM-D1, were used to draw a carbonization continuum diagram showing two carbonization stages. While non-Archean samples can be seen to dominate the first stage, the second stage mostly consists of the Archean samples. In this diagram, some Archean samples fall at the boundary with non-Archean samples, which thus demonstrates a low degree of carbonization when compared to most Archean CM. As a result, these samples constitute candidates that may contain preserved molecular signatures of Archean CM. Therefore, with regard to the search for the oldest molecular traces of life on Earth, we propose the use of this carbonization continuum diagram to select the Archean CM samples.

KEY WORDS

Archean-Early life-Kerogen-Raman spectroscopy-Carbonization. Astrobiology 16, 407-417.

Epigenetic therapy as a novel approach for GFI136N-associated murine/human AML

Epigenetic changes can contribute to development of acute myeloid leukemia (AML), a malignant disease of the bone marrow. A single-nucleotide polymorphism of transcription factor growth factor independence 1 (GFI1) generates a protein with an asparagine at position 36 (GFI1(36N)) instead of a serine at position 36 (GFI1(36S)), which is associated with de novo AML in humans. However, how GFI1(36N) predisposes to AML is poorly understood. To explore the mechanism, we used knock-in mouse strains expressing GFI1(36N) or GFI1(36S). Presence of GFI1(36N) shortened the latency and increased the incidence of AML in different murine models of myelodysplastic syndrome/AML. On a molecular level, GFI1(36N) induced genomewide epigenetic changes, leading to expression of AML-associated genes. On a therapeutic level, use of histone acetyltransferase inhibitors specifically impeded growth of GFI1(36N)-expressing human and murine AML cells in vitro and in vivo. These results establish, as a proof of principle, how epigenetic changes in GFI1(36N)-induced AML can be targeted.

Histone chaperones FACT and Spt6 prevent histone variants from turning into histone deviants

Histone variants are specialized histones which replace their canonical counterparts in specific nucleosomes. Together with histone post-translational modifications and DNA methylation, they contribute to the epigenome. Histone variants are incorporated at specific locations by the concerted action of histone chaperones and ATP-dependent chromatin remodelers. Recent studies have shown that the histone chaperone FACT plays key roles in preventing pervasive incorporation of two histone variants: H2A.Z and CenH3/CENP-A. In addition, Spt6, another histone chaperone, was also shown to be important for appropriate H2A.Z localization. FACT and Spt6 are both associated with elongating RNA polymerase II. Based on these two examples, we propose that the establishment and maintenance of histone variant genomic distributions depend on a transcription-coupled epigenome editing (or surveillance) function of histone chaperones.

Repression of p53-target gene Bbc3/PUMA by MYSM1 is essential for the survival of hematopoietic multipotent progenitors and contributes to stem cell maintenance

p53 is a central mediator of cellular stress responses, and its precise regulation is essential for the normal progression of hematopoiesis. MYSM1 is an epigenetic regulator essential for the maintenance of hematopoietic stem cell (HSC) function, hematopoietic progenitor survival, and lymphocyte development. We recently demonstrated that all developmental and hematopoietic phenotypes of Mysm1 deficiency are p53-mediated and rescued in the Mysm1(-/-)p53(-/-) mouse model. However, the mechanisms triggering p53 activation in Mysm1(-/-) HSPCs, and the pathways downstream of p53 driving different aspects of the Mysm1(-/-) phenotype remain unknown. Here we show the transcriptional activation of p53 stress responses in Mysm1(-/-) HSPCs. Mechanistically, we find that the MYSM1 protein associates with p53 and colocalizes to promoters of classical p53-target genes Bbc3/PUMA (p53 upregulated modulator of apoptosis) and Cdkn1a/p21. Furthermore, it antagonizes their p53-driven expression by modulating local histone modifications (H3K27ac and H3K4me3) and p53 recruitment. Using double-knockout mouse models, we establish that PUMA, but not p21, is an important mediator of p53-driven Mysm1(-/-) hematopoietic dysfunction. Specifically, Mysm1(-/-)Puma(-/-) mice show full rescue of multipotent progenitor (MPP) viability, partial rescue of HSC quiescence and function, but persistent lymphopenia. Through transcriptome analysis of Mysm1(-/-)Puma(-/-) MPPs, we demonstrate strong upregulation of other p53-induced mediators of apoptosis and cell-cycle arrest. The full viability of Mysm1(-/-)Puma(-/-) MPPs, despite strong upregulation of many other pro-apoptotic mediators, establishes PUMA as the essential non-redundant effector of p53-induced MPP apoptosis. Furthermore, we identify potential mediators of p53-dependent but PUMA-independent Mysm1(-/-)hematopoietic deficiency phenotypes. Overall, our study provides novel insight into the cell-type-specific roles of p53 and its downstream effectors in hematopoiesis using unique models of p53 hyperactivity induced by endogenous stress. We conclude that MYSM1 is a critical negative regulator of p53 transcriptional programs in hematopoiesis, and that its repression of Bbc3/PUMA expression is essential for MPP survival, and partly contributes to maintaining HSC function.