Biology subjects

Mann, A.

Publications and source records attributed to Mann, A..

18 recordsLinked to original sources

bioRxiv2026

Loop extrusion dynamics and cooperative activation independently regulate enhancer-driven transcription

How enhancers transmit their activation signals to target promoters is a fundamental unanswered question. Gene activation by distal enhancers is affected by the three-dimensional organisation of chromatin driven by cohesin-mediated loop extrusion, but how the dynamic loop extrusion cycle shapes transcriptional outcomes is not fully understood. In addition, genes are typically regulated by multiple enhancers and cases of cooperativity between enhancers have been observed that depend on the relative position of enhancers and gene. The reason for such context-dependent cooperativity is unknown, and whether it is linked to loop extrusion has not been explored. Here, we use synthetic gene activation to show that NIPBL depletion, which decreases loop extrusion rate, reduces long-range activation in a dose-dependent manner. In contrast, WAPL depletion, which reduces cohesin turnover, can both increase and decrease distal gene activation depending on the presence of adjacent CTCF binding sites. These effects on gene activation correlate with the impact on chromatin contacts. Depletion of the co-activator BRD4 also affects long-range activation, but not by changing chromatin contacts. Synthetic activation from two locations results in super-additive responses, which can be predicted by an independently determined response model. These predictions hold for dual activation from proximal and/or distal sites, and with perturbed NIPBL, WAPL, or BRD4. Distal activation therefore appears to be equivalent in nature to proximal activation, and context-dependent cooperativity can arise simply from different level of activation inputs operating on a non-linear response function.

molecular biology↗

bioRxiv2026

Reduced expression of an essential blood-stage Plasmodium phosphatidylserine synthase does not modulate parasite resistance to PfATP4 inhibitors

Plasmodium falciparum ATP4 mutations A211V and G223R allow parasites to survive the lethal effects of antimalarials PA21A092 (PA92) and cipargamin (CIP), respectively. An A211V mutant line (Dd2A211V) treated with PA92 showed enhanced levels of lipid production, which prompted the idea that components of the phospholipid biosynthesis pathway could be involved in the survival mechanism of PfATP4 mutant parasites. As phosphatidylserine synthase (PfPSS) is the only enzyme that produces phosopholipid phosphatidylserine (PS) in P. falciparum parasites, we hypothesized that PfPSS is both essential for parasite survival and that reduced PfPSS expression would cause resistant PfATP4 mutant parasites to become susceptible to PA92 or CIP. We created a CIP-resistant G223R mutant line (Dd2G223R) via CRISPR-Cas9 and integrated a conditional PfPSS knockdown construct into a Dd2A211V ({downarrow}PSS-Dd2A211V) and our Dd2G223R line ({downarrow}PSS-Dd2G223R). We treated these knockdown lines with PA92 or CIP to determine the half-maximal effective concentration (EC50) of each antimalarial with normal or reduced PfPSS levels. While we found that PfPSS is essential for parasite survival, we did not find any significant alterations to the EC50 values of PA92 or CIP based on the reduced levels of PfPSS in our mutant lines. Although PfPSS does not appear to be involved, other components of the phospholipid production pathway could still affect the resistance mechanism of PfATP4 mutations. Identification of novel targets to counteract the mechanism by which PfATP4 mutant parasites resist lethal drug effects is crucial for the successful application of antimalarials in endemic countries where resistance is on the rise.

microbiology↗

bioRxiv2026

Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice

The genomic locus that encodes the Leucine-rich repeat kinase 2 (LRRK2) gene is highly pleiotropic, being associated with both Parkinsons disease (PD) and Crohns disease (CD). Coding variants associated with risk of PD and CD act as gain of function kinase mutations increasing phosphorylation of RAB substrates, and non-coding variants in the promoter region of LRRK2 increase expression of the gene, notably in immune cells. If regulation of LRRK2 expression is a causal contributor to age-related diseases, it is important to understand the mechanism(s) by which LRRK2 is regulated, particularly in the context of inflammation. Here, we show that interferon-{gamma} exposure induces robust LRRK2 activation in human iPSC-derived microglia through signaling of the Janus-activated Kinase complex to phosphorylate STAT1, which then binds to the LRRK2 promoter and is associated with remodeling of chromatin structure in this genomic locus. Additional regulatory mechanisms include the stress-induced transcription factor and long non-coding RNA encoded at the same locus, resulting in increased LRRK2 mRNA levels. We also show evidence of the same effect in acutely cultured human brain slices. While we were unable to demonstrate any induction of Lrrk2 mRNA in the mouse brain, the introduction of a human bacterial artificial chromosome transgene into the mouse genome recapitulated sensitivity to interferon-{gamma} in microglia. A comparative genomic analysis across mammals suggests that these species differences are driven by regulatory regions upstream of LRRK2 that are specific to anthropoid primates. These results demonstrate that there are differences between species in how genes associated with human diseases are regulated and provide important information that should be incorporated in disease modeling.

neuroscience↗

bioRxiv2026

Within-host adaptive evolution is limited by genetic drift in experimental human influenza A virus infections

Selection of advantageous mutations drives the emergence of dominant variants during seasonal influenza epidemics. However, within-host detection of such variants remains rare, limiting our understanding of how selection operates at the scale of individual hosts. In this study, we used a controlled human infection model to examine the within-host evolutionary dynamics in thirteen participants intranasally infected with a seasonal H3N2 influenza A virus. Although this clinical trial is ongoing, our work represents a pre-planned, interim, exploratory analysis. Results in this system were contrasted with those observed in a ferret model of infection. The inoculum, used in both humans and ferrets, carried standing diversity that enabled evaluation of variant trajectories during infection. Although the dynamics were variable among participants, in humans, the minor variants in the PA and NP gene segments tended to increase in frequency as infection progressed. Variant dynamics were more consistent among ferrets but showed differences from humans in the fate of the minor NP allele. Based on these observations, we fit a population genetic model to longitudinal measurements of variant frequencies. Estimates of variant selection coefficients and effective viral population sizes indicated that in humans the two minor variants had a selective advantage over the major variants, but genetic drift was strong, limiting the efficiency of selection. In ferrets, the PA minor variant also was estimated to have a selective advantage, while the NP minor variant was estimated to have a selective disadvantage. Moreover, effective viral population sizes were estimated to be considerably higher in ferrets than in humans, indicating that genetic drift was weaker in ferrets. Our analyses reveal differing selective environments acting on influenza viruses in human and ferret hosts and indicate that selection at the within-host level is weakened by genetic drift.

microbiology↗

bioRxiv2025

Metagenomic Profiling of Bacterial (16S) and Fungal (ITS) Communities on D'Anjou Pears during Long-Term Controlled Atmosphere Storage

DAnjou pears are routinely stored for up to nine months under controlled atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. Overall, fungal communities exhibited lower estimated Chao1 alpha diversity (mean 18.3) compared to bacterial communities (mean 166.4). No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability or being bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas and Acinetobacter. Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium, Penicillium, Botrytis, and Mucor present at different storage stages. SignificanceThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and improve food safety throughout the supply chain.

microbiology↗

bioRxiv2025

Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection

Quantifying T cell response during primary infection in humans is crucial for understanding adaptive immunity. Leveraging a controlled human challenge to SARS-CoV-2, we characterized antigen-specific T cell response within and across individuals. Notably, individual clones reached similar maximum frequencies despite differences in the timing of their peak expansion. Mathematical modeling showed that this observation is consistent with precursor frequency, but not TCR signal strength, as the source of inter-clonal variability. Single-cell profiling revealed distinct temporal programs for CD4+ and CD8+ T cells, with CD4+ cells expanding earlier but contracting to a lower frequency. Clones with similar receptors, likely recognizing the same antigen, expanded at similar times. Together, these findings highlight how clone-intrinsic properties such as precursor frequency and lineage shape T cell clonal kinetics. These insights provide a quantitative framework for understanding T cell response in humans, with implications for vaccine design.

biophysics↗

bioRxiv2025

Integrative analysis reveals generalizable human neurodegenerative disease-associated glial states

Glial cells are known to respond transcriptionally in multiple neurodegenerative diseases (NDDs). In particular, microglial states have been characterized in Alzheimers disease and mouse models of amyloidosis as disease-associated microglia. Although single-cell transcriptomic technologies have increased the dimensionality of information available across cell states, few studies have systematically tested for changes in glial transcription across brain regions and disease states. Here, we report a statistical framework for glial annotation, disease association, and transcriptional profiling, which facilitate identification of generalizable glial states that are present across a spectrum of NDDs (Alzheimers disease, Parkinsons disease, amyotrophic lateral sclerosis, and frontotemporal dementia) by re-analyzing data available in four multi-region atlases. We identify seven astrocyte substates, 14 microglia/myeloid substates, and five oligodendrocyte substates where transcriptional variability is attributable to region, disease, or study-specific effects. Regional heterogeneity of astrocytes masked disease associations, even within cortical subregions. We found only limited oligodendrocyte transcriptional heterogeneity, resulting in few substates for further interrogation. Notably, microglia showed the strongest evidence for disease association. We show, for the first time, that this association exists across different NDDs. Using latent factor analysis, we created a consensus human neurodegenerative disease-associated microglia (hnDAM) signature, which we experimentally validated in 11 independent sample series. We demonstrate that the hnDAM signature is a statistically testable biomarker for conserved microglial activation in NDDs by: i) comparing to murine DAM-like signatures, ii) performing transcription factor analysis, and iii) modeling transcriptional reprogramming perturbations in iPSC-derived microglia. Importantly, we find for the first time a way to make direct comparisons between DAM-like activation profiles in separate studies and propose a novel modeling paradigm via PIKfyve inhibition. Taken together, this work broadens our understanding of glial activation across neuropathologies and reveals hnDAM as a putative therapeutic target that can be utilized in any transcriptomic study of patients suffering from NDDs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/678630v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1863095org.highwire.dtl.DTLVardef@dfa6c8org.highwire.dtl.DTLVardef@13e95f1org.highwire.dtl.DTLVardef@1e6165e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

A CYCLIC PEPTIDE TARGETS GLIOBLASTOMA BY BINDING TO ABERRANTLY EXPOSED SNAP25

Disease-specific changes in tumors and other diseased tissues are an important target of research because they provide clues on the pathophysiology of the disease as well as uncovering potentially useful markers for diagnosis and treatment. Here, we report a new cyclic peptide, CESPLLSEC (CES), that specifically accumulated (homed) in intracranial U87MG and the WT-GBM model of glioblastoma from intravenous (IV) injection, associating with the vasculature. Affinity chromatography of U87MG tumor extracts on insolubilized CES peptide identified Synaptosomal Associated Protein 25 (SNAP25) as a candidate target molecule (receptor) for CES. Several results supported the identification of SNAP25 as the CES receptor. IV-injected FAM-CES colocalized with SNAP25 in the tumors, and direct binding studies showed specific CES peptide binding to recombinant human SNAP25. A CES peptide-drug conjugate designed for photodynamic therapy showed selective cytotoxicity to SNAP25+ glioblastoma cell lines. Specific accumulation of systemically injected anti-SNAP25 antibody in U87MG glioblastoma, and labeling of intact U87MG cells with anti-SNAP in flow cytometry showed that SNAP25 is available from the circulation but not in normal tissues and that it is present at the cell surface. Using an array of ECM proteins and surface plasmon resonance revealed that SNAP25 binds moderately to collagen V and strongly to collagen VI. Modeling studies suggested that CES and collagen VI compete for the same binding site on SNAP25. Our results introduce CES as a valuable targeting peptide for drug delivery, and its receptor SNAP25 as a possible molecular marker of interest for glioblastoma.

cancer biology↗

bioRxiv2023

Transmissibility of clinically relevant atovaquone-resistant Plasmodium falciparum by anopheline mosquitoes

Rising numbers of malaria cases and deaths underscore the need for new interventions. Long-acting injectable medications, such as those now in use for HIV prophylaxis, offer the prospect of a malaria "chemical vaccine", combining the efficacy of a drug (like atovaquone) with the durability of a biological vaccine. Of concern, however, is the possible selection and transmission of drug-resistant parasites. We addressed this question by generating clinically relevant, highly atovaquone-resistant, Plasmodium falciparum mutants competent to infect mosquitoes. Isogenic paired strains, that differ only by a single Y268S mutation in cytochrome b, were evaluated in parallel in southeast Asian (Anopheles stephensi) or African (Anopheles gambiae) mosquitoes, and thence in humanized mice. Fitness costs of the mutation were evident along the lifecycle, in asexual parasite growth in vitro and in a progressive loss of parasites in the mosquito. In numerous independent experiments, microscopic exam of salivary glands from hundreds of mosquitoes failed to detect even one Y268S sporozoite, a defect not rescued by coinfection with wild type parasites. Furthermore, despite uniformly successful transmission of wild type parasites from An. stephensi to FRG NOD huHep mice bearing human hepatocytes and erythrocytes, multiple attempts with Y268S-fed mosquitoes failed: there was no evidence of parasites in mouse tissues by microscopy, in vitro culture, or PCR. These studies confirm a severe-to-lethal fitness cost of clinically relevant atovaquone-resistant P. falciparum in the mosquito, and they significantly lessen the likelihood of their transmission in the field. SignificanceNew tools are needed to protect individuals from malaria and to control malaria in the field. Atovaquone plus proguanil is a commonly used and well-tolerated medicine to prevent malaria. No drug resistance has been reported from its prophylactic use, but tablets must be taken daily. Giving atovaquone as a single injection may provide much longer-lasting protection, against both falciparum and vivax malaria, but there is concern this may create drug resistance. In this study we showed that clinically relevant atovaquone-resistant malaria parasites survive poorly, if at all, in mosquitoes, and that mosquitoes do not transmit drug-resistant parasites to humanized mice. These findings lessen the likelihood that an atovaquone "chemical vaccine" would lead to the spread of atovaquone resistance.

microbiology↗

bioRxiv2022

Targeted editing of GTR1 and GTR2 homologs directs the development of ideal low-seed and high-leaf glucosinolate oilseed mustard

Glucosinolate content in the Brassica oilseed crops has been reduced to the globally accepted Canola quality levels, making the seed meal useful as a protein-rich animal feed. However, the overall lower glucosinolate content in such plants renders them vulnerable to pests. We report CRISPR/Cas9-based editing of glucosinolate transporter (GTR) family genes to develop ideal oilseed mustard lines with the desired low levels of seed glucosinolates while maintaining high glucosinolate levels in leaves and pod walls, without affecting the seed yield and seed quality traits. The low-seed and high-leaf glucosinolate mustard lines with improved nutritional and defense traits will raise its international trade potential both as oilseed and feed crop.

plant biology↗

bioRxiv2022

The mitochondrion of Plasmodium falciparum generates essential acetyl-CoA for protein acetylation

Coenzyme A (CoA) biosynthesis is an excellent target for antimalarial intervention. While most studies have focused on the use of CoA to produce acetyl-CoA in the apicoplast and the cytosol of malaria parasites, mitochondrial acetyl-CoA production is less well understood. In the current study, we performed metabolite labeling experiments to measure endogenous metabolites in Plasmodium falciparum lines with genetic deletions affecting mitochondrial dehydrogenase activity. Our results show that mitochondrial acetyl-CoA biosynthesis is essential for parasite growth and identify a catalytic redundancy between the two main ketoacid dehydrogenase enzymes, both of which are able to produce acetyl-CoA. The activity of these enzymes is dependent on the lipoate attachment enzyme LipL2, which is essential for parasite survival solely based on its role in supporting acetyl-CoA metabolism. We also find that acetyl-CoA produced in the mitochondrion is essential for the acetylation of histones and other proteins outside of the mitochondrion. Taken together, our results demonstrate that the mitochondrion is an essential de novo source of acetyl-CoA and is required for P. falciparum protein acetylation critical to parasite survival.

microbiology↗

bioRxiv2020

Q-STARZ: Quantitative Spatial and Temporal Assessment of Regulatory element activity in Zebrafish

Noncoding regions of the genome harbouring cis-regulatory elements (CREs) or enhancers drive spatial and temporal gene expression. Mutations or single nucleotide polymorphisms (SNPs) in enhancers have been widely implicated in human diseases and disease-predispositions. However, our ability to assay the regulatory potential of genetic variants in enhancers is currently very limited, in part because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type (Wt) and disease-associated, mutant (Mut) human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. Using this single transgenic cassette, the functional activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing the simultaneous visualisation of the activity of both alleles. This can reveal where and when in embryonic development the wild-type allele is active and how this activity is altered by the disease-associated mutation.

genetics↗

bioRxiv2020

The WD and linker domains of ATG16L1 required for non canonical autophagy limit lethal influenza A virus infection at epithelial surfaces.

Respiratory viruses such as influenza A virus (IAV) and SARS-CoV-2 (Covid-19) cause pandemic infections where cytokine storm syndrome, lung inflammation and pneumonia lead to high mortality. Given the high social and economic cost of these viruses, there is an urgent need for a comprehensive understanding of how the airways defend against virus infection. Viruses entering cells by endocytosis are killed when delivered to lysosomes for degradation. Lysosome delivery is facilitated by non-canonical autophagy pathways that conjugate LC3 to endo-lysosome compartments to enhance lysosome fusion. Here we use mice lacking the WD and linker domains of ATG16L1 to demonstrate that non-canonical autophagy protects mice from lethal IAV infection of the airways. Mice with systemic loss of non-canonical autophagy are exquisitely sensitive to low-pathogenicity murine-adapted IAV where extensive viral replication throughout the lungs, coupled with cytokine amplification mediated by plasmacytoid dendritic cells, leads to fulminant pneumonia, lung inflammation and high mortality. IAV infection was controlled within epithelial barriers where non-canonical autophagy slowed fusion of IAV with endosomes and reduced activation of interferon signalling. This was consistent with conditional mouse models and ex vivo analysis showing that protection against IAV infection of lung was independent of phagocytes and other leukocytes. This establishes non-canonical autophagy pathways in airway epithelial cells as a novel innate defence mechanism that can restrict IAV infection and lethal inflammation at respiratory surfaces.

microbiology↗

bioRxiv2019

Genetic and functional diversification of chemosensory pathway receptors in filarial nematode parasites

Lymphatic filariasis (LF) afflicts over 60 million people worldwide and leads to severe pathological outcomes in chronic cases. The nematode parasites (Nematoda: Filarioidea) that cause LF require both arthropod (mosquito) intermediate hosts and mammalian definitive hosts for their propagation. The invasion and migration of filarial worms through host tissues are complex and critical to survival, yet little is known about the receptors and signaling pathways that mediate directed migration in these medically important species. In order to better understand the role of chemosensory signaling in filarial worm taxis, we employ comparative genomics, transcriptomics, reverse genetics, and chemical approaches to identify putative chemosensory receptor proteins and perturb chemotaxis phenotypes in filarial worms. We find that chemoreceptor family size is correlated with the presence of environmental (extra-host) stages in nematode life cycles, and that filarial worms contain a compact and highly-diverged chemoreceptor complement and lineage-specific ion channels that are predicted to operate downstream of chemoreceptor activation. In Brugia malayi, an etiological agent of LF, chemoreceptor expression patterns correspond to distinct parasite migration events across the life cycle. To interrogate the role of chemosensation in the migration of larval worms, arthropod infectious stage (microfilariae) and mammalian infectious stage (L3) Brugia parasites were incubated in nicotinamide, an agonist of the nematode transient receptor potential (TRP) channel OSM-9. Exposure of microfilariae to nicotinamide alters intra-mosquito migration while exposure of L3s reduces chemotaxis towards host-associated cues in vitro. Nicotinamide also potently modulates thermosensory responses in L3s, suggesting a polymodal sensory role for Brugia osm-9. Reverse genetic studies implicate both Brugia osm-9 and the cyclic nucleotide-gated (CNG) channel subunit tax-4 in larval chemotaxis towards host serum, and these ion channel subunits rescue sensory defects in C. elegans osm-9 and tax-4 knock-out strains. Together, these data reveal genetic and functional diversification of chemosensory signaling proteins in filarial worms, and encourage a more thorough investigation of clade and parasite-specific facets of nematode sensory receptor biology.

microbiology↗

bioRxiv2019

Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets

Identifying cellular functions dysregulated by disease associated variants could implicate novel pathways for drug targeting or modulation in cell therapies. Variants associated with immune diseases point towards the role of CD4+ regulatory T cells (Tregs), cell type critical for immune homeostasis. To translate the effects of immune disease alleles on Treg function we mapped genetic regulation (QTL) of gene expression and chromatin activity in Tregs. We identified 123 loci where Treg QTLs colocalized with immune disease variants. These colocalizations indicated that dysregulation of key Treg pathways, including cell activation via CD28 and IL-2 signalling mediated by STAT5A contribute to the shared pathobiology of immune diseases. Finally, using disease GWAS signals colocalizing with Treg QTLs, we identified 34 known drug targets and 270 targets with drug tractability evidence. Our study is the first in-depth characterization of immune disease variant effects on Treg gene expression modulation and dysregulation of Treg function.

genetics↗

bioRxiv2018

Heteromerization of endogenous mu and delta opioid receptors tunes mu opioid receptor signaling and trafficking

Increasing evidence indicates that native mu and delta opioid receptors can associate to form heteromers in discrete brain neuronal circuits. However, little is known about their signaling and trafficking. Using double fluorescent knock-in mice, we investigated the impact of neuronal co-expression on the internalization profile of mu and delta opioid receptors in primary hippocampal cultures and in vivo. We established ligand selective mu-delta co-internalization upon activation by exogenous ligands and provide evidence for mu-delta co-internalization by the endogenous opioid peptide met-enkephalin, but not {beta}-endorphin. Co-internalization was driven by the delta opioid receptor, required an active conformation of both receptors and led to sorting to the lysosomal compartment. This alteration in the mu opioid receptor intracellular fate was accompanied by sustained ERK1/2 phosphorylation. In addition, increased mu-delta neuronal co-localization in the rostral ventromedial medulla in a chronic neuropathic state suggests that mu-delta heteromers are involved in the regulation of nociceptive transmission

neuroscience↗

bioRxiv2017

Tex19.1 Restricts LINE-1 Mobilisation in Mouse Embryonic Stem Cells

Mobilisation of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution. In humans, retrotransposon mobilisation is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilise in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilisation. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, we show that loss of Tex19.1 increases L1-ORF1p levels and mobilisation of L1 reporters in pluripotent mouse embryonic stem cells implying that Tex19.1 prevents new retrotransposition-mediated mutations from arising in the germline genome. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in the epigenetically dynamic developing mammalian germline.

genetics↗

bioRxiv2016

Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types

BackgroundA healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.\n\nResultsWe applied a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16- monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naive T cells, from the same 125 healthy individuals. We discovered substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression were found to be implicated in key immune pathways and to associate with cellular properties and environmental exposure. We also observed increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites were enriched at dynamic chromatin regions and active enhancers.\n\nConclusionsOur data highlight the importance of transcriptional and epigenetic variability for the neutrophils key role as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability.

molecular biology↗