Biology subjects

Simon, M.

Publications and source records attributed to Simon, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination

Somatic hypermutation (SHM) and class switch recombination (CSR) diversify immunoglobulin (Ig) genes and are initiated by the activation induced deaminase (AID), a single-stranded DNA cytidine deaminase that is thought to engage its substrate in the context of RNA polymerase II (RNAPII) transcription. Through a loss of function genetic screen, we identified numerous potential factors involved in SHM including ELOF1, a component of the RNAPII elongation complex that has been shown to function in DNA repair and transcription elongation. Loss of ELOF1 strongly compromises SHM, CSR, and AID targeting and alters RNAPII transcription by reducing RNAPII pausing downstream of transcription start sites and levels of serine 5 but not serine 2 phosphorylated RNAPII throughout transcribed genes. ELOF1 must bind to RNAPII to be a proximity partner for AID and to function in SHM and CSR. We propose that ELOF1 helps create the appropriate stalled RNAPII substrate on which AID acts. HighlightsO_LIA CRISPR knockout screen has identified numerous potential SHM factors. C_LIO_LISHM, CSR, and AID targeting are strongly compromised in the absence of ELOF1. C_LIO_LIELOF1 must interact with RNAPII to be an AID proximity partner and support AID targeting. C_LIO_LIELOF1 supports RNAPII pausing and generation of the substrate for AID action. C_LI

immunology↗

bioRxiv2024

TBX15 regulates a network of immune response genes in adipose tissue and alters fat mass and depot weight in heterozygous knockout mice

Adipose tissue distribution in the body is an indicator of metabolic disease risk, independent of body mass index (BMI), and is indirectly measured by waist-hip-ratio (WHR). T-Box transcription factor-15 (TBX15) has been implicated in regulation of adipose distribution in multiple human and mouse studies, and the TBX15-WARS2 genome-wide association study locus has been associated with BMI-adjusted-WHR signals in multiple investigations. As a potential mediator of this signal, we investigated the role of Tbx15 using heterozygous and homozygous mouse knockout models to determine if loss of this gene alters adipose physiology, and to identify the transcriptional network regulated by Tbx15 in adipose tissue and preadipocyte cells. In a metabolic phenotyping experiment we provided either low fat diet (LFD) or high fat diet (HFD) to male and female heterozygous Tbx15+/- and wildtype Tbx15+/+mice from weaning and maintained for 24 weeks. Only Tbx15+/-mice maintained on LFD weighed less than wildtype LFD controls, and female LFD Tbx15+/- mice had lower fat mass overall. We found that in LFD Tbx15+/- mice, multiple visceral fat depots weighed less than wildtype controls, and this was maintained when corrected for body mass for both gonadal and mesenteric visceral adipose depots. When comparing adipocyte size in multiple adipose depots, some reduction in number of larger adipocytes was detected in the perirenal adipose tissue of female HFD Tbx15+/- vs Tbx15+/+ mice, mesenteric adipose tissue from female LFD Tbx15+/- vs Tbx15+/+ mice and male HFD Tbx15+/- vs Tbx15+/+mice. RNA-sequencing of subcutaneous (inguinal) adipose tissues from 12-week old male and female knockout Tbx15-/-, Tbx15+/- and Tbx15+/+ mice raised on a standard chow diet identified 897 upregulated genes and 2328 downregulated genes in female Tbx15-/- mice compared to Tbx15+/+mice. We then combined this dataset with TBX15 ChIP-sequencing data from mouse preadipocyte 3T3-L1 cells overexpressing TBX15 to identify a credible set of genes directly regulated by TBX15. These 52 genes were enriched for B- and T-cell receptor signalling, JAK-STAT signalling and haematopoietic cell lineage pathways; suggesting a direct regulatory role for TBX15 in these pathways in adipose tissue. Together, these data highlight a role for TBX15 in regulation of differential adipose tissue expansion, particularly under low caloric conditions. Further, we identify a potentially important role for TBX15 in the well described adipocyte-immune cell crosstalk associated with obesity and type 2 diabetes mellitus.

physiology↗

bioRxiv2024

Quantifying immune cell telomere content at single-cell resolution in context of PD-1 checkpoint immunotherapy

Biological processes such as aging, carcinogenesis, and immune responses depend on the ability of cells to maintain or rapidly expand populations. This capacity is constrained by a cells replicative potential, which is reflected in its telomere content. Despite the central role of telomeres in cancer and immunity, their analysis at single-cell resolution across diverse cell types remains challenging. Here we show that scATAC-seq data enables quantitative telomeromics when key technical and biological confounders are accounted for. We present a computational framework that addresses read sparsity, telomere representation, and chromatin-state-dependent competition for sequencing signal, enabling robust estimation of telomere content and telomeric variant repeat composition from scATAC-seq data. By inferring global chromatin condensation directly from scATAC-seq profiles, our approach corrects for cell-cycle-associated biases while simultaneously capturing chromatin-state dysregulation in cancer. Applied to a large cancer atlas, this framework reveals patient-specific telomere maintenance phenotypes, including telomerase-associated and alternative lengthening of telomeres (ALT)-like profiles preserved across subclonal populations. Extending beyond cancer cells, we observe that telomere content in exhausted T cell subpopulations prior to immunotherapy is predictive for effective response to PD-1 checkpoint blockade. Together, these results establish scATAC-seq as a robust platform for single-cell telomeromics in cancer and immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/609339v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4f9498org.highwire.dtl.DTLVardef@a4b787org.highwire.dtl.DTLVardef@d1e25org.highwire.dtl.DTLVardef@136196b_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Popp, F. (2026) https://BioRender.com/mi2jove

immunology↗

bioRxiv2024

Metabolic and transcriptomic analyses of nectaries reveal differences in the mechanism of nectar production between monocots (Ananas comosus) and dicots (Nicotiana tabacum)

BackgroundNectar is offered by numerous flowering plants to attract pollinators. To date, the production and secretion of nectar have been analyzed mainly in eudicots, particularly rosids such as Arabidopsis. However, due to the enormous diversity of flowering plants, further research on other plant species, especially monocots, is needed. Ananas comosus (monocot) is an economically important species and ideal for such analyses because it produce easily accessible nectar in sufficient quantities. In addition, the analyses were also carried out with Nicotiana tabacum (dicot, asterids) for comparison. ResultsWe performed transcriptome sequencing (RNA-Seq) analyses of the nectaries of Ananas comosus and Nicotiana tabacum, to test whether mechanisms described for nectar production and secretion in Arabidopsis are also present in these plant species. The focus of these analyses is on carbohydrate metabolism and transport (e.g., sucrose-phosphate synthases, invertases, sucrose synthases, SWEETs and further sugar transporters). In addition, the metabolites were analyzed in the nectar, nectaries and leaves of both plant species to address the question whether concentration gradients for different metabolites exist between the nectaries and nectar. The nectar of N. tabacum contains large amounts of glucose, fructose and sucrose, and the sucrose concentration in the nectar appears to be similar to the sucrose concentration in the nectaries. Nectar production and secretion in this species closely resembles corresponding processes in some other dicots, including sucrose synthesis in nectaries and sucrose secretion by SWEET9. The nectar of A. comosus also contains large amounts of glucose, fructose and sucrose and in this species the sucrose concentration in the nectar appears to be higher than the sucrose concentration in the nectaries. Furthermore, orthologs of SWEET9 appear to be generally absent in A. comosus and other monocots. Therefore, sucrose export by SWEETs from the nectaries into the nectar can be excluded, rather, other mechanisms, such as active sugar export or exocytosis, are more likely. ConclusionThe mechanisms of nectar production and secretion in N. tabacum appear to be largely similar to those in other dicots, whereas in the monocotyledonous species A. comosus, different synthesis and transport processes are involved.

plant biology↗

bioRxiv2024

Mimosa species endemic to acidic soils in central Brazil are nodulated by a high diversity of Paraburkholderia genotypes, but widespread species are nodulated by Paraburkholderia, Cupriavidus or Rhizobium depending on soil characteristics

Neotropical Beta-rhizobia have a particular affinity to the large legume (Fabaceae) genus Mimosa and some of its relatives in the tribe Mimosae of the Caesalpinioideae subfamily. However, little is still known about the ecology of this interaction, especially the relationship between the rhizobia of "widespread" pan-tropical Mimosa species like M. pudica and the rhizobia that nodulate endemic Mimosa species that are very restricted in their habitats. The objective of this study was to examine the microsymbionts of Mimosa spp. and some other mimosoids in climates ranging from tropical to subtropical, humid to semi-arid, with varied soil characteristics and altitudes, with the aim of testing the hypothesis that widespread species have more cosmopolitan symbiont preferences than endemic ones. Nodules were sampled from more than 40 Mimosa spp. and related taxa in eleven Brazilian states, many endemics or biome-restricted, but particular attention was paid to sample nodules from the widespread species M. pudica at all locations. The Mimosa symbionts comprised 19 potential 16S rRNA and recA groups at the species level, with 16 belonging to the genus Paraburkholderia, including six lineages that may represent new species. The remaining genotypes consisted of 14 strains in two lineages of Cupriavidus that were mainly isolated from M. pudica growing at low altitudes, plus a single lineage of Rhizobium also from M. pudica. It is concluded that a high diversity of Paraburkholderia strains dominate as symbionts of Mimosa in the acidic soils of its main center of radiation in Central Brazil but that Cupriavidus and Rhizobium comprise a significant minority of symbionts of widespread Mimosa spp., especially M. pudica, in lowland or disturbed areas with less acidic soils. Mimosa symbiont diversity is thus driven either by edapho-climatic characteristics for widespread species and/or by co-evolution of the symbiotic partners for endemic species.

plant biology↗

bioRxiv2024

TLR4 deficiency does not alter glaucomatous progression in a mouse model of chronic glaucoma

Glaucoma is a leading cause of irreversible blindness worldwide. Toll-like receptor 4 (TLR4) is a pattern-recognition transmembrane receptor that induces neuroinflammatory processes in response to injury. Tlr4 is highly expressed in ocular tissues and is known to modulate inflammatory processes in both anterior and posterior segment tissues. TLR4 activation can lead to mitochondrial dysfunction and metabolic deficits in inflammatory disorders. Due to its effects on inflammation and metabolism, TLR4 is a candidate to participate in glaucoma pathogenesis. It has been suggested as a therapeutic target based on studies using acute models, such as experimentally raising IOP to ischemia-inducing levels. Nevertheless, its role in chronic glaucoma needs further evaluation. In the current study, we investigated the role of TLR4 in an inherited mouse model of chronic glaucoma, DBA/2J. To do this, we analyzed the effect of Tlr4 knockout (Tlr4-/-) on glaucoma-associated phenotypes in DBA/2J mice. Our studies found no significant differences in intraocular pressure, iris disease, or glaucomatous progression in Tlr4-/- compared to Tlr4+/+ DBA/2J mice. These data do not identify a role for TLR4 in this chronic glaucoma, but further research is warranted to understand its role in other glaucoma models and different genetic contexts.

neuroscience↗

bioRxiv2024

The unusual orf117Sha locus causes desynchronization of pollen development in the Arabidopsis gametophytic Sha CMS

Cytoplasmic male sterility (CMS) is of major agronomical relevance in hybrid breeding. In gametophytic CMS, abortion of pollen is determined by the grain genotype, while in sporophytic CMS, it is determined by the mother plant genotype. While several CMS mechanisms have been dissected at the molecular level, gametophytic CMS has not been straightforwardly accessible. We used the gametophytic Sha-CMS in Arabidopsis to characterize the cause and process of pollen abortion by implementing in vivo biosensing in single pollen and mitoTALEN mutagenesis. We obtained conclusive evidence that orf117Sha is the CMS-causing gene, despite distinct characteristics from other CMS-genes. We measured the in vivo cytosolic ATP content in single pollen, followed pollen development and analyzed pollen mitochondrial volume in two genotypes that differed only by the presence of the orf117Sha locus. Our results show that the Sha-CMS is not triggered by ATP deficiency. Instead, we observed desynchronization of a pollen developmental program. Pollen death occurred independently in pollen grains at diverse stages and was preceded by mitochondrial swelling. We conclude that pollen death is grain-autonomous in Sha-CMS and propose that mitochondrial permeability transition, which was previously described as a hallmark of developmental and environmental-triggered cell death programs, precedes pollen death in Sha-CMS. HighlightThe Arabidopsis CMS-causing gene orf117Sha does not limit pollen ATP supply. Pollen-centered approaches show desynchronization of development and mitochondrial swelling before pollen death, which occurred at diverse stages.

plant biology↗

bioRxiv2023

High-volume, label-free imaging for quantifying single-cell dynamics in induced pluripotent stem cell colonies

To facilitate the characterization of unlabeled induced pluripotent stem cells (iPSCs) during culture and expansion, we developed an AI pipeline for nuclear segmentation and mitosis detection from phase contrast images of individual cells within iPSC colonies. The analysis uses a 2D convolutional neural network (U-Net) plus a 3D U-Net applied on time lapse images to detect and segment nuclei, mitotic events, and daughter nuclei to enable tracking of large numbers of individual cells over long times in culture. The analysis uses fluorescence data to train models for segmenting nuclei in phase contrast images. The use of classical image processing routines to segment fluorescent nuclei precludes the need for manual annotation. We optimize and evaluate the accuracy of automated annotation to assure the reliability of the training. The model is generalizable in that it performs well on different datasets with an average F1 score of 0.94, on cells at different densities, and on cells from different pluripotent cell lines. The method allows us to assess, in a non-invasive manner, rates of mitosis and cell division which serve as indicators of cell state and cell health. We assess these parameters in up to hundreds of thousands of cells in culture for over 20 hours, at different locations in the colonies, and as a function of excitation light exposure.

systems biology↗

bioRxiv2023

Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states

Schlemms canal (SC) is central in intraocular pressure regulation but requires much characterization. It has distinct inner and outer walls, each composed of Schlemms canal endothelial cells (SECs) with different morphologies and functions. Recent transcriptomic studies of the anterior segment added important knowledge, but were limited in power by SEC numbers or did not focus on SC. To gain a more comprehensive understanding of SC biology, we performed bulk RNA sequencing on C57BL/6J SC, blood vessel, and lymphatic endothelial cells from limbal tissue ([~]4500 SECs). We also analyzed mouse limbal tissues by single-cell and single-nucleus RNA sequencing (C57BL/6J and 129/Sj strains), successfully sequencing 903 individual SECs. Together, these datasets confirm that SC has molecular characteristics of both blood and lymphatic endothelia with a lymphatic phenotype predominating. SECs are enriched in pathways that regulate cell-cell junction formation pointing to the importance of junctions in determining SC fluid permeability. Importantly, and for the first time, our analyses characterize 3 molecular classes of SECs, molecularly distinguishing inner wall from outer wall SECs and discovering two inner wall cell states that likely result from local environmental differences. Further, and based on ligand and receptor expression patterns, we document key interactions between SECs and cells of the adjacent trabecular meshwork (TM) drainage tissue. Also, we present cell type expression for a collection of human glaucoma genes. These data provide a new molecular foundation that will enable the functional dissection of key homeostatic processes mediated by SECs as well as the development of new glaucoma therapeutics. Significance statementSchlemms canal is a critical ocular drainage structure that maintains intraocular pressure with important consequences for glaucoma. Despite this, Schlemms canal has been relatively understudied with the molecular process that mediate its function, maintain its health, or that are compromised in glaucoma needing much deeper characterization. This study is important as it provides the most comprehensive molecular characterization of Schlemms canal cells to date providing a wealth of molecular details. In addition to highlighting important biological pathways, this information will guide studies to develop new treatments against glaucoma.

genomics↗

bioRxiv2023

Incorporating strontium enriched amorphous calcium phosphate granules in collagen/collagen-magnesium-hydroxyapatite osteochondral scaffold improves subchondral bone repair

To date, osteochondral defect repair with a collagen/collagen-magnesium-hydroxyapatite (Col/Col-Mg-HAp) scaffold has demonstrated good clinical results. However, subchondral bone repair has been suboptimal, potentially leading to damage to the regenerated overlying neocartilage. This study aimed at improving the bone repair potential of this scaffold by incorporating strontium (Sr) ion enriched amorphous calcium phosphate (Sr-ACP) granules (100-150 {micro}m). Sr concentration of Sr-ACP was determined with ICP-MS at 2.49 {+/-} 0.04 wt.%. Then 30 wt.% ACP or Sr-ACP granules were integrated into the scaffold prototypes. The ACP or Sr-ACP granules were well distributed and embedded in the collagenic matrix demonstrated by micro-CT and scanning electron microscopy/energy dispersive x-ray spectrometry. Good cytocompatibility of ACP/Sr-ACP granules and ACP/Sr-ACP enriched scaffolds was confirmed in in vitro cytotoxicity assays. An overall promising early tissue response and good biocompatibility of both ACP and Sr-ACP enriched scaffolds were demonstrated in a subcutaneous mouse model. In a goat osteochondral defect model, significantly more bone observed at 6 months with the treatment of Sr-ACP enriched scaffolds compared to scaffold only in particular in the weight-bearing femoral condyle subchondral bone defect. Overall, the incorporation of osteogenic Sr-ACP granules in Col/Col-Mg-HAp scaffolds showed to be a feasible and promising strategy to improve subchondral bone repair.

bioengineering↗

bioRxiv2023

Multiple myeloma long-term survivors display sustained immune alterations decades after first line therapy

The long-term consequences of cancer or cancer therapy on the patients immune system years after cancer-free survival remain poorly understood. Here, we have performed an in-depth characterization of the bone marrow ecosystem of multiple myeloma long-term survivors at initial diagnosis and up to 17 years following cancer-free survival. Using comparative single-cell analyses in combination with molecular, genomic and functional approaches, we demonstrate that multiple myeloma long-term survivors display pronounced alterations in their bone marrow microenvironment associated with impaired immunity. These immunological alterations were frequently driven by an inflammatory immune circuit fueled by the long-term persistence or resurgence of residual myeloma cells. Notably, even in the complete absence of any detectable residual disease for decades, sustained changes in the immune system were observed, suggesting an irreversible immunological scarring caused by the initial exposure to the cancer and therapy. Collectively, our study provides key insights into the molecular and cellular bone marrow ecosystem of multiple myeloma long-term survivors, revealing reversible and irreversible alterations of the immune compartment, which can serve as diagnostic and predictive tools. Statement of significanceLarge-scale single-cell profiling of a unique cohort of multiple myeloma long-term survivors uncovered that exposure to cancer and its treatment causes both reversible and irreversible immune alterations associated with impaired immunity. These findings have far-reaching implications for the understanding of long-term immune alterations in cancer, which need to be considered also in the context of immune therapeutic approaches. Furthermore, our study demonstrates how cancer-associated immune trafficking can be used to predict disease re-initiation in the bone marrow, opening new avenues for minimally invasive disease monitoring.

cancer biology↗

bioRxiv2023

Assessing diatom-associated bacteria by a specific CARD-FISH protocol

The cell surfaces of phytoplankton algae including diatoms are usually colonized by specific bacterial populations which interact with and affect growth of the host species. Catalyzed Reported Deposition Fluorescence in situ Hybridizazion (CARD-FISH) is a well-suited technique to visualize and identify algal-associated bacterial cells. Autofluorescence and the strongly structured cell surface of the algal cell make it difficult to quantify distinct populations of the colonizing bacterial communities. To overcome these limitations, we adopted a CARD-FISH method to this specific application by reducing the algal autofluorescence by an extra ethanol treatment and by stacking epifluorescence micrographs taken at different focal planes and merging them into a composite image. Cells of the diatom Thalassiosira rotula were used as host and incubated with a consortium of different bacterial strains and a natural bacterial community. Samples were concentrated either by filtration onto polycarbonate membranes or by centrifugation and analyzed with probes CF319a, GAM42a and ROS536. The results showed easily quantifiable bacterial cells and did not reveal any significant differences in the abundance of diatom-associated bacterial populations assessed by both methods. Our CARD-FISH protocol persuasively demonstrated that bacterial populations can be easily and reliably enumerated on diatom cells and presumably also on other algal cells and autotrophic biofilms.

microbiology↗

bioRxiv2023

Targeting Transferrin Receptor to Transport Antisense Oligonucleotides Across the Blood-Brain Barrier

Antisense oligonucleotides (ASO) are promising therapies for neurological disorders, though they are unable to cross the blood-brain barrier (BBB) and must be delivered directly to the central nervous system (CNS). Here, we use a human transferrin receptor (TfR)-binding molecule to transport ASO across the BBB in mice and non-human primates, termed oligonucleotide transport vehicle (OTV). Systemically delivered OTV drives significant, cumulative, and sustained knockdown of the ASO target across multiple CNS regions and all major cell types. Further, systemic OTV delivery enables more uniform ASO biodistribution and knockdown compared to two other clinically relevant ASO delivery routes: a standard, high affinity TfR antibody, or direct ASO delivery to the CSF. Together, our data support systemically delivered OTV as a potential therapeutic platform for neurological disorders. One-Sentence SummarySystemically dosed OTV delivered via TfR1 targeting shows widespread and cumulative target knockdown in the mouse and NHP CNS.

neuroscience↗

bioRxiv2023

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1

The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes suggesting the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.

biochemistry↗

bioRxiv2023

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two splicing factors commonly mutated in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. HIGHLIGHTS- Oncogenic mutations in SF3B1 and U2AF1 cause a gene body RNAPII transcription elongation defect - The elongation defect is linked to impaired assembly of early spliceosome complexes and leads to replication stress and changes to chromatin landscape - RNAPII elongation defects in SF3B1K700E are normalized by modulating epigenetic factors but 3 cryptic splicing events are not reversed - Targeting the Sin3/HDAC pathway to normalize RNAPII elongation defect is a potential therapeutic approach in these disorders GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/530019v3_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@dc6d22org.highwire.dtl.DTLVardef@180f36borg.highwire.dtl.DTLVardef@ed341forg.highwire.dtl.DTLVardef@f8dfb2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

A tissue-specific ubiquitin switch coordinates brain, craniofacial, and skin development

The molecular mechanisms that coordinate patterning of the embryonic ectoderm into spatially distinct lineages to form the nervous system, epidermis, and craniofacial structures are unclear. Here, biochemical disease-variant profiling reveals a posttranslational pathway that drives early ectodermal differentiation in the vertebrate head. The anteriorly expressed ubiquitin ligase CRL3-KLHL4 restricts signaling of the ubiquitous cytoskeletal regulator CDC42. The major substrate of CRL3-KLHL4 is the canonical CDC42 effector kinase PAK1 that monoubiquitylation switches into a CDC42 inhibitor. Loss of CRL3-KLHL4 or a disease-associated KLHL4 variant reduce PAK1 ubiquitylation causing overactivation of CDC42 signaling and defective ectodermal patterning and neurulation. Thus, tissue-specific, ubiquitin-dependent restriction of CDC42 signaling is essential for face, brain, and skin formation, demonstrating how cell-fate and morphometric changes are coordinated for faithful organ development.

developmental biology↗

bioRxiv2022

Differential kinetic analysis using nucleotide recoding RNA-seq and bakR

Conventional RNA sequencing (RNA-seq) provides limited information about the kinetic mechanisms underlying changes in RNA levels. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) are widely used approaches to identify changes in RNA synthesis and degradation kinetics, yet no software exists to rigorously compare the parameters of RNA kinetics between experimental conditions. We developed bakR to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Using simulated and real data, we validate bakR and demonstrate how it provides new insights into the kinetics of RNA metabolism.

bioinformatics↗

bioRxiv2022

Sniffing behaviour of Barbary macaques at Affenberg Salem

Olfaction is one of the evolutionarily oldest senses and plays a fundamental role in foraging and social interactions across mammals. In primates, the role of olfaction is now well recognized, but better investigated in strepsirrhine and platyrrhine primates than in catarrhines. We observed the sniffing behavior of semi-free ranging Barbary macaques, Macaca sylvanus, at Affenberg Salem, Germany, to assess how frequently macaques sniff and in which contexts, and how sniffing is affected by sex and age. Focal observations of 24 males and 24 females aged 1 to 25 years showed that Barbary macaques sniffed, on average, 5.3 times per hour, with more than 80% of sniffs directed at food. Irrespective of the context, younger individuals sniffed more often than older ones. Females sniffs were more often directed at food than male sniffs, while males sniffed more often than females in a social context. Sniffs at conspecifics occurred primarily in a sexual context, with 70% of social sniffs directed at female anogenital swellings performed by males. Of the observed 176 anogenital inspections, 51 involved sniffing of the swelling. Olfactory inspections were followed by copulation significantly less often than merely visual inspections, suggesting that anogenital odors provided additional information guiding male mating decisions. In sum, results show that Barbary macaques routinely use olfaction during feeding, but also in a social context. Our study further suggests that odors may guide mating decisions, but the role of olfaction in sexual interactions warrants further investigations.

animal behavior and cognition↗