Biology subjects

Wilson, M. J.

Publications and source records attributed to Wilson, M. J..

15 recordsLinked to original sources

bioRxiv2025

Metadomain and metaloop genome interactions in mammalian T cells

Recent studies have advanced our understanding of chromosomal organization and its principal role in gene regulation. However, most analyses have focused on short-range interactions (<2 Mb), limiting insight into broader regulatory architecture. In particular, the relationships between topologically associating domains (TADs), sub-TAD loops, long-range cross-TAD interactions, and higher-order chromosomal compartmentalization remain poorly understood. Here, we identify extensive multi-megabase and interchromosomal interactions (metaloops) in T lymphocytes, which organize into larger meta-TAD associations (metadomains). Metaloops bridge distal promoters and regulatory elements of key T cell-specific genes such as Ctla4, Ikzf2, Il2ra, Ets1, Lef1, Runx1, Bach2, Foxo1 and others, and are both shared and cell type-specific across functionally distinct T cell lineages. Reanalysis of published data confirms the reproducibility of these interactions in both mouse and human T cells and their dependence on superenhancers. Genome-wide clustering of metadomains reveals three interchromosomal hubs with distinct epigenomic profiles, including a superenhancer-enriched hub associated with T cell-specific gene activation. By integrating a compendium of new and public T cell epigenomic data, we infer distinct architectural factors associated with short-range loops and long-range metaloops. Altogether, our study reveals new features of T cell-specific 3D genome organization across scales, and our computational framework is broadly applicable to analyses of chromatin architecture across different cell types and experimental systems. Highlights- Ultra-long-range (>2 Mb) chromatin interactions linked to gene regulation in T cells - A new algorithm identifies distal and interchromosomal meta-TADs and metaloops - An interchromosomal T cell-specific active hub emerges from metadomain clustering - Epigenomic compendium implicates TFs associated with long-range interactions

genomics↗

bioRxiv2025

The cellular architecture of wheat leaves supports a conservation of spatial patterning of the mesophyll in grasses

Classical botany identifies a clear adaxial/abaxial (palisade/spongy) patterning of the mesophyll in leaves of eudicots but suggest that there is no comparable overt pattern within the mesophyll of most grasses. In this paper, we report on an analysis of leaves from across ploidy levels of Triticum species which reveals a patterning of mesophyll cellular architecture that has been maintained during the evolution/selection of wheat. Taking a quantitative approach to the analysis of 2D and 3D images, we show that upper and lower mesophyll cells are larger than the middle mesophyll cells, which are themselves more lobed than the mesophyll cells adjoining the upper and lower epidermis. This mesophyll patterning is superimposed on a gradual increase of cell size with ploidy, suggesting that it is evolutionarily ancient. Taken in the context of data revealing patterning of the rice mesophyll, our data support the hypothesis that grass leaves do display distinct cellular patterning across the adaxial/abaxial axis, the functional significance of which awaits full elucidation.

plant biology↗

bioRxiv2024

Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis: Insights into tissue specialization and blastogenesis

Botrylloides diegensis is a colonial ascidian that has been the focus of developmental, evolutionary, and regeneration research. In this study, we performed single-cell RNA sequencing (scRNA-seq) of an entire B. diegensis colony, including zooids, buds, and vascular tunics, to resolve cellular heterogeneity and identify cell and tissue markers. We identified 29 major cell clusters within the colony and used in situ hybridization to examine the spatial expression of cluster marker genes. Numerous tissue types were identified at the molecular level, including blood cells and zooid tissues such as the branchial epithelium, stomach, and endostyle. Distinct cluster markers were identified for specific regions of the stomach epithelium, highlighting the specialization of these regions and the strength of using scRNA-seq to explore their functionality. Cell trajectory projections highlighted the early appearance of progenitor clusters, whereas more differentiated zooid-related tissues appeared later in the developmental path. This study provides a valuable resource for understanding the development, tissue function, and regeneration of B. diegensis. This demonstrates the power of scRNA-seq to define cell types and tissues in complex colonial organisms. Summary statementSingle-cell RNA sequencing of Botrylloides diegensis revealed cellular heterogeneity, identified 29 major cell clusters, and provided insights into tissue specialization and blastogenesis.

developmental biology↗

bioRxiv2023

Structural basis for inhibition of βFXIIa by garadacimab

FXIIa is the principal initiator of the plasma contact system and can activate both procoagulant and proinflammatory pathways. Its activity is important in the pathophysiology of Hereditary Angioedema (HAE). Here, we describe a high-resolution cryo-EM structure of the beta-chain from FXIIa ({beta}FXIIa) complexed with the Fab fragment of garadacimab. Garadacimab binds to {beta}FXIIa through an unusually long CDR-H3 that inserts into the S1 pocket in a non-canonical way. This atypical structural mechanism is likely the primary contributor in the inhibition of activated FXII proteolytic activity in HAE. Garadacimab Fab-{beta}FXIIa structure also reveals critical determinants of high-affinity binding of garadacimab to activated FXII. Structural analysis with other bonafide FXIIa inhibitors, such as benzamidine and C1-INH, reveals a conserved mechanism of {beta}FXIIa inhibition, a novel finding of this study. In summary, garadacimab Fab-{beta}FXIIa structure provides crucial insights into its mechanism of action and delineates primary and auxiliary paratopes/epitopes. This work reaffirms the benefits of cryo-EM as a primary tool to study antigen-antibody complexes in near native state, particularly where other methods have fallen short.

biochemistry↗

bioRxiv2023

Deletion of a conserved genomic region associated with adolescent idiopathic scoliosis leads to vertebral rotation in mice.

Adolescent idiopathic scoliosis (AIS) is the most common form of scoliosis, in which spinal curvature develops in adolescence, and 90% of patients are female. Scoliosis is a debilitating disease that often requires bracing or surgery in severe cases. AIS affects 2-5.2 percent of the population; however, the biological origin of the disease remains poorly understood. In this study, we aimed to determine the function of a highly conserved genomic region previously linked to AIS using a mouse model generated by CRISPR-CAS9 gene editing to knockout this area of the genome to better understand the biological cause of AIS, which we named AIS_CRM{Lambda}. We also investigated the upstream factors that regulate the activity of this enhancer in vivo, whether the spatial expression of the LBX1 protein would change with the loss of AIS-CRM function, and whether any phenotype would arise after deletion of this region. We found a significant increase in mRNA expression in the developing neural tube at E10.5, and E12.5, for not only Lbx1 but also other neighboring genes. Adult knockout mice showed vertebral rotation and proprioceptive deficits, also observed in human AIS patients. In conclusion, our study sheds light on the elusive biological origins of AIS, by targeting and investigating a highly conserved genomic region linked to AIS in humans. These findings provide valuable insights into the function of the investigated region and contribute to our understanding of the underlying causes of this debilitating disease.

genetics↗

bioRxiv2023

High-fat diet-induced obesity increases susceptibility to endogenous and ethyl carbamate-induced somatic mutagenesis

Obesity and dietary fat consumption are associated with increased risk for certain cancers. We conducted a set of experiments designed to investigate both the inherent mutagenicity of high-fat diet (HFD) and the effect of HFD exposure on sensitivity to ethyl carbamate, a known mutagen. Greater body mass in females was associated with higher frequency of Pig-a mutant erythrocytes and HFD-induced obese female mice exhibited increased sensitivity to ethyl carbamate-induced mutagenesis compared to control mice. Together, these findings indicate that HFD exposure induces both endogenously generated changes related to mutagenesis and interacts with the mutagenic effects of ethyl carbamate.

pharmacology and toxicology↗

bioRxiv2022

Stomatal density affects rice mesophyll cell size and shape and modulates a conserved pattern of cells through the leaf

The structure of the mesophyll influences how light, CO2 and water travels inside a leaf, affecting the rates of both photosynthesis and transpiration. Recent studies in wheat and Arabidopsis have shown that the structure of the mesophyll is influenced by the density and activity of stomata, consistent with the hypothesis that gas flow via stomata can modulate internal cell growth and separation to co-ordinate leaf structure and function. To investigate whether this also occurs in rice, a staple food crop for a large fraction of the worlds population, we examined mesophyll structure in rice mutants with altered stomatal density. Our data show that stomatal function modulates mesophyll structure in rice. Variation in the degree of mesophyll lobing made a major contribution to altered mesophyll structure, suggesting that modified leaf gas flux through stomata influences an aspect of cell shape directly linked to gas exchange capacity in rice. In addition, our analysis revealed a previously unreported underlying pattern in cell size, shape and axiality across layers of the rice mesophyll, which further investigation revealed is present in a range of rice species and cultivars. The potential origin and significance of this mesophyll patterning are discussed. HIGHLIGHTWe describe a previously unreported cellular pattern in rice leaves and show that it is modulated by stomata. These results shed new light on leaf structure and function.

plant biology↗

bioRxiv2022

Variation in whole-body regeneration between Botrylloides morphs and species

Regeneration is a characteristic of the animal kingdom, and regenerative capacity is limited to higher taxonomical levels. In contrast, some basal animals like urochordates maintain a unique regeneration capacity, such as undergoing whole-body regeneration (WBR), an ability not observed in other chordates. Botryllids are colonial urochordates that can recreate new bodies through WBR from solely vascular tissue within ~2 weeks. To date, some species from the botryllid family were reported to orchestrate WBR, including B. diegensis. This study provided two novel records of WBR of B. jacksonianum and B. aff. anceps along with the two distinct morphs of B. diegensis. Interestingly, B. aff. anceps executed twin-body regeneration while this was limited to one-body for B. jacksonianum and B. diegensis. Histological sections validate the formation of multiple niches during WBR. Furthermore, the process of regeneration is phenotypically more similar between B. aff. anceps and B. diegensis. In contrast, the type of WBR in B. jacksonianum is similar to vascular budding as the niches were built from the vascular epithelium without undergoing significant tissue remodelling.

developmental biology↗

bioRxiv2022

Lhx9 haploinsufficiency alters transcription in the adult mouse ovary, causing subfertility and abnormal epithelium

Understanding the molecular pathways that underpin ovarian development and function is vital for improving the research approaches to investigating fertility. Despite a significant improvement in our knowledge of molecular activity in the ovary, many questions remain unanswered in the quest to understand factors influencing fertility and ovarian pathologies such as cancer. Here we present an investigation into the expression and function of developmental transcription factor LIM Homeobox 9 (LHX9) in the adult mouse ovary. We have characterised Lhx9 expression in several cell types of the mature ovary across follicle stages. To elucidate the function of this expression, we carried out an investigation of ovarian anatomy and transcription in a Lhx9+/- knockout mouse model displaying subfertility. Despite a lack of gross anatomical differences between genotypes, RNA-sequencing found that 90 genes were differentially expressed between Lhx9+/- and Lhx9+/+ mice. Gene ontology analyses revealed a downregulation of genes with major roles in ovarian steroidogenesis and an upregulation of genes with implications for ovarian cancer. Analysis of the ovarian epithelium revealed Lhx9+/- mice have a disorganised epithelial phenotype and a significant increase in epithelial marker gene expression. These results provide an analysis of Lhx9 in the adult mouse ovary and a new candidate for fertility research and ovarian epithelial cancer. Summary sentenceLhx9 haploinsufficient mice are subfertile with altered expression of steroid genes in the adult ovary and abnormal ovarian surface epithelium.

developmental biology↗

bioRxiv2021

Identification and characterisation of Botrylloides species from Aotearoa New Zealand coasts

Ascidians are marine filter feeder primitive chordates. Botrylloides ascidians possess diverse biological abilities like whole-body regeneration (WBR), hibernation/aestivation, blastogenesis, metamorphosis, and natural chimerism. However, the absence of distinctive morphological features often makes identification problematic. Botrylloides diegensis is an ascidian that has been misidentified in previous studies and is recorded in GenBank as Botrylloides leachii due to the high morphological similarity between the sister species. More available sequences and strategies around identification would help resolve some of the confusion currently surrounding its ambiguous nature. We collected several Botrylloides samples from 7 locations around New Zealand - Dunedin, Christchurch, Picton, Nelson, Whangateau, New Plymouth and Invercargill - and barcoded the species based on Cytochrome Oxidase I, Histone 3, 18S, and 28S ribosomal RNA markers. Network and Bayesian trees confirmed the presence of three Botrylloides species: B. diegensis, B. jacksonianum, and B. aff. anceps. Additionally, morphotypes of three species were investigated regarding zooid size, area, tentacle numbers and colonial arrangement.

genetics↗

bioRxiv2021

Characterization of a novel Lbx1 loss of function mouse line

Adolescent Idiopathic Scoliosis (AIS) is the most common type of spine deformity affecting 2-3% of the population worldwide. The etiology of this disease is still poorly understood. Several GWAS studies have identified single nucleotide polymorphisms (SNPs) located near the gene LBX1 that is significantly correlated with AIS risk. LBX1 is a transcription factor with roles in myocyte precursor migration, cardiac neural crest specification, and neuronal fate determination in the neural tube. Here, we further investigated the role of LBX1 in the developing spinal cord of mouse embryos using a CRISPR-generated mouse model expressing a truncated version of LBX1 (Lbx1{Delta}). Homozygous mice died at birth, likely due to cardiac abnormalities. To further study the neural tube phenotype, we used RNA-sequencing to identify 410 genes differentially expressed between the neural tubes of E12.5 wildtype and Lbx1{Delta}/{Delta} embryos. Genes with increased expression in the deletion line were involved in neurogenesis and those with broad roles in embryonic development. Many of these genes have also been associated with scoliotic phenotypes. In comparison, genes with decreased expression were primarily involved in skeletal development. Subsequent skeletal and immunohistochemistry analysis further confirmed these results. This study aids in understanding the significance of links between Lbx1 function and AIS susceptibility.

developmental biology↗

bioRxiv2020

A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome

Tonne-Kalscheuer syndrome (TOKAS) is an X-linked intellectual disability syndrome associated with variable clinical features including craniofacial abnormalities, hypogenitalism and diaphragmatic hernia. TOKAS is caused exclusively by variants in the gene encoding the E3 ubiquitin ligase gene RLIM, also known as. Here we report identification of a novel RLIM missense variant, c.1262A>G p.(Tyr421Cys) adjacent to the regulatory basic region, which causes a severe form of TOKAS resulting in perinatal lethality by diaphragmatic hernia. Inheritance and X-chromosome inactivation patterns implicate RLIM p.(Tyr421Cys) as the likely pathogenic variant in the affected individual and within the kindred. We show that the RLIM p.(Tyr421Cys) variant disrupts both expression and function of the protein in an embryonic stem cell model. RLIM p.(Tyr421Cys) is correctly localised to the nucleus, but is readily degraded by the proteasome. The RLIM p.(Tyr421Cys) variant also displays significantly impaired E3 ubiquitin ligase activity, which interferes with RLIM function in Xist long-non-coding RNA induction that initiates imprinted X-chromosome inactivation. Our data uncover a highly disruptive missense variant in RLIM that causes a severe form of TOKAS, thereby expanding our understanding of the molecular and phenotypic spectrum of disease severity.

developmental biology↗

bioRxiv2018

Genome-wide analysis of H3K4me3 and H3K27me3 modifications throughout the mouse urogenital ridge at E11.5.

In mammals, the adrenal gland, testis and ovary arise from a common progenitor tissue known as the urogenital ridge (UGR). This small population of cells will adopt a number of different cell fates following sex determination, including forming the precursors of somatic cells (such as Sertoli and granulosa cells) and steroidogenic cells. In addition, this tissues also contains the Wolffian and Mullerian ducts that later form components of the reproductive tracts. A potential mechanism to maintain developmental plasticity of the UGR until gonad formation is through the epigenetic modification of histone proteins.\n\nIn order to provide a resource for future studies, we used chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) for two histone modifications, H3K4me3 and H3K27me3, in the E11.5 mouse UGR. These marks are both known to reflect the active, repressive or a poised chromatin state. We found that enrichment for each histone mark reflected transcriptional activity in precursor cells of the developing gonad. From the analysis of potential enhancer/regulator peak regions for DNA binding motifs, we identified several candidate transcription factors that may contribute to gonadal cell lineage specification. We additionally identified signaling pathway genes that are targeted by both chromatin modifications. Together, these datasets provide a useful resource for investigating gene regulatory networks functioning during UGR development at E11.5.

developmental biology↗

bioRxiv2017

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution.

Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. This chordate subphylum contains a particularly diverse range of reproductive methods, regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of chordate traits. To gain further insights into the evolution of the tunicate phylum, we have sequenced the genome of the colonial Stolidobranchian Botrylloides leachii.\n\nWe have produced a high-quality (90 % BUSCO genes) 159 Mb assembly, containing 82 % of the predicted total 194 Mb genomic content. The B. leachii genome is much smaller than that of Botryllus schlosseri (725 Mb), but comparable to those of Ciona robusta and Molgula oculata (both 160 Mb). We performed an orthologous clustering between five tunicate genomes that highlights sets of genes specific to some species, including a large group unique to colonial ascidians with gene ontology terms including cell communication and immune response.\n\nBy analysing the structure and composition of the conserved gene clusters, we identified many examples of multiple cluster breaks and gene dispersion, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. In addition, we investigate lineage-specific gene gain and loss within the Wnt, Notch and retinoic acid pathways. Such examples of genetic change within these highly evolutionary conserved pathways commonly associated with regeneration and development may underlie some of the diverse regenerative abilities observed in the tunicate subphylum. These results supports the widely held view that tunicate genomes are evolving particularly rapidly.

genomics↗

bioRxiv2017

Histological and haematological analysis of the ascidian Botrylloides leachii (Savigny, 1816) during whole-body regeneration

Abstract (250 words)Whole-body regeneration, the formation of an entire adult from only a small fragment of its own tissue, is extremely rare among chordates. Exceptionally, in the colonial ascidian Botrylloides leachii, a fully functional adult is formed from their common vascular system, upon ablation of all adults from the colony, in just 10 days thanks to their high blastogenetic potential. While previous studies have identified key genetic markers and morphological changes, no study has yet focused on the haematological aspects of regeneration despite the major involvement of the remaining vascular system and the contained haemocytes in this process. To dissect this process, we analysed colony blood flow patterns using time-lapse microscopy to obtain a quantitative description of the velocity, reversal pattern, and average distance travelled by haemocytes. We also observed that flows present during regeneration are powered by temporally and spatially synchronized contractions of the terminal ampullae. In addition, we revised previous studies on B. leachii haematology as well as asexual development using histological sectioning, and compared the role of haemocytes during whole-body regeneration. We found that regeneration starts with a rapid healing response characterized by blood clotting and infiltration of immunocytes, followed by increased activity of haemoblasts, recruitment of macrophage-like cells for clearing the tissues of debris, and their subsequent disappearance from the circulation concomitant with the maturation of a single regenerated adult. Overall, we provide a uniquely detailed account of the haematological properties of regenerating B. leachii colonies, providing novel lines of inquiry towards the decipherment of regeneration in chordates.

cell biology↗