Biology subjects

Gillis, A.

Publications and source records attributed to Gillis, A..

15 recordsLinked to original sources

bioRxiv2025

Hierarchical buffering of cellular RNA polymerase II pools maintains transcriptional homeostasis

RNA polymerase II (Pol II) abundance and transcriptional output are coordinated across diverse conditions to maintain mRNA homeostasis. To determine whether Pol II acts as a limiting factor for transcription, we combined acute perturbations with quantitative single-cell imaging and genome-wide profiling. We find that transcription remains stable across 70-180% of normal Pol II levels in human cells. This robustness emerges from hierarchical buffering mechanisms operating on distinct timescales. Within tens of minutes after monoallelic depletion of Pol II subunit POLR2A, cells maintain steady transcriptional output by drawing polymerases from a nucleoplasmic reserve pool. However, over hours, cellular Pol II holoenzyme levels also recover, driven by constitutive excess POLR2A subunit production rather than feedback sensing. Finally, strong depletion over days activates additional compensatory mechanisms. Together, these results reveal how temporal separation of buffering mechanisms provides robustness to perturbations of essential machinery, illuminating how cells maintain homeostatic control of essential complexes.

cell biology↗

bioRxiv2025

Accounting for the influence of dissimilarity gradientson community uniqueness

Compositional uniqueness has become increasingly relevant for understanding how local communities contribute to regional biodiversity. The most widely used metric is the Local Contribution to Beta Diversity (LCBD), which is typically regressed against environmental predictors. However, LCBD can vary either because of environmental processes that affect the overall variance in community composition, or because communities change directionally along environmental gradients. The latter implies that LCBD-environment relationships can strongly depend on how the environment is sampled. To address this issue, we introduce Generalised Dissimilarity Uniqueness Models (GDUM), a framework that embeds effects on community uniqueness within pairwise dissimilarity modelling. GDUMs are consistent with conventional uniqueness models, while explicitly accounting for directional changes in composition. This distinction disentangles directional and non-directional drivers of beta diversity, such as environmental filtering versus stochastic processes. By improving interpretability and generalizability, GDUM is a useful tool for understanding beta diversity patterns and projecting biodiversity responses.

ecology↗

bioRxiv2025

Evolution of Cajal-Retzius Cells in Vertebrates from an Ancient Class of Tp73+ Neurons

Evolutionary changes of cortical development were instrumental for the emergence of the mammalian neocortex. Cajal-Retzius cells, a transient neuron type discovered over a century ago, are critical players in the development of mammalian-specific cortical features such as inside-out corticogenesis. However, it is unclear whether Cajal-Retzius cells exist only in mammals, or if they are ancestral in vertebrates but acquired new functions during mammalian brain development. To trace the evolution of this cell type, we probe the presence of Cajal-Retzius cells in chicken, salamander, zebrafish, and little skate. First, through comparative transcriptomics and spatial analysis we show that Cajal-Retzius cells are conserved in vertebrates. However, only amniote Cajal-Retzius cells gained robust expression of Reelin, a secreted glycoprotein crucial for mammalian cortical development. Second, we find that Cajal-Retzius cells are part of a larger and diverse family of neuron types, and are closely related to Tp73+ external tufted cells in the olfactory bulb, which express most of the "canonical" Cajal-Retzius transcription factors. Our results indicate that Cajal-Retzius cells emerged early in vertebrate history, using a regulatory program largely shared with neurons in the olfactory system, and that transcriptomic novelties underlie their specialized roles in mammalian cortical development. This is an extreme example of how cell types may diverge in morphology and function over the course of evolution even when their core transcriptomic profile is broadly preserved.

neuroscience↗

bioRxiv2025

Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs

FoxQ2 is a highly conserved class of Forkhead-box transcription factors expressed on the anterior side of the body in cnidarians and bilaterians. Despite this conserved expression pattern, recent phylogenetic analyses have revealed a complex and rapid evolution of this class, with several taxon-specific duplications and losses. Until recently, FoxQ2 was thought to be lost in most vertebrate lineages, and its presence and localization in different vertebrate groups remains unclear. To reconcile these conflicting reports of conservation and divergence, here we present a comprehensive analysis of the phylogenetic relationships and expression patterns of FoxQ2 genes across metazoans. By combining phylogenetics and synteny analyses of FoxQ2 sequences from 21 animal phyla, we uncover the presence of three ancient FoxQ2 paralogs in bilaterians, which we name FoxQ2a, FoxQ2b and FoxQ2c. All three FoxQ2 paralogs are present in the chordate lineage and two are conserved in vertebrates, indicating a richer repertoire of vertebrate Fox genes than previously estimated. To investigate the expression of FoxQ2 genes across bilaterians, we mined expression data from existing single cell transcriptomic datasets of mollusk, acoel, amphioxus and zebrafish development, and expanded it using fluorescent in situ hybridization in amphioxus, lamprey, skate, zebrafish and chicken. Our analysis demonstrates the conserved anterior expression of FoxQ2a and FoxQ2b paralogs while also revealing a novel domain of FoxQ2c expression within the chordate endoderm, including in amphioxus, lamprey and skate. Finally, we devise a method to predict conserved transcription factor binding sites across the three extant amphioxus genera with specificity to developmental stage and cell-type identity. This suggests conserved regulatory interactions for the expression of FoxQ2a across deuterostomes. Overall, this work clarifies the complex evolutionary history of FoxQ2 genes and identifies a newly discovered endodermally-expressed Fox gene, FoxQ2c. We further propose that the early duplication of FoxQ2a and FoxQ2b, along with their redundant functions, provided the ideal background for subfunctionalization, contributing to the fast evolutionary rate of FoxQ2 sequences observed in bilaterians.

evolutionary biology↗

bioRxiv2023

The skate spiracular organ develops from a unique neurogenic placode, distinct from lateral line placodes

The spiracular organ is an epithelial pouch or tube lined with mechanosensory hair cells, found embedded in the wall of the spiracle/spiracular chamber (remnant of the first pharyngeal cleft) in many non-teleost jawed fishes. It is innervated via a branch of the anterior lateral line nerve and usually considered a specialised lateral line organ, although it most likely functions as a proprioceptor for jaw movement. It is homologous to the paratympanic organ: a hair cell-lined epithelial pouch embedded in the wall of the middle ear (which evolved from the spiracular chamber) of birds, alligators and Sphenodon. A previous fate-mapping study showed that the chicken paratympanic organ and its afferent neurons originate from a molecularly distinct placode immediately dorsal to the geniculate (first epibranchial) placode. Here, DiI fate-mapping in a cartilaginous fish (little skate, Leucoraja erinacea) shows that the spiracular organ derives from a previously unrecognised neurogenic placode immediately dorsal to the geniculate placode and molecularly distinct from lateral line placodes. These findings further support the developmental and evolutionary independence of this unique jawed-vertebrate mechanosensory organ from the lateral line system. Summary statementFate-mapping in a cartilaginous fish supports the developmental independence from the lateral line system of the mechanosensory spiracular organ, consistent with its homology with the amniote paratympanic organ.

developmental biology↗

bioRxiv2022

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

microbiology↗

bioRxiv2022

Gill developmental program in the teleost mandibular arch

Whereas no known living vertebrate possesses gills derived from the jaw-forming mandibular arch, it has been proposed that the jaw arose through modifications of an ancestral mandibular gill. Here we show that the zebrafish pseudobranch, which regulates blood pressure in the eye, develops from mandibular arch mesenchyme and first pouch epithelia and shares gene expression, enhancer utilization, and developmental gata3 dependence with the gills. Combined with work in chondrichthyans, our findings in a teleost fish point to the presence of a mandibular pseudobranch with serial homology to gills in the last common ancestor of jawed vertebrates, consistent with a gill origin of vertebrate jaws.

developmental biology↗

bioRxiv2021

The pseudobranch of jawed vertebrates is a mandibular arch-derived gill

The pseudobranch is a gill-like epithelial elaboration that sits behind the jaw of most fishes. This structure was classically regarded as a vestige of the ancestral gill-arch like condition of the gnathostome jaw. However, more recently, hypotheses of jaw evolution by transformation of a gill arch have been challenged, and the pseudobranch has alternatively been considered a specialised derivative of the second (hyoid) pharyngeal arch. Here, we demonstrate by cell lineage tracing in a cartilaginous fish, the skate (Leucoraja erinacea), that the pseudobranch does, in fact, derive from the mandibular arch, and that it shares gene expression features and cell types with gills. We also show that the mandibular arch pseudobranch is supported by a spiracular cartilage that is patterned by a shh-expressing epithelial signalling centre. This closely parallels the condition seen in the gill arches, where cartilaginous appendages called branchial rays supporting the respiratory lamellae of the gills are patterned by a shh-expressing gill arch epithelial ridge (GAER). Taken together, these findings support serial homology of the pseudobranch and gills, and an ancestral origin of gill arch-like anatomical features from the gnathostome mandibular arch.

developmental biology↗

bioRxiv2021

Wildlife in Cameroon harbor diverse coronaviruses including many isolates closely related to human coronavirus 229E

Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. SARS-CoV-2 highlights the global impact emergence events can have. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n=8) and beta (n=9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human derived HCoV-229E isolates closest to those from camels in terms of the S and N genes, but closest to isolates from bats for the E, M, and RdRp genes. The CoV RNA positivity rate in bats varied significantly (p<0.001) between the wet (8.2%) and dry season (4.5%). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.

microbiology↗

bioRxiv2020

Coronavirus surveillance in Congo basin wildlife detects RNA of multiple species circulating in bats and rodents

Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 Alpha- and 6 Beta-coronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.

microbiology↗

bioRxiv2020

Coronavirus surveillance of wildlife in the Lao People's Democratic Republic detects viral RNA in rodents

Coronaviruses can become zoonotic as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia facilitates an increased risk for such incidents. We sampled and tested rodents (851) and other mammals, and found Betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters, and relate closely to known rodent coronaviruses detected in the region, and distantly to human coronaviruses OC43 and HKU1. Considering close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks.

microbiology↗

bioRxiv2020

Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer

Whereas the gill chambers of extant jawless vertebrates (lampreys and hagfish) open directly into the environment, jawed vertebrates evolved skeletal appendages that promote the unidirectional flow of oxygenated water over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here we find that these divergent gill cover patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a Pou3f3 arch enhancer that is deeply conserved from cartilaginous fish through humans but undetectable in lampreys, with minor sequence differences in the bony versus cartilaginous fish enhancers driving the corresponding single versus multiple gill arch expression patterns. In zebrafish, loss of Pou3f3 gene function disrupts gill cover formation, and forced expression of Pou3f3b in the gill arches generates ectopic skeletal elements resembling the multiple gill cover pattern of cartilaginous fishes. Emergence of this Pou3f3 enhancer >430 mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution.

developmental biology↗

bioRxiv2019

Adult chondrogenesis and spontaneous cartilage repair in the skate, Leucoraja erinacea

Mammalian articular cartilage is an avascular tissue with poor capacity for spontaneous repair. Here, we show that embryonic development of cartilage in the skate (Leucoraja erinacea) mirrors that of mammals, with developing chondrocytes co-expressing genes encoding the transcription factors Sox5, Sox6 and Sox9. However, in skate, transcriptional features of developing cartilage persist into adulthood, both in peripheral chondrocytes and in cells of the fibrous perichondrium that ensheaths the skeleton. Using pulse-chase label retention experiments and multiplexed in situ hybridization, we identify a population of cycling Sox5/6/9+ perichondral progenitor cells that generate new cartilage during adult growth, and we show that persistence of chondrogenesis in adult skates correlates with ability to spontaneously repair cartilage injuries. Skates therefore offer a unique model for adult chondrogenesis and cartilage repair and may serve as inspiration for novel cell-based therapies for skeletal pathologies, such as osteoarthritis.

developmental biology↗

bioRxiv2019

Resegmentation is an ancestral feature of the gnathostome vertebral skeleton

The vertebral skeleton is a defining feature of vertebrate animals. However, the mode of vertebral segmentation varies considerably between major lineages. In tetrapods, adjacent somite halves recombine to form a single vertebra through the process of \"resegmentation\". However, in teleost fishes, there is considerable mixing between cells of the anterior and posterior somite halves, without clear resegmentation. To determine whether resegmentation is a tetrapod novelty, or an ancestral feature of jawed vertebrates, we tested the relationship between somites and vertebrae in a cartilaginous fish, the skate (Leucoraja erinacea). Using cell lineage tracing, we show that skate trunk vertebrae arise through tetrapod-like resegmentation, with anterior and posterior halves of each vertebra deriving from adjacent somites. We further show that tail vertebrae also arise through resegmentation, despite a duplication of the number of vertebrae per body segment. These findings resolve axial resegmentation as an ancestral feature of the jawed vertebrate body plan.

developmental biology↗

bioRxiv2017

Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales

It is almost a cliche that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae, Siphoviridae, and Podoviridae. Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae. Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.

microbiology↗