Biology subjects

Vaquerizas, J. M.

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

At least 19 recordsLinked to original sources

bioRxiv2026

Locus-specific spatial and transcriptional dynamics direct T cell lineage choice in the thymus

Decades of investigation have made the choice between CD4 and CD8 T cell lineages in the thymus a key paradigm for mammalian cell commitment and differentiation, yet how transcriptional diversification is coordinated with 3D genome organisation remains largely unexplored. Here, using single-molecule transcript quantification and region capture Pico-C (RCPC), we resolve distinct transcriptional and spatial chromatin dynamics at the lineage-defining loci Cd4 and Cd8. We find early Cd4/Cd8 transcriptional divergence driven by MHC-dependent bias in Cd8a transcript copy number, which unfolds gradually across both CCR7- and CCR7+ differentiation stages. Unexpectedly, Cd4 and Cd8 loci show fundamentally different spatial contact dynamics: transiently reduced mesoscale (10-100kb) contacts at Cd8 provide a permissive chromatin environment throughout the transcriptional diversification process. By contrast, Cd4 undergoes switch-like contact changes limited to the microscale (1kb) late in differentiation, associated with lineage stabilization by ThPOK and/or RUNX3. These results place distinct, locus-specific chromatin environments at the centre of transcriptional diversification during T cell lineage choice.

genetics↗

bioRxiv2026

A single-nucleus multiomic and spatial atlas of gene regulation in human spermatogenesis

Gametogenesis, the production of oocytes and sperm, ensures the faithful transmission of genetic material to the next generation. In males, spermatogenesis occurs within the testis, where germ cells progress through a highly ordered developmental programme in close association with supporting somatic cells. Defects in this process cause infertility, yet the gene regulatory mechanisms coordinating normal and dysfunctional human spermatogenesis remain incompletely defined. Here we generate a single-nucleus multiomic and spatial atlas of human spermatogenesis by profiling chromatin accessibility and gene expression in the same nuclei and integrating these data with spatial transcriptomics of intact testicular tissue. We infer high-confidence gene regulatory networks that resolve stage-specific activity of known and novel candidate regulators across germline and somatic compartments, and map spatially restricted signalling interactions within the seminiferous tubule niche. Integration with infertility-associated genetic variation links non-coding risk loci to candidate enhancers and target genes in cell-type-specific regulatory contexts. Finally, profiling clinical cryptozoospermia samples as in vivo perturbations supports the ability of this network to capture downstream transcriptional consequences of disease-associated regulatory disruption. Together, these data provide a spatially resolved regulatory framework for human spermatogenesis and a foundation for interpreting the molecular basis of male infertility.

genomics↗

bioRxiv2026

Temporally distinct CDX programmes preconfigure vagal and trunk neural crest

Neural crest cells (NCCs) are progenitor cells vital in establishing the head, heart, gut and peripheral nervous system of vertebrate embryos. Disruptions to NCC development underlie neurocristopathies, which constitute a wide array of congenital anomalies. Yet how NCCs acquire defined regional identities that enable them to generate distinct derivatives along the body axis remains unclear. Here, we identify an epiblast progenitor population in mouse embryos that transiently contributes to vagal neural crest cells and trunk-to-tail derivatives. Using single-cell spatial transcriptomics across successive stages of neural crest migration, we generate a cervicothoracic cell atlas that resolves vagal and trunk neural crest cells in situ. Combining in vivo lineage tracing with in vitro models of neural crest induction, we show that despite transiently sharing a lineage, vagal and trunk neural crest arise through separate mechanisms. Temporally discrete regionalisation events mediated by CDX transcription factors establish HOX states that define vagal versus trunk identity. These findings revise models of NCC formation by demonstrating that temporally separate epiblast regionalisation events preconfigure neural crest and neural progenitor identities. More broadly, the results suggest that primary regionalisation events coordinately govern multiple cell lineages at the cervicothoracic transition, with implications for understanding neurocristopathies involving combined enteric and trunk derivatives.

developmental biology↗

bioRxiv2026

Convergent evolution of cluster-wide Hox gene regulation in Bilateria

The anteroposterior collinear expression of Hox genes is a hallmark of animal development that underpins the diversification of body plans1 and life cycles2. However, the origin and drivers of this coordinated expression remain elusive: while vertebrates rely on complex cluster-wide Hox gene regulation3-8, insects define gene-specific, sub-cluster regulatory domains9-11. Here, we discover a new mode of Hox gene regulation in segmented worms (Annelida). By combining chromatin conformation data with histone modifications profiling in Owenia fusiformis, we show that a large distal enhancer forms developmentally regulated, long-range contacts across the Hox cluster, and its activation coincides with the consolidation of a cluster-wide topologically associating domain (TAD), loss of Polycomb-mediated repression, and Hox gene transcription. This chromatin structure also occurs in the annelids Dimorphilus gyrociliatus and Capitella teleta, the latter showing additional subTAD structures that correlate with Hoxs temporal collinearity12. Moreover, related phyla with intact, organised Hox clusters and spatial collinearity, such as nemerteans and chitons, show annelid-like chromatin organisations, whereas phyla with disorganised13 Hox clusters do not. Coordinated Hox gene regulation from a "global control region" is thus ancestral to Lophotrochozoa, indicating that complex regulatory logics based on cluster-wide, long-range chromatin interactions with distal enhancers evolved convergently in vertebrates and spiralians.

developmental biology↗

bioRxiv2026

Spermatogonial stem cells and their differentiation roadmap throughout marmoset development

Sperm transfer genetic information from one generation to the next. These cells originate from gonocytes, which are specified during early embryonal development. To date however, there is limited information on the transcriptional gatekeepers governing the key events leading to sperm production: transition of gonocytes out of pluripotency around the time of birth, formation of the spermatogonial compartment prior to puberty, and initiation of germ cell differentiation at the time of puberty. We address this knowledge gap by employing the marmoset monkey (Callithrix jacchus) as a model for human postnatal testicular development. We analysed the transcriptional profiles of [~]48,000 neonatal, pre-pubertal, pubertal, and adult testicular cells and correlated these with histomorphometric measurements. We uncovered a transcriptional state linking gonocytes and spermatogonia characterized by CITED2 expression. Moreover, we propose NANOS2 and DPPA4 as regulators of spermatogonial plasticity from pre-puberty onwards and identify molecular gatekeepers of male germ cell differentiation.

developmental biology↗

bioRxiv2026

Self-organization of Drosophila chromatin architecture in a cell-free system

Metazoan genomes are organized by folding of the nucleosome fiber into loops and domains that support long-range regulatory interactions. Although cohesin-mediated loop extrusion and architectural DNA-binding proteins are central to current models of genome organization, how these mechanisms integrate to generate higher-order structure remains incompletely understood. Early Drosophila melanogaster embryogenesis provides a unique window into the emergence of chromatin architecture, as rapid syncytial nuclear divisions occur largely in the absence of transcription. However, probing the mechanisms underlying this primordial folding in vivo is technically challenging. Here, we establish an in vitro system that reconstitutes complex chromatin using extracts from syncytial embryos. Nucleosome mapping and Micro-C analyses reveal that long-range interactions, including loops and topologically associating domains (TADs), emerge spontaneously from soluble extract components. While some structures resemble those observed in early embryos, others represent latent interaction potentials that are constrained in vivo. Focusing on the eve locus, we find that TAD formation is incompatible with a simple loop extrusion model and instead requires direct pairing of boundary elements mediated by the insulator protein Suppressor-of-hairy-wing Su(Hw). Together, our work demonstrates that key features of 3D genome organization can be reconstituted in a cell-free system and provides a tractable platform for mechanistic dissection of chromatin folding in Drosophila.

genomics↗

bioRxiv2025

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

BackgroundPolycomb Repressive Complex 2 (PRC2) modulates chromatin accessibility and architecture to direct tissue-specific gene expression. PRC2 function is frequently altered in cancer by loss-of-function mutation or deletion, but the downstream effects on transcriptional regulation are incompletely understood. ResultsTo gain insights into these mechanisms, we performed a holistic analysis of epigenomic and transcriptional changes in an isogenic model of acute myeloid leukemia (AML) with heterozygous EZH2 deletion that mimics reduced PRC2 function in patient leukemias. PRC2-depleted cells had diverse gene expression changes, including a bias towards more immature monocyte-lineage transcriptional signatures. PRC2 depletion also correlated with marked increases in chromatin accessibility genome-wide, with 10-45% increases in ATAC-seq peaks in EZH2+/- clones. These changes were accompanied by decreased H3K27me3 and increased H3K27ac levels in CUT+RUN assays that were incompletely linked to transcriptional activity. Despite these generalised changes, 3D chromatin architecture assessed by Hi-C was largely maintained, with H3K27me3 preferentially lost in regions with low DNA-DNA contact frequency. Surprisingly, some regions gained broad H3K27me3 domains at heavily compacted chromatin. We notably saw compartmentalisation changes upstream of the transcriptionally upregulated fetal hematopoiesis gene LIN28B in EZH2+/- cells, with corresponding activation of a LIN28B-specific transcriptional program, including upregulation of the CDK6 oncogene. These results correlated with EZH2+/- cell phenotype, including decreased cellular proliferation and increased resistance to CDK6 inhibitor palbociclib. ConclusionsOur findings suggest that PRC2 depletion pleiotropically affects AML transcriptional regulation to directly impact cell phenotype and treatment responsiveness, which may partially explain the aggressive biology seen in these cases.

cancer biology↗

bioRxiv2025

Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes

The fates of differentiated cells in our body can be induced to change by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling can be produced. However, the efficiency of this process is low, partly due to properties of somatic donor nuclei which stabilize their differentiated fate but also act as barriers reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood. Here, we developed an artificial intelligence-based approach to model nuclear reprogramming and used it to identify the chromatin modification H3K27ac as an epigenetic barrier to reprogramming-induced cell fate changes. Using reprogramming by nuclear transfer (NT) to eggs of Xenopus laevis as a model system, we profiled chromatin modifications in differentiated cell types alongside gene expression patterns before and after reprogramming. Our model integrated the data and by leveraging model predictions, we find that genes resisting inactivation during reprogramming display chromatin modification barcodes. This revealed H3K27ac as a novel candidate barrier to NT reprogramming. Reducing H3K27ac levels using p300/CBP inhibitors before reprogramming led to an improved downregulation of genes linked to H3K27ac-modified enhancers after reprogramming. Importantly, these effects were accompanied by improved embryonic development of the resulting nuclear transfer embryos. In summary, our study identified H3K27ac as a safeguarding mechanism of cellular identities and as a reprogramming barrier during NT. Hence, the here-developed Digital Reprogramming" approach is capable of modelling and improving current cell-fate reprogramming strategies.

genomics↗

bioRxiv2024

PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites

PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514, revealing dynamic regulation by kinase and phosphatase activities. To identify more PBK targets, we analysed loss of mitotic phosphorylation events in Pbk-/-preB cells and performed proteomic comparisons on isolated mitotic chromosomes. Among a large pool of C2H2-zinc finger targets, PBK is essential for evicting the CCCTC-binding protein CTCF and zinc finger proteins encoded by Ikzf1, Ikzf3, Znf131 and Zbtb11. PBK-deficient cells were able to divide but showed altered chromatin accessibility and nucleosome positioning consistent with CTCF retention. Our studies reveal that PBK controls the dissociation of selected factors from condensing mitotic chromosomes and contributes to their compaction.

molecular biology↗

bioRxiv2023

Genome-wide DNA methylation changes in human spermatogenesis

Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global-decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatid-specific methylome. Hypomethylated regions in spermatids were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.

genetics↗

bioRxiv2023

Specific photoreceptor cell fate pathways are differentially altered in NR2E3-associated diseases

Mutations in NR2E3 cause two retinal dystrophies with a distinct phenotype. NR2E3 encodes an orphan nuclear transcription factor that contributes to photoreceptor cell fate determination by repressing cone while activating rod genes. To dissect NR2E3 function, we performed scRNA-seq in the retinas of wild type and two different Nr2e3 mouse models that show phenotypes similar to patients carrying NR2E3 mutations. Our results reveal that rod and cone populations are not homogeneous and can be separated into different sub- classes. We identify a previously unreported cone pathway that generates hybrid cones that co-express both cone- and rod-related genes. In mutant retinas, this hybrid cone subpopulation is more abundant, as it includes a subpopulation of rods transitioning towards a cone cell fate. Hybrid photoreceptors with high misexpression of cone- and rod-related genes are prone to regulated necrosis. Overall, our results shed light on the role of NR2E3 in modulating photoreceptor differentiation towards cone and rod fates and explain how mutations in NR2E3 lead to different visual disorders in humans. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/543550v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@bc8118org.highwire.dtl.DTLVardef@1bf5f72org.highwire.dtl.DTLVardef@11351f5org.highwire.dtl.DTLVardef@169e7df_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISMutations in the gene encoding the retinal transcription factor NR2E3 cause two different inherited retinal dystrophies: retinitis pigmentosa and enhanced S-cone syndrome. O_LIscRNA-seq in retinas of wild type and two Nr2e3 mouse models reveal that rod and cone populations are not homogeneous and can be classified into different sub-classes. C_LIO_LIA previously unreported cone pathway that generates hybrid cones co- expressing both cone- and rod-related genes is identified. C_LIO_LIHybrid photoreceptors with high misexpression of cone- and rod-related genes are prone to regulated necrosis. C_LIO_LIExpression of rod and cone signature genes change in response to different NR2E3 mutations thus providing a frame to understand the molecular basis of distinct NR2E3-associated diseases. C_LI

genetics↗

bioRxiv2021

SSIM can robustly identify changes in 3D genome conformation maps

We previously presented Comparison of Hi-C Experiments using Structural Similarity (CHESS), an approach that applies the concept of the structural similarity index (SSIM) to Hi-C matrices1, and demonstrated that it could be used to identify both regions with similar 3D chromatin conformation across species, and regions with different chromatin conformation in different conditions. In contrast to the claim of Lee et al.2 that the SSIM output of CHESS is independent of the input data, here we confirm that SSIM depends on both local and global properties of the input Hi-C matrices. We provide two approaches for using CHESS to highlight regions of differential genome organisation for further investigation, and expanded guidelines for choosing appropriate parameters and controls for these analyses.

genomics↗

bioRxiv2021

DNA motif analysis of shear stress responsive endothelial enhancers reveals differential association of KLF and ETV/ETS binding sites with gained and lost enhancers

Endothelial cells (EC) lining blood vessels are exposed to mechanical forces, such as shear stress exerted by the flowing blood. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation in addition to cell size and shape. Despite a good understanding of the genes and signaling pathways responding to shear stress, our insights into the transcriptional regulation of these responses is much more limited. In particular, we do not know the different sets of regulatory elements (enhancers) that might control increases or decreases in gene expression. Here, we set out to study changes in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 hours of laminar shear stress. Our results show a correlation of gained and lost enhancers with up- and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized shear stress responsive genes in ECs of zebrafish embryos using RNA-Seq. Together, our results reveal the presence of shear stress responsive DNA regulatory elements and lay the groundwork for the future exploration of these elements and the TFs binding to them in controlling EC biology.

genomics↗

bioRxiv2021

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

developmental biology↗

bioRxiv2021

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

genomics↗

bioRxiv2020

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

The relationship between the 3D organisation of chromatin inside the nucleus and the regulation of gene expression remains unclear. While disruption of domains and domain boundaries can lead to mis-expression of developmental genes, acute depletion of key regulators of genome organisation, such as CTCF and cohesin, and major reorganisation of genomic regions have relatively small effects on gene expression. Therefore, it is unclear whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell type-specific activation of genes and their regulatory elements. Here, using the Drosophila melanogaster dorsoventral patterning system as a model, we demonstrate the independence of 3D chromatin organisation and developmental gene regulation. We define tissue-specific enhancers and link them to expression patterns at the single-cell level using single cell RNA-seq. Surprisingly, despite tissue-specific differences in chromatin state and gene expression, 3D chromatin organisation is maintained across tissues. Our results provide strong evidence that tissue-specific chromatin conformation is not required for tissue-specific gene expression, but rather acts as an architectural framework to facilitate proper gene regulation during development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗

bioRxiv2020

FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C and its derivatives, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data (https://github.com/vaquerizaslab/fanc). Due to its comprehensiveness and compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

genomics↗

bioRxiv2020

Germ plasm localisation dynamics mark distinct phases of transcriptional and post-transcriptional regulation control in primordial germ cells

In many animal models, primordial germ cell (PGC) development depends on maternally-deposited germ plasm to avoid somatic cell fate. Here, we show that PGCs respond to regulatory information from the germ plasm in two distinct phases and mechanisms in zebrafish. We show that PGCs commence zygotic genome activation together with the rest of the embryo with no demonstrable differences in transcriptional and chromatin accessibility levels. Thus, cytoplasmic germ plasm determinants only affect post-transcriptional stabilisation of RNAs to diverge transcriptome from somatic cells, which, unexpectedly, also activate germ cell-specific genes. Perinuclear relocalisation of germ plasm is coupled to dramatic divergence in chromatin opening and transcriptome from somatic cells characterised by PGC-specific chromatin topology. Furthermore, we reveal Tdrd7, regulator of germ plasm localisation, as crucial determinant of germ fate acquisition.

developmental biology↗