Juan M. Vaquerizas

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

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

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

This study creates a single-nucleus multiomic and spatial atlas of human spermatogenesis, linking gene regulatory networks to infertility-associated genetic variation and disease perturbations.

Temporally distinct CDX programmes preconfigure vagal and trunk neural crest

The paper identifies temporally distinct CDX-driven regionalisation events that preconfigure vagal and trunk neural crest identities in mouse embryos.

Convergent evolution of cluster-wide Hox gene regulation in Bilateria

The paper identifies a conserved global control region for Hox gene regulation in annelids and shows convergent evolution of cluster-wide regulatory mechanisms in vertebrates and spiralians.

Spermatogonial stem cells and their differentiation roadmap throughout marmoset development

This study identifies transcriptional states and regulators of spermatogonial stem cell differentiation in marmoset testes across developmental stages.

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

This study reconstitutes Drosophila chromatin architecture in a cell-free system, revealing spontaneous formation of long-range interactions and TADs.

LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis

This study shows that LBR and LAP2 tether heterochromatin to the nuclear periphery, and their loss disrupts genome homeostasis by repositioning heterochromatin and altering gene expression.

Global re-organisation of genome architecture at the transition to gametogenesis

This study reveals a unique 3D genome architecture in premeiotic gonadal germ cells, linked to epigenetic reprogramming and loss of TADs, alongside DNA demethylation.

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

This study investigates how PRC2 depletion in AML affects epigenomic and transcriptional changes, revealing altered chromatin accessibility, H3K27me3 levels, and gene expression patterns that impact cell phenotype and treatment response.

Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes

This study identifies H3K27ac as an epigenetic barrier to reprogramming-induced cell fate changes using an AI-based approach and shows that reducing H3K27ac improves reprogramming efficiency.

Genome-wide DNA methylation changes in human spermatogenesis

This study identifies genome-wide DNA methylation changes during human spermatogenesis and their disruption in disturbed spermatogenesis, highlighting hypomethylation at specific regions and transposable elements.

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

The paper shows PBK/TOPK phosphorylates Ikaros, Aiolos, and CTCF to displace them from mitotic chromosomes, altering chromatin accessibility at specific zinc finger protein sites.

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

The paper uses scRNA-seq to study NR2E3 mutations in mouse retinas, identifying hybrid photoreceptors and their role in disease.

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

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

This study characterizes zebrafish transposable elements (TEs) using bulk and single-cell RNA sequencing, revealing their dynamic genomic distribution and spatiotemporal expression patterns during embryogenesis.

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

SSIM can robustly identify changes in 3D genome conformation maps

The paper confirms that SSIM depends on Hi-C matrix properties and provides improved methods for identifying differential 3D genome conformation.

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

The paper shows that 3D chromatin organisation and gene regulation are independent during Drosophila dorsoventral patterning, with chromatin structure maintaining consistency across tissues despite differences in gene expression.

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

FAN-C simplifies Hi-C data analysis by providing a comprehensive tool with matrix generation, analysis, and visualization capabilities, compatible with common Hi-C formats.

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

The paper shows zebrafish primordial germ cells use germ plasm in two phases to regulate transcriptome divergence from somatic cells through post-transcriptional mechanisms and chromatin changes.

Cohesin disrupts polycomb-dependent chromosome interactions

The paper shows cohesin disrupts polycomb-dependent chromosomal interactions to regulate gene repression in embryonic stem cells.

Transposable elements drive reorganisation of 3D chromatin during early embryogenesis

Hi-C in 2-cell-like mouse cells ties MERVL retroelement transcription to transient insulating domain boundaries, with insertions differing between strains, placing retroelements at the origin of embryonic genome architecture.

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

The paper introduces Low-C, a low-input Hi-C method, demonstrating its reproducibility and application in analyzing chromatin conformation in primary B-cells from a lymphoma patient.

A comprehensive manually-curated Compendium of Bovine Transcription Factors

The paper curates a list of 865 bovine transcription factors and analyzes their domain families, conservation, and tissue-specific expression.