Biology subjects

Rico, D.

Publications and source records attributed to Rico, D..

18 recordsLinked to original sources

bioRxiv2026

Genome mutations and environmental perturbations reshape the epigenomic topology to drive functional collapse in digital cells

Understanding how genetic and environmental perturbations drive cellular dysfunction remains a challenge. Using digital somatic cells, we evaluate the functionality of over eight thousand genomes across thousands of environments alongside systematic mutational screens. We find that environmental perturbations induce loss of function with a higher probability than point mutations. Crucially, however, most mutations causing loss of function, rather than acting as direct sequence-level damage, converge with environmental stress by triggering reorganization of the epigenomic topology. Our data suggest that loss of functionality is best understood not as cumulative damage, but as a perturbation-driven state transition within a reconfigurable epigenetic landscape

systems biology↗

bioRxiv2026

An enhancer-centric approach applied to human immune system epigenomes revealed the association of macrophage enhancers with cardiovascular disease

Complex diseases are influenced by both genetic and environmental factors. Immune cells are key mediating interactions with the environment, but the impact of genetic variation on the immune system and how it influences complex diseases is not fully understood. Moreover, most genome-wide analyses (GWAS) variants associated with complex diseases are non-coding and difficult to interpret. Here, we investigated the association of non-coding variants with immune cell enhancers. As part of BLUEPRINT and the International Human Epigenome (IHEC) consortia, we generated and analysed a comprehensive set of epigenomes for human primary immune cells, including 107 epigenomes derived from 749 ChIP-Seq experiments across 24 cell types. We identified multicell enhancer activity patterns across the genome and examined their links with non-coding variants from 518 GWAS traits. This analysis revealed 117 significant associations, including novel links between cardiovascular disease variants and macrophage-specific enhancers that regulate genes involved in lipid metabolism and immunity, such as the gene encoding for the nuclear receptor LXR-alpha (NR1H3) and many of its known target genes. Together, these data will help to better understand the influence of genetic variability in immune function and related diseases.

genomics↗

bioRxiv2026

Toward a probabilistic definition of chromatin accessible regions at the single-cell level

Understanding cis-regulatory elements (CREs) at the single cell level is fundamental to deciphering transcriptional changes during development, cell differentiation, and homeostasis. Recent studies have shown that arbitrary peak-calling thresholds complicate data interpretation and cross-study comparisons. Furthermore, due to the inherent sparsity of single-nuclei ATAC-seq (snATAC-seq) data, distinguishing between truly inaccessible regions and technical dropouts remains challenging. Our analysis of snATAC-seq experiments performed in a well-established cell line suggests that the dichotomy between accessible (open) or inaccessible (close) CREs is misleading. Thousands of accessible regions are present in a very small fraction of cells of the population but they are repeatedly identified, suggesting that they have a low accessibility or are only transiently accessible. However, depending on the detection threshold selected they could be considered as either genuine CREs or noise. To resolve this inconsistency, we propose a model where chromatin accessibility is treated as a continuum, defined by a probability of accessibility (Pa) for each accessible region across cell types and conditions. Through computational simulations, we demonstrate that snATAC-seq results can be explained by a simple "balls into bins" probability model, offering a theoretical framework for calculating Pa distributions from any snATAC-seq dataset. Furthermore, we examine how Pa distributions shift following activation of the TGF{beta} signaling pathway. This probabilistic approach removes the reliance on arbitrary thresholds and supports a more quantitative, and dynamic understanding of accessible regions function.

genomics↗

bioRxiv2025

Three-Dimensional Epigenome Roadmap of Human B-cell Differentiation Uncovers Mechanisms of Humoral Immunity and Oncogenesis

Human B-cell differentiation underlies humoral immunity, and its disruption leads to cancer, autoimmunity, and immunodeficiencies. However, the enhancer-based regulatory mechanisms governing this process remain poorly understood. To address this gap, we generated the first three-dimensional epigenomic roadmap of human B-cell differentiation in vivo. By profiling nine differentiation stages, we linked nearly half a million enhancers to their target genes through chromatin interactions, defined their activity states, and predicted bound transcription factors. We show that the acquisition of B-cell identity, distinct from common cellular processes, relies on large enhancer networks acting additively and synergistically to finely tune transcription. We further identify a 3D epigenetic priming mechanism underlying immune memory, whereby memory B cells retain primed DNA loops that enable faster responses to antigen re-exposure. Extending this roadmap to disease, we demonstrate that B-cell malignancies preserve enhancer signatures of their cell of origin while silencing distal tumor suppressor control. Finally, we uncover a previously unappreciated oncogenic mechanism in which intragenic deletions disrupt distal gene regulation via enhancer loss. Together, this resource provides a framework for understanding the genetic and epigenetic basis of humoral immunity and immune-related diseases.

genomics↗

bioRxiv2025

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

BackgroundDNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. ResultsManufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. ConclusionsThe RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

genomics↗

bioRxiv2025

PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.

Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), which enables, in the same workflow, to identify the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions and ubiquitin(-like) modified proteins. We validated PLAMseq with two well characterized proteins, RNA polymerase II and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, which study has remained elusive due to the lack of specific reagents, and found that SETDB1 binds to SUMOylated histone H1.2 and H1.4 which also colocalize with H3K9me3 at repetitive regions of the genome.

molecular biology↗

bioRxiv2024

Breastmilk IgG engages the neonatal immune system to instruct host-microbiota mutualism

Maternal antibodies fundamentally regulate infant immunity to the developing gut microbiota, yet the mechanisms underlying this process remain elusive. Here, we show that maternal IgG, ingested in the first week of life, functions to restrain microbiota-dependent adaptive immune responses and reduce offspring susceptibility to intestinal inflammation weeks later, following weaning. To exert these functions, efficient binding of IgG to gut bacterial antigens and engagement of Fc and complement dependent effector functions in offspring was required. These discoveries reveal a novel mechanism wherein maternal IgG engages the offspring immune system to calibrate responses to gut microbes. This mode of maternal immune instruction may provide adaptability to developmental shifts in microbiota necessary for establishing host-microbiota mutualism and limiting susceptibility to inflammatory disease. One sentence abstractIngestion of maternal IgG during a discrete postnatal window calibrates neonatal immunity to the gut microbiota.

immunology↗

bioRxiv2023

The discovery of an evolutionarily conserved enhancer within the MYEOV locus suggests an unexpected role for this non-coding region in cancer

The myeloma overexpressed gene (MYEOV) has been proposed to be a proto-oncogene due to high RNA transcript levels found in multiple cancers, including myeloma, breast, lung, pancreas and esophageal cancer. The presence of an open reading frame (ORF) in humans and other primates suggests protein-coding potential. Yet, we still lack evidence of a functional MYEOV protein. It remains undetermined how MYEOV overexpression affects cancerous tissues. In this work, we show that MYEOV has originated and may still function as an enhancer, possibly regulating CCND1. Firstly, MYEOV 3 end enhancer activity was confirmed in humans using publicly available ATAC-STARR-seq data, performed on B-cell-derived GM12878 cells. We detected enhancer histone marks H3K4me1 and H3K27ac overlapping MYEOV in multiple healthy human tissues, which include B cells, liver and lung tissue. The analysis of 3D genome datasets revealed chromatin interactions between the MYEOV-3-enhancer and the proto-oncogene CCND1. BLAST searches and multi-sequence alignments results showed that this human enhancer element is conserved from the amphibians/amniotes divergence, with a 273 bp conserved region also found in all mammals, and even in chickens, and it consistently located near the corresponding CCND1 orthologues. Furthermore, we observed conservation of active enhancer state in the MYEOV orthologues of four non-human primates, dog, rat and mouse. When studying this homologous region in mice, where the ORF of MYEOV is absent, we not only observed an enhancer chromatin state but also found interactions between the mouse enhancer homolog and Ccnd1 using 3D-genome interaction data. This is similar to the interaction observed in humans and, interestingly, coincides with CTCF binding sites in both species. Taken together, this suggests that MYEOV is a primate-specific gene with a de novo ORF that originated at an evolutionarily older enhancer region. This deeply conserved enhancer element is possibly regulating CCND1 in both humans and mice, opening the possibility of studying MYEOV regulatory functions in cancer using non-primate animal models.

genomics↗

bioRxiv2023

Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation

Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where particular combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognise trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me3 during mitosis. We find that H3K4me3 hinders adjacent H3T3ph deposition in cells, and that the PHD domain of TAF3 can bind H3K4me3 in mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.

cell biology↗

bioRxiv2022

Esearch3D: Propagating gene expression in chromatin networks to illuminate active enhancers

Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. Currently, enhancer-associated features such as histone modifications, co-activators or bi-directional transcription are used in lieu of any definitive and universal enhancer feature. We present Esearch3D, a new approach that leverages network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D-genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bi-directional CAGE-seq, STARR-seq, P300 and RNA polymerase II ChIP-seq, and expression quantitative trait loci (eQTL). Esearch3D successfully leverages the relationship between chromatin architecture and global transcription and represents a novel approach to predict active enhancers and understand the complex underpinnings of regulatory networks. The method is available at: https://github.com/InfOmics/Esearch3D.

bioinformatics↗

bioRxiv2021

Vertebrate whole genome duplications shaped the current 3D genome architecture

Topologically associated domains (TADs) are interaction sub-networks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localise by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localisation patterns between the genes born during vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggests that TADs could play a role in organising ancestral functions and evolutionary novelty. HighlightsO_LITADs coincide with clusters of genes that are close in their evolutionary age. C_LIO_LIWhole genome duplications mark a transition in gene age co-localisation clusters. C_LIO_LIGene age co-localisation patterns are associated with TAD insulation. C_LIO_LIYoung essential genes share TADs and interact with old genes. C_LI

genomics↗

bioRxiv2021

High-resolution simulations of chromatin folding at genomic rearrangements in malignant B-cells provide mechanistic insights on proto-oncogene deregulation

Genomic rearrangements are known to result in proto-oncogene deregulation in many cancers, but the link to genome 3D structure remains poorly understood. Here we used the highly-predictive heteromorphic polymer (HiP-HoP) model to predict chromatin conformations at the proto-oncogene CCND1 in healthy and malignant B-cells. After confirming that the model gives good predictions of Hi-C data for the non-malignant human B-cell derived cell line GM12878, we generated predictions for two cancer cell lines, U266 and Z-138. These possess genome rearrangements involving CCND1 and the immunoglobulin heavy chain locus (IGH), which we mapped using targeted genome sequencing. Our simulations showed that a rearrangement in U266 cells where a single IGH super-enhancer is inserted next to CCND1 leaves the local topologically associated domain (TAD) structure intact. We also observed extensive changes in enhancer-promoter interactions within the TAD, suggesting that it is the downstream chromatin remodelling which gives rise to the oncogene activation, rather than the presence of the inserted super-enhancer DNA sequence per se. Simulations of the IGH-CCND1 reciprocal translocation in Z-138 cells revealed that an oncogenic fusion TAD is created, encompassing CCND1 and the IGH super-enhancers. We predicted how the structure and expression of CCND1 changes in these different cell lines, validating this using qPCR and fluorescence in situ hybridization microscopy. Our work demonstrates the power of polymer simulations to predict differences in chromatin interactions and gene expression for different translocation break-points.

genomics↗

bioRxiv2020

Epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking

Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B-cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterised the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B-cell (MAF, MYC and FGFR3/NSD2) and T-cell malignancies (LMO2, TLX3 and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.

genomics↗

bioRxiv2018

Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils

Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide a complete epigenetic and functional overview of their differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration of epigenetic and transcriptome dynamics reveals an enforced regulation of differentiation, through cellular functions such as: release of proteases, respiratory burst, cell cycle regulation and apoptosis. We observe an early establishment of the cytotoxic capability, whilst the signaling components that activate antimicrobial mechanisms are transcribed at later stages, outside the bone marrow, thus preventing toxic effects in the bone marrow niche. Altogether, these data reveal how the developmental dynamics of the epigenetic landscape orchestrate the daily production of large number of neutrophils required for innate host defense and provide a comprehensive overview of the epigenomes of differentiating human neutrophils.\n\nKey pointsO_LIDynamic acetylation enforces human neutrophil progenitor differentiation.\nC_LI\n\nO_LINeutrophils cytotoxic capability is established early at the (pro)myelocyte stage.\nC_LI\n\nO_LICoordinated signaling component expression prevents unwanted toxic effects to the bone marrow niche.\nC_LI

immunology↗

bioRxiv2017

Comparative analysis of neutrophil and monocyte epigenomes

Neutrophils and monocytes provide a first line of defense against infections as part of the innate immune system. Here we report the integrated analysis of transcriptomic and epigenetic landscapes for circulating monocytes and neutrophils with the aim to enable downstream interpretation and functional validation of key regulatory elements in health and disease. We collected RNA-seq data, ChIP-seq of six histone modifications and of DNA methylation by bisulfite sequencing at base pair resolution from up to 6 individuals per cell type. Chromatin segmentation analyses suggested that monocytes have a higher number of cell-specific enhancer regions (4-fold) compared to neutrophils. This highly plastic epigenome is likely indicative of the greater differentiation potential of monocytes into macrophages, dendritic cells and osteoclasts. In contrast, most of the neutrophil-specific features tend to be characterized by repressed chromatin, reflective of their status as terminally differentiated cells. Enhancers were the regions where most of differences in DNA methylation between cells were observed, with monocyte-specific enhancers being generally hypomethylated. Monocytes show a substantially higher gene expression levels than neutrophils, in line with epigenomic analysis revealing that gene more active elements in monocytes. Our analyses suggest that the overexpression of c-Myc in monocytes and its binding to monocyte-specific enhancers could be an important contributor to these differences. Altogether, our study provides a comprehensive epigenetic chart of chromatin states in primary human neutrophils and monocytes, thus providing a valuable resource for studying the regulation of the human innate immune system.

genomics↗

bioRxiv2017

Widespread population variability of intron size in evolutionary old genes: implications for gene expression variability

Introns can be extraordinarily large and they account for the majority of the DNA sequence in human genes. However, little is known about their population patterns of structural variation and their functional implication. By combining the most extensive maps of CNVs in human populations, we have found that intronic losses are the most frequent copy number variants (CNVs) in protein-coding genes in human, with more than 12,986 intronic deletions, affecting 4,147 genes (including 1,154 essential genes and 1,638 disease-related genes). These intronic length variation results in dozens of genes showing extreme population variability in size, with 40 genes with 10 or more different sizes and up to 150 allelic sizes. Intronic losses are frequent in evolutionarily ancient genes that are highly conserved at the protein sequence level. This result contrasts with losses overlapping exons, which are observed less often than expected by chance and almost exclusively affect primate-specific genes. An integrated analysis of CNVs and RNA-seq data showed that intronic loss can be associated with significant differences in gene expression levels in the population (CNV-eQTLs). These intronic CNV-eQTLs regions are enriched for intronic enhancers and can be associated with expression differences of other genes showing long distance intron-promoter 3D interactions. Our data suggests that intronic structural variation of protein-coding genes can exert an important role in maintaining the variability of gene expression and splicing in human populations.\n\nAuthor SummaryMost human genes have introns that have to be removed after a gene is transcribed from DNA to RNA because they not encode information to translate RNA into proteins. As mutations in introns do not affect protein sequences, they are usually ignored when looking for normal or pathogenic genomic variation. However, introns comprise about half of the human non-coding genome and they can have important regulatory roles. We show that deletions of intronic regions appear more frequent than previously expected in the healthy population, with a significant proportion of genes with evolutionary ancient and essential functions carrying them. This finding was very surprising, as ancient genes tend to have high conservation of their coding sequence. However, we show that deletions of their non-coding intronic sequence can produce considerable changes in their locus length. We found that a significant number of these intronic deletions are associated with under- or over-expression of the affected genes or distant genes interacting in 3D. Our data suggests that the frequent gene length variation in protein-coding genes resulting from intronic CNVs might influence their regulation in different individuals.

genomics↗

bioRxiv2016

Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types

BackgroundA healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.\n\nResultsWe applied a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16- monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naive T cells, from the same 125 healthy individuals. We discovered substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression were found to be implicated in key immune pathways and to associate with cellular properties and environmental exposure. We also observed increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites were enriched at dynamic chromatin regions and active enhancers.\n\nConclusionsOur data highlight the importance of transcriptional and epigenetic variability for the neutrophils key role as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability.

molecular biology↗

bioRxiv2016

Searching for the chromatin determinants of human hematopoiesis

Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify forty-two human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet

genomics↗