A5043261082- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Estrogen and related hormone effects
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Ubiquitin and proteasome pathways
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- PARP inhibition in cancer therapy
- Reproductive System and Pregnancy
- DNA Repair Mechanisms
- Protein Degradation and Inhibitors
- Genomic variations and chromosomal abnormalities
- Endometriosis Research and Treatment
- RNA and protein synthesis mechanisms
- Scientific Computing and Data Management
- Research Data Management Practices
- Cytokine Signaling Pathways and Interactions
- Chemokine receptors and signaling
- RNA Interference and Gene Delivery
- Hippo pathway signaling and YAP/TAZ
- CRISPR and Genetic Engineering
- Endometrial and Cervical Cancer Treatments
- Cancer Cells and Metastasis
- Retinoids in leukemia and cellular processes
Center for Genomic Science
2025
Barcelona Institute for Science and Technology
2016-2024
Centre for Genomic Regulation
2013-2023
Universitat Pompeu Fabra
2012-2022
Institute of Science and Technology
2017
Ferioli & Gianotti (Italy)
2017
Centro Nacional de Análisis Genómico
2014
Centre National de la Recherche Scientifique
2007-2011
Institut de Recherche en Santé, Environnement et Travail
2011
Université de Rennes
2007-2011
The human genome is segmented into topologically associating domains (TADs), but the role of this conserved organization during transient changes in gene expression not known. Here we describe distribution progestin-induced chromatin modifications and transcriptional activity over TADs T47D breast cancer cells. Using ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing), Hi-C (chromosome capture followed by three-dimensional (3D) modeling techniques, found that...
Key nuclear processes in eukaryotes, including DNA replication, repair, and gene regulation, require extensive chromatin remodeling catalyzed by energy-consuming enzymes. It remains unclear how the ATP demands of such are met response to rapid stimuli. We analyzed this question context massive regulation changes induced progestins breast cancer cells found that is generated cell nucleus via hydrolysis poly(ADP-ribose) ADP-ribose. In presence pyrophosphate, ADP-ribose used pyrophosphatase...
Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA (RNA-seq), immunoprecipitation (ChIP-seq) CCCTC-binding factor (CTCF) meiotic cohesins, coupled with confocal super-resolution microscopy. Spermatogonia presents well-defined...
Eukaryotic gene regulation implies that transcription factors gain access to genomic information via poorly understood processes involving activation and targeting of kinases, histone-modifying enzymes, chromatin remodelers chromatin. Here we report progestin in breast cancer cells requires a rapid transient increase poly-(ADP)-ribose (PAR), accompanied by dramatic decrease cellular NAD could have broad implications cell physiology. This nuclear PARylation is mediated PAR polymerase PARP-1...
CXCR4 and CXCR7 are the two receptors for chemokine CXCL12, a key mediator of growth effect estrogens (E2) in estrogen receptor (ER)-positive breast cancers. In this study we examined E2-regulation CXCL12 axis components their involvement cancer cells. were differentially regulated by E2 which enhanced expression both but repressed CXCR7. Formaldehyde-associated isolation regulatory elements (FAIRE) revealed that E2-mediated transcriptional regulation these genes is linked to control...
A close chromatin conformation precludes gene expression in eukaryotic cells. Genes activated by external cues have to overcome this repressive state locally changing structure a more open state. Although much is known about hormonal activation, how basal repression of regulated genes targeted the correct sites throughout genome not well understood. Here we report that breast cancer cells, unliganded progesterone receptor (PR) binds genomic and targets complex containing HP1γ...
Lamins (A/C and B) are major constituents of the nuclear lamina (NL). Structurally conserved lamina-associated domains (LADs) formed by genomic regions that contact NL. also found in nucleoplasm, with a yet unknown function. Here we map genome-wide localization lamin B1 an euchromatin-enriched fraction mouse genome follow its dynamics during epithelial-to-mesenchymal transition (EMT). Lamin associates actively expressed open euchromatin regions, forming dynamic B1-associated (eLADs) about...
In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which transcription is coordinately regulated in response to steroid hormones. Here we further describe that responsive TADs contain 20- 100-kb-long clusters of intermingled estrogen receptor (ESR1) and progesterone (PGR) binding sites, hereafter called hormone-control regions (HCRs). T47D identified more than 200 HCRs, are frequently bound by unliganded ESR1 PGR. These HCRs...
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet impact genome reshuffling this organization remains unclear. Here, we take advantage chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis crossover events to study how higher-order chromatin recombination landscapes are affected by chromosomal fusions mammalian germ line. We demonstrate that alter nuclear architecture during meiosis,...
Highlights•PADI2 citrullinates arginine1810 (cit1810) at CTD of RNA polymerase II (RNAP2)•PADI2 and R1810 regulate transcription proliferation breast cancer cells•Absence cit1810 leads to RNAP2 accumulation proximal promoter regions•Cit1810 facilitates interaction with P-TEFb complexSummaryThe post-translational modification key residues the C-terminal domain (RNAP2-CTD) coordinates transcription, splicing, processing by modulating its capacity act as a landing platform for variety protein...
The three-dimensional conformation of genomes is an essential component their biological activity. advent the Hi-C technology enabled unprecedented progress in our understanding genome structures. However, subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed remove those biases, but issue abnormal karyotypes received little attention. Many experiments are performed cancer cell lines, which typically harbor large-scale copy number...
Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization dynamically modulated to permit rapid and transient changes in response environmental challenges remains unclear. Here we show that hyperosmotic stress disrupts different levels organization, ranging from A/B compartment reduction number insulation topologically associating domains (TADs). Concomitantly, transcription greatly affected, TAD borders weaken, RNA Polymerase II...
Abstract Up to seven members of the histone H1 family may contribute chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down multiple variants deregulates many genes, promotes appearance genome-wide accessibility sites triggers an interferon response via activation heterochromatic repeats. However, how these changes expression profile relate re-distribution as well genome conformational have not been yet studied. Here, we combined ChIP-seq five...
Steroid hormones regulate gene expression by interaction of their receptors with hormone responsive elements (HREs) and recruitment kinases, chromatin remodeling complexes, coregulators to target promoters. Here we show that in breast cancer cells the BAF, but not closely related PBAF complex, is required for progesterone induction several genes including MMTV, where it catalyzes localized displacement histones H2A H2B subsequent NF1 binding. PCAF also needed acetylates histone H3 at K14, an...
Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha PR), are major determinants in the development progression of endometrial carcinomas, However, precise mechanism action role other transcription factors involved not entirely clear. Using Ishikawa cancer cells, we report that E2 treatment exposes a set progestin-dependent PR binding sites which include both progestin target genes. ChIP-seq results from hormone-treated cells revealed non-random distribution PAX2...
ABSTRACT Ewing sarcoma (ES) is an aggressive bone and soft tissue neoplasm characterized by EWSR1/ETS rearrangements whose cellular origin remains unclear. EWS-FLI1 expression in human pediatric mesenchymal stem cells (hpMSCs) induces a quantitatively qualitatively different transcriptional response than its adult MSCs (haMSCs), but fails to form tumors vivo . ES have early developmental lineage signatures distinct from postnatal MSCs. Here, we generated experimental teratomas out of...
Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes cancer and a major bladder tumor suppressor. Little known about how its inactivation contributes to tumorigenesis. Here, we analyze genomic distribution perform loss-of-function experiments using RT112 cells; then effects by integrating gene expression chromatin interaction data. Functional compartmentalization between cohesin complexes: cohesin-STAG2 displays distinctive mediates short...