A5001055945- Chromatin Remodeling and Cancer
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- Cancer-related molecular mechanisms research
- Protein Degradation and Inhibitors
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Fibromyalgia and Chronic Fatigue Syndrome Research
- School Health and Nursing Education
- Plant Virus Research Studies
- Health, psychology, and well-being
- Advanced biosensing and bioanalysis techniques
- Cancer Mechanisms and Therapy
- Acute Myeloid Leukemia Research
- Environmental and Sediment Control
- Human Health and Disease
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Pluripotent Stem Cells Research
- Cancer-related gene regulation
- Biochemical and Molecular Research
Centre for Genomic Regulation
2020-2025
University of Parma
2012-2024
Of the ∼1.3 million Alu elements in human genome, only a tiny number are estimated to be active transcription by RNA polymerase (Pol) III. Tracing individual loci from which transcripts originate is complicated their highly repetitive nature. By exploiting RNA-Seq data sets and unique DNA sequences, we devised bioinformatic pipeline allowing us identify Pol III-dependent of elements. When applied ENCODE transcriptomes seven cell lines, this search strategy identified ∼1300 corresponding...
Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert stem cells (ESCs) 2C-like cells. This conversion is marked by a global reorganization and dispersion H3K9me3-heterochromatin foci, which then reversibly formed upon re-entry into pluripotency. By profiling chromatin-bound...
Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment in mice, we generated an inducible system to convert stem cells (ESCs) 2C-like cells. This conversion is marked by a global reorganization and dispersion H3K9me3-heterochromatin foci, which then reversibly formed upon re-entry into pluripotency. By profiling...
Cellular phenotypic heterogeneity is an important hallmark of many biological processes and understanding its origins remains a substantial challenge. This often reflects variations in the chromatin structure, influenced by factors such as viral infections cancer, which dramatically reshape cellular landscape. To address challenge identifying distinct cell states, we developed artificial intelligence nucleus (AINU), deep learning method that can identify specific nuclear signatures at...
Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B lymphocytes, leads to the generation bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits nuclei a multipotent state. Interrogation regulatory network gene expression signatures identifies 8 candidate master regulator proteins. Of these candidates,...
Embryo size, specification, and homeostasis are regulated by a complex gene regulatory signaling network. Here we used expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse engineer an mESC We identify NKX1-2 as novel master regulator preimplantation embryo development. find that Nkx1-2 inhibition reduces nascent RNA synthesis, downregulates genes controlling ribosome biogenesis, translation, transport, induces severe alteration nucleolus structure,...
An opaque biochemical definition, an insufficient functional characterization, interpolated database description, and a beautiful 3D structure with wrong reaction. All these are elements of exemplar case misannotation in biological databases confusion the scientific literature concerning genes enzymes acting on ureidoglycolate, intermediate purine catabolism. Here we show evidence for relocation assigned to EC 3.5.3.19 (ureidoglycolate hydrolase, releasing ammonia), such as allA Escherichia...
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% the human genome and one most numerous family potential targets for RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while issue expression has not been extensively addressed. We applied dedicated bioinformatic pipeline ENCODE RNA-Seq datasets seven cell lines and, first...
Fibromyalgia (FM) has been explained as a result of gene-environment interactions. The present study aims to verify DNA methylation differences in eleven candidate genome regions previously associated FM, evaluating patterns potential disease biomarkers. was analyzed through bisulfite sequencing, comparing 42 FM women and their healthy sisters. associations between the level these were further explored network analysis. Lastly, logistic regression model investigated potentially with when...
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate RNAs, represent the most numerous non-coding (ncRNA) gene family in human genome. is generally kept extremely low levels tight epigenetic silencing, but it has been reported increase under different types of cell perturbation, such as viral infection and cancer. being able act expression modulators, may be directly involved mechanisms determining cellular behavior perturbed states. To...
Abstract Objectives The present pilot study aims to investigate DNA methylation changes of genes related fibromyalgia (FM) development and its main comorbid symptoms, including sleep impairment, inflammation, depression other psychiatric disorders. Epigenetic modifications might trigger or perpetuate complex interplay between pain transduction/transmission, central processing experienced stressors in vulnerable individuals. Methods We conducted analysis by targeted bisulfite NGS sequencing...
SINE retrotransposons of the Alu subfamily are most numerous active mobile DNA elements in human genome. transcription by RNA polymerase III is subjected to tight epigenetic silencing, but activated response viral infection, genotoxic anticancer agents and other stimuli, through uncharacterized switches interspersed throughout The elucidation roles cell biology pathology has long been hampered difficulties their profiling at single-locus resolution, due repetitive nature. We recently found...
Abstract Alu retrotransposons, which form the largest family of mobile DNA elements in human genome, have recently come to attention as a potential source regulatory novelties, most notably by participating enhancer function. Even though transcription RNA polymerase III is subjected tight epigenetic silencing, their expression has long been known increase response various types stress, including viral infection. Here we show that, primary fibroblasts, adenovirus small e1a triggered...
Abstract In the last two decades, we have witnessed an impressive crescendo of non-coding RNA studies, due to both development high-throughput RNA-sequencing strategies and ever-increasing awareness involvement newly discovered ncRNA classes in complex regulatory networks. Together with excitement for possibility explore previously unknown layers gene regulation, these advancements led realization need shared criteria data collection analysis novel integrative perspectives tools aimed at...
Abstract Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert stem cells (ESCs) 2C-like cells. This conversion is marked by a global reorganization and dispersion H3K9me3-heterochromatin foci, which then reversibly formed upon re-entry into pluripotency. By profiling...
Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert stem cells (ESCs) 2C-like cells. This conversion is marked by a global reorganization and dispersion H3K9me3-heterochromatin foci, which then reversibly formed upon re-entry into pluripotency. Profiling chromatin-bound...
Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert stem cells (ESCs) 2C-like cells. This conversion is marked by a global reorganization and dispersion H3K9me3-heterochromatin foci, which then reversibly formed upon re-entry into pluripotency. Profiling chromatin-bound...