Browsing by Author "Carnevali, Davide"

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  • A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features
    Carnevali, Davide; Zhong, Limei; González-Almela, Esther; Viana, Carlotta; Rotkevich, Mikhail; Wang, Aiping; Franco-Barranco, Daniel; González-Marfil, Aitor; Neguembor, Maria Victoria; Castells García, Àlvaro, 1991-; Arganda-Carreras, Ignacio; Cosma, Maria Pia (Springer, 2024)
    Cellular phenotypic heterogeneity is an important hallmark of many biological processes and understanding its origins remains a substantial challenge. This heterogeneity often reflects variations in the chromatin structure, ...
  • Alu RNA modulates the expression of cell cycle genes in human fibroblasts
    Cantarella, Simona; Carnevali, Davide; Morselli, Marco; Conti, Anastasia; Pellegrini, Matteo; Montanini, Barbara; Dieci, Giorgio (MDPI, 2019)
    Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is ...
  • DNA methylation changes in fibromyalgia suggest the role of the immune-inflammatory response and central sensitization
    Gerra, Maria Carla; Carnevali, Davide; Ossola, Paolo; González-Villar, Alberto; Pedersen, Inge Søkilde; Triñanes, Yolanda; Donnini, Claudia; Manfredini, Matteo; Arendt-Nielsen, Lars; Carrillo-de-la-Peña, Maria Teresa (MDPI, 2021)
    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 to FM, evaluating DNA ...
  • SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state
    Sebastián Pérez, Rubén; Nakagawa, Shoma; Tu, Xiaochuan; Aranda Aragón, Sergio; Pesaresi, Martina; Gómez García, Pablo; Alcoverro-Bertran, Marc; Gómez Vázquez, José Luis; Carnevali, Davide; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Martin, Laura; Nissim Rafinia, Malka; Meshorer, Eran; Neguembor, Maria Victoria; Di Croce, Luciano; Cosma, Maria Pia (eLife, 2023)
    Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin ...
  • The master regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state
    Arumugam, Karthik; Shin, William; Schiavone, Valentina; Vlahos, Lukas; Tu, Xiaochuan; Carnevali, Davide; Kesner, Jordan; Paull, Evan O.; Romo Saladrigas, Neus, 1982-; Subramanian, Prem; Worley, Jeremy; Tan, Xiangtian; Califano, Andrea; Cosma, Maria Pia, 1970- (Science Direct, 2020)
    Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, ...
  • The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development
    Nakagawa, Shoma; Carnevali, Davide; Tan, Xiangtian; Alvarez, Mariano J.; Parfitt, David-Emlyn; Di Vicino, Umberto; Arumugam, Karthik; Shin, William; Aranda, Sergi; Normanno, Davide; Sebastián Pérez, Rubén; Cannatá, Chiara; Cortes, Paola; Neguembor, Maria Victoria; Shen, Michael M.; Califano, Andrea; Cosma, Maria Pia (Elsevier, 2024)
    Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse ...
  • Transcription-mediated supercoiling regulates genome folding and loop formation
    Neguembor, Maria Victoria; Martin, Laura; Castells García, Àlvaro, 1991-; Gómez García, Pablo; Vicario, Chiara; Carnevali, Davide; Abed, Jumana AlHaj; Granados, Alba; Sebastián Pérez, Rubén; Sottile, Francesco, 1988-; Solon, Jérôme; Wu, Chao-Ting; Lakadamyali, Melike; Cosma, Maria Pia, 1970- (Elsevier, 2021)
    The chromatin fiber folds into loops, but the mechanisms controlling loop extrusion are still poorly understood. Using super-resolution microscopy, we visualize that loops in intact nuclei are formed by a scaffold of cohesin ...

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