Zobrazeno 1 - 10
of 16
pro vyhledávání: '"polymer physic"'
Autor:
Andrea Esposito, Simona Bianco, Andrea M. Chiariello, Alex Abraham, Luca Fiorillo, Mattia Conte, Raffaele Campanile, Mario Nicodemi
The mammalian genome has a complex, functional 3D organization. However, it remains largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we infer from only Hi-C the cell-type-specific arrangement of DNA binding sites suffi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f1bfcba61149e223eb28dfefee690a7
http://edoc.mdc-berlin.de/21513/7/21513suppl.zip
http://edoc.mdc-berlin.de/21513/7/21513suppl.zip
Autor:
Luca Fiorillo, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Francesco Flora, Andrea Esposito, Mattia Conte, Mario Nicodemi, Francesco Musella
Publikováno v:
Methods in Molecular Biology ISBN: 9781071613894
Novel technologies revealed a nontrivial spatial organization of the chromosomes within the cell nucleus, which includes different levels of compartmentalization and architectural patterns. Notably, such complex three-dimensional structure plays a cr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8f7bd94aeec57697976d93df7a76dc09
http://hdl.handle.net/11588/863906
http://hdl.handle.net/11588/863906
Autor:
Andrea M. Chiariello, Simone Serio, Paolo Kunderfranco, Mario Nicodemi, Mattia Conte, Christina Pagiatakis, Arianna Felicetta, Silvia Crasto, Gianluigi Condorelli, Roberto Papait, Elisa Di Pasquale, Paola Cattaneo, Luca Fiorillo, Simona Bianco, Irene Salamon
Publikováno v:
iScience
iScience, Vol 23, Iss 9, Pp 101539-(2020)
iScience, Vol 23, Iss 9, Pp 101539-(2020)
Summary Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cc90309adac4284bc2deeb11cc86a92d
http://hdl.handle.net/11588/826412
http://hdl.handle.net/11588/826412
Autor:
Mario Nicodemi, Davide Marenduzzo, J. Johnson, Alexander Morozov, Davide Michieletto, Chris A. Brackley, Peter R. Cook
Publikováno v:
Nucleus
Brackley, C A, Johnson, J, Michieletto, D, Morozov, A N, Nicodemi, M, Cook, P R & Marenduzzo, D 2018, ' Extrusion without a motor : a new take on the loop extrusion model of genome organization ', Nucleus, pp. 1-10 . https://doi.org/10.1080/19491034.2017.1421825
Brackley, C A, Johnson, J, Michieletto, D, Morozov, A N, Nicodemi, M, Cook, P R & Marenduzzo, D 2018, ' Extrusion without a motor : a new take on the loop extrusion model of genome organization ', Nucleus, pp. 1-10 . https://doi.org/10.1080/19491034.2017.1421825
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9b26bd3c8f143f0766fef0dfe17d994d
Autor:
Mario Nicodemi, Andrea Esposito, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Carlo Annunziatella
Publikováno v:
Wiley Interdiscip Rev Syst Biol Med
The depth and complexity of data now available on chromosome 3D architecture, derived by new technologies such as Hi-C, have triggered the development of models based on polymer physics to explain the observed patterns and the underlying molecular fo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3c0ee7b966a964e4985cebe237651bf
http://hdl.handle.net/11588/728751
http://hdl.handle.net/11588/728751
Autor:
Mario Nicodemi, Andrea Esposito, Andrea M. Chiariello, Carlo Annunziatella, Mattia Conte, Raffaele Campanile, Luca Fiorillo, Guillaume Andrey, Antonella Prisco, Simona Bianco
Publikováno v:
Cell Reports, Vol. 28, No 6 (2019) pp. 1574-1583.e4
Cell reports 28 (2019): 1574–1583. doi:10.1016/j.celrep.2019.07.013
info:cnr-pdr/source/autori:Bianco S.; Annunziatella C.; Andrey G.; Chiariello A.M.; Esposito A.; Fiorillo L.; Prisco A.; Conte M.; Campanile R.; Nicodemi M./titolo:Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells/doi:10.1016%2Fj.celrep.2019.07.013/rivista:Cell reports/anno:2019/pagina_da:1574/pagina_a:1583/intervallo_pagine:1574–1583/volume:28
Cell reports 28 (2019): 1574–1583. doi:10.1016/j.celrep.2019.07.013
info:cnr-pdr/source/autori:Bianco S.; Annunziatella C.; Andrey G.; Chiariello A.M.; Esposito A.; Fiorillo L.; Prisco A.; Conte M.; Campanile R.; Nicodemi M./titolo:Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells/doi:10.1016%2Fj.celrep.2019.07.013/rivista:Cell reports/anno:2019/pagina_da:1574/pagina_a:1583/intervallo_pagine:1574–1583/volume:28
Complex architectural rearrangements are associated to the control of the HoxD genes in different cell types; yet, how they are implemented in single cells remains unknown. By use of polymer models, we dissect the locus 3D structure at the single DNA
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::efa49ddbdcf4c3828788be2400b150d9
https://pubmed.ncbi.nlm.nih.gov/31390570
https://pubmed.ncbi.nlm.nih.gov/31390570
Autor:
Esposito, S, Cofini, M, Rigante, D, Leonardi, A, Lucchetti, L, Cipolla, C, Lanciotti, L, Penta, L.
In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of experimental data emerging from new technologies such as Hi-C or GAM, in a principled way. Here we
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8bfb5d7117c53d61c5c3f9f8129281e4
http://hdl.handle.net/11391/1432814
http://hdl.handle.net/11391/1432814
Autor:
Carlo Annunziatella, Verena Heinrich, Guillaume Andrey, Robert Schöpflin, Martin Franke, Christina Paliou, Katerina Kraft, Philine Guckelberger, Michael Pechstein, Bjørt K Kragesteen, Andrea M. Chiariello, Lars Wittler, Malte Spielmann, Bernd Timmermann, Stefan Mundlos, Andrea Esposito, Axel Visel, Ivana Jerković, Darío G. Lupiáñez, Martin Vingron, Simona Bianco, Mario Nicodemi, Wing Lee Chan, Izabela Harabula
Publikováno v:
Nat Genet
Nature Genetics, Vol. 50, No 10 (2018) pp. 1463-1473
Nature genetics, vol 50, iss 10
Nature Genetics, Vol. 50, No 10 (2018) pp. 1463-1473
Nature genetics, vol 50, iss 10
The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of transcription factors. By studying Pitx1, a regulator of hindlimb development, we show that dynamic cha
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a6e213ebb7016b20a563d747a739dae
http://hdl.handle.net/11588/723498
http://hdl.handle.net/11588/723498
Autor:
Andrea M. Chiariello, Andrea Esposito, Carlo Annunziatella, Simona Bianco, Luca Fiorillo, Antonella Prisco, Mario Nicodemi
Publikováno v:
Frontiers in Neuroscience
Frontiers in Neuroscience, Vol 11 (2017)
Frontiers in neuroscience (Online) 11 (2017). doi:10.3389/fnins.2017.00559
info:cnr-pdr/source/autori:Chiariello, Andrea M.; Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Fiorillo, Luca; Prisco, Antonella; Nicodemi, Mario/titolo:A Polymer Physics Investigation of the Architecture of the Murine Orthologue of the 7q11.23 Human Locus/doi:10.3389%2Ffnins.2017.00559/rivista:Frontiers in neuroscience (Online)/anno:2017/pagina_da:/pagina_a:/intervallo_pagine:/volume:11
Frontiers in Neuroscience, Vol 11 (2017)
Frontiers in neuroscience (Online) 11 (2017). doi:10.3389/fnins.2017.00559
info:cnr-pdr/source/autori:Chiariello, Andrea M.; Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Fiorillo, Luca; Prisco, Antonella; Nicodemi, Mario/titolo:A Polymer Physics Investigation of the Architecture of the Murine Orthologue of the 7q11.23 Human Locus/doi:10.3389%2Ffnins.2017.00559/rivista:Frontiers in neuroscience (Online)/anno:2017/pagina_da:/pagina_a:/intervallo_pagine:/volume:11
In the last decade, the developments of novel technologies, such as Hi-C or GAM methods, allowed to discover that chromosomes in the nucleus of mammalian cells have a complex spatial organization, encompassing the functional contacts between genes an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f19677577e098a20fb29671bc036d5ba
http://europepmc.org/articles/PMC5641313
http://europepmc.org/articles/PMC5641313
Autor:
Andrea M. Chiariello, Guillaume Andrey, Ana Pombo, Katerina Kraft, Mario Nicodemi, Carlo Annunziatella, Simona Bianco, Robert Schöpflin, Darío G. Lupiáñez, Martin Vingron, Stefan Mundlos, Lars Wittler
Publikováno v:
Nature Genetics
Nature Genetics, Vol. 50, No 5 (2018) pp. 662-667
Nature Genetics, Vol. 50, No 5 (2018) pp. 662-667
Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::96f85a198393516207e80d1b27c75476
https://pubmed.ncbi.nlm.nih.gov/29662163
https://pubmed.ncbi.nlm.nih.gov/29662163