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Publications

  1. Lab of environmental epigenetics

 

 

PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stability
Year: 2024 ISSN:EMBO J (2024) DOI:https://doi.org/10.1038/s44318-024-00267-2
Authors: Peng Liu ,Seba Nadeef, Maged F Serag, Andreu Paytuví-Gallart, Maram Abadi, Francesco Della Valle, Santiago Radío, Xènia Roda htt, Jaïr Dilmé Capó, Sabir Adroub, Nadine Hosny El Said, Bodor Fallatah, Mirko Celii, Gian Marco Messa, Mengge Wang, Mo Li, Paola Tognini, Lorena Aguilar,Arnal, Satoshi Habuchi, Selma Masri, Paolo Sassone-Corsi, , and Valerio Orlando

21 October 2024

https://doi.org/10.1038/s44318-024-00267-2

LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory response
Year: 2024 DOI:https://doi.org/10.1038/s44318-024-00143-z
Authors: Arianna Mangiavacchi, Gabriele Morelli, Sjur Reppe,   Alfonso Saera-Vila, , Peng Liu, Benjamin Eggerschwiler, Huoming Zhang, Dalila Bensaddek, Elisa A Casanova, Carolina Medina Gomez,, Vid Prijatelj, Francesco Della Valle, Nazerke Atinbayeva, Juan Carlos Izpisua Belmonte, Fernando Rivadeneira, Paolo Cinelli, Kaare Morten Gautvik, Valerio Orlando,

DOI: EMBO J (2024)

https://doi.org/10.1038/s44318-024-00143-z

TDP-43 Epigenetic Facets and Their Neurodegenerative Implications
Year: 2023 DOI:10.3390/ijms241813807
Authors: Juliette Gimenez, Alida Spalloni, Sara Cappelli, Francesca Ciaiola,, Valerio Orlando,, Emanuele Buratti, and Patrizia Longone
Int J Mol Sci. 2023 Sep; 24(18): 13807.
Published online 2023 Sep 7.
PMCID: PMC10530927
PMID: 37762112
Epigenome changes in active and inactive Polycomb‐group‐controlled regions
Year: 2023 DOI:https://doi.org/10.15252/embr.202357607
Authors: Achim Breiling, Laura P O'Neill, Donatella D'Eliseo, Bryan M Turner, and Valerio Orlando
EMBO rep (2023) 24: e57607

Dynamic Interactome of PRC2-EZH1 Complex Using Tandem-Affinity Purification and Quantitative Mass Spectrometry
Year: 2023
Authors: Peng Liu, Huoming Zhang, Francesco Della Valle &  Valerio Orlando

First Online: 23 May 2023

Synaptic and transcriptomic features of cortical and amygdala pyramidal neurons predict inefficient fear extinction
Year: 2023 DOI:https://doi.org/10.1016/j.celrep.2023.113066
Authors: Daniela Laricchiuta , Juliette Gimenez, Giuseppe Sciamanna, Andrea Termine, Carlo Fabrizio,, Francesco Della Valle , Silvia Caioli, Luana Saba, Marco De Bardi, Francesca Balsamo, Anna Panuccio, Noemi Passarello, Anna Mattioni, Elisa Bisicchia, Cristina Zona,, Valerio Orlando,, Laura Petrosini

Published:August 31, 2023

Liver and muscle circadian clocks cooperate to support glucose tolerance in mice
Year: 2023 DOI:https://doi.org/10.1016/j.celrep.2023.112588
Authors: Jacob G. Smith, Kevin B. Koronowski, Thomas Mortimer, Tomoki Sato , Carolina M. Greco, Paul Petrus , Amandine Verlande, Siwei Chen , Muntaha Samad, Ekaterina Deyneka, Lavina Mathur, Ronnie Blazev, Jeffrey Molendijk, Arun Kumar, Oleg Deryagin, Mireia Vaca-, Ronnie Blazev, Jeffrey Molendijk, Arun Kumar, Oleg Deryagin, Mireia Vaca-Dempere,, Valentina Sica, Peng Liu,, Valerio Orlando,, Benjamin L. Parker Paolo Sassone-Corsi
27 June 2023, 112588
Epigenetics and Brain Plasticity: Back to Function
Year: 2023
Authors: Gabriele Morelli†, Francesco Della Valle  , Valerio Orlando
Detecting Cell Compartment-Specific PRC2-RNA Interactions via UV-RIP
Year: 2023
Authors: Francesco Della Valle, Peng Liu, Gabriele Morelli†, Valerio Orlando
Behind the scenes: How RNA orchestrates the epigenetic regulation of gene expression
Year: 2023 DOI:https://doi.org/10.3389/fcell.2023.1123975
Authors: Arianna Mangiavacchi, Gabriele Morelli†, Valerio Orlando
Front. Cell Dev. Biol., 25 January 2023
Sec. Epigenomics and Epigenetics
Volume 11 - 2023 | https://doi.org/10.3389/fcell.2023.1123975
LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes
Year: 2022 DOI:10.1126/scitranslmed.abl6057
Authors: Francesco Della Valle, Pradeep Ready, Mako Yamamoto, Peng Lui, Alfonso Sera-Vila, Dalila BinSadeek, Homing Zhang, Javier Martinez, Leila Abassi, Mirko Celii, Alejandro Ocampo, Estrella Delicado, Arianna Mangiavacchi, Riccardo Aiese Cgliano, Conception Estebban, Steve Horvath, Juan Carlos Belamonte, Valerio Orlando
10 Aug 2022
Vol 14, Issue 657
 
Transcriptomic and Network Analyses Reveal Immune Modulation by Endocannabinoids in Approach/Avoidance Traits
Year: 2022 DOI:10.3390/ijms23052538
Authors: Andrea Termine , Carlo Fabrizio, Juliette Gimenez , Anna Panuccio, Francesca Balsamo , Noemi Passarello , Silvia Caioli, Luana Saba , Marco De Bardi, Francesco Della Valle  , Valerio Orlando, Laura Petrosini, Daniela Laricchiuta
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Year: 2015 DOI:10.1126/science.1259418
Authors: Erik Arner, Carsten O Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drabløs, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic, Tom C Freeman, Ahmad M N Alhendi, Peter Arner, Richard Axton, J Kenneth Baillie, Anthony Beckhouse, Beatrice Bodega, James Briggs, Frank Brombacher, Margaret Davis, Michael Detmar, Anna Ehrlund,, Mitsuhiro Endoh, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Geoffrey J Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley Forrester, Daniel Goldowitz, Reto Guler, Thomas Ha, Mitsuko Hara, Meenhard Herlyn, Tomokatsu Ikawa, Chieko Kai, Hiroshi Kawamoto, Valerio Orlando, Please refer to the link to find the other authors
 2015 Feb 27;347(6225):1010-4.-doi: 10.1126/science.1259418. Epub 2015 Feb 12.

Repetitive elements dynamics in cell identity programming, maintenance, and disease
Year: 2014 DOI:10.1016/j.ceb.2014.09.002
Authors: Beatrice Bodega, Valerio Orlando
2014 Dec;31:67-73._ doi: 10.1016/j.ceb.2014.09.002.
A promoter-level mammalian expression atlas
Year: 2014 DOI:DOI: 10.1038/nature13182
Authors: FANTOM Consortium and the RIKEN PMI and CLST (DGT), Alistair R R Forrest, Hideya Kawaji, Michael Rehli, J Kenneth Baillie, Michiel J L de Hoon, Vanja Haberle, Timo Lassmann, Ivan V Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J Mungall,, Terrence F Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A Semple, Yuri Ishizu, Robert S Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M Altschuler, Takahiro Arakawa, John A C Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J Balwierz, Anthony G Beckhouse, Swati Pradhan-Bhatt, Judith A Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A Maxwell Burroughs, Andrea Califano, Carlo V Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C Clevers, Emiliano Dalla, Carrie A Davis, Michael Detmar, Valerio Orlando, Please refer to the link to find the other authors
 2014 Mar 27;507(7493):462-70._doi: 10.1038/nature13182.
PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C
Year: 2013 DOI:10.1371/journal.pgen.1003283
Authors: Federica Lo Sardo, Chiara Lanzuolo, Federico Comoglio, Marco De Bardi, Renato Paro, Valerio Orlando
. 2013;9(2):e1003283. doi: 10.1371/journal.pgen.1003283. Epub 2013 Feb 21.
RNA-interference components are dispensable for transcriptional silencing of the drosophila bithorax-complex
Year: 2013 DOI:10.1371/journal.pone.0065740
Authors: Filippo M Cernilogar, A Maxwell Burroughs, Chiara Lanzuolo, Achim Breiling, Axel Imhof, Valerio Orlando
  • PMID: 23785447_PMCID: PMC3681981_DOI: 10.1371/journal.pone.0065740
    •   
Characterization of piRNAs across postnatal development in mouse brain
Year: 2016 DOI:10.1038/srep25039
Authors: Yanal Ghosheh, Loqmane Seridi, Taewoo Ryu, Hazuki Takahashi, Valerio Orlando, Timothy Ravasi
Sci Rep. 2016 Apr 26;6:25039. doi: 10.1038/srep25039.PMID: 27112104
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Year: 2020 DOI:10.1038/s41467-020-14337-6
Authors: Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ,, Ghilotti M, Cameron CJF,, Valentine M, Medvedeva YA, Noguchi S,, Agirre E, Kashi K, Samudyata, Luginbühl J,, Cazzoli R, Agrawal S, Luscombe NM,, Blanchette M, Kasukawa T, Hoon M, Arner E,, Lenhard B, Plessy C, Castelo-Branco G,, Orlando V, Carninci P.
 Nat Commun. 2020 Feb 24;11(1):1018. doi: 10.1038/s41467-020-14337-6.PMID: 32094342
Functional annotation of human long noncoding RNAs via molecular phenotyping
Year: 2020 DOI:10.1101/gr.254219.119
Authors: Ramilowski JA, Yip CW, Agrawal S,, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC,, Ouyang JF, Parkinson N, Petri A, Roos L,, Severin J, Yasuzawa K, Abugessaisa I,, Akalin A, Antonov IV, Arner E,, Bonetti A, Bono H, Borsari B, Brombacher F,, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M,, Chang H, Dostie J, Ducoli L, Favorov A, Fort A,, Garrido D, Gil N, Gimenez J,, Guler R, Handoko L, Harshbarger J,, Hasegawa A, Hasegawa Y, Hashimoto K,, Hayatsu N, Heutink P, Hirose T,, Imada EL, Itoh M, Kaczkowski B, Kanhere A,, Kawabata E, Kawaji H, Kawashima T,, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T,, Kratz A, Kurowska-Stolarska M, Kwon ATJ,, Leek J, Lennartsson A, Lizio M, López-Redondo F,, Luginbühl J, Maeda S, Makeev VJ, Marchionni L,, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M,, Murata M, Nishiyori H, Nitta KR,, Noguchi S, Noro Y, Nurtdinov R,, Okazaki Y, Orlando V,, Please refer to the link to find the other authors
Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27.PMID: 32718982 
Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories and Modulates Amygdala Pyramidal Neuron Transcriptome
Year: 2021
Authors: Daniela Laricchiuta, Giuseppe Sciamanna, Juliette Gimenez, Andrea Termine, Carlo Fabrizio, Silvia Caioli, Francesca Balsamo, Anna Panuccio, Marco De Bardi, Luana Saba, Noemi Passarello, Debora Cutuli, Anna Mattioni, Cristina Zona, Valerio Orlando, Laura Petrosini

/ 2021 Jan 15;22(2):810./doi: 10.3390/ijms22020810.

New insights into the functional role of retrotransposon dynamics in mammalian somatic cells
Year: 2021 DOI:10.1007/s00018-021-03851-5
Authors: Mangiavacchi A, Liu P, Della Valle F, Orlando V.
Cell Mol Life Sci. 2021 Jul;78(13):5245-5256. doi: 10.1007/s00018-021-03851-5. Epub 2021 May 14.PMID: 33990851
Malat-1-PRC2-EZH1 interaction supports adaptive oxidative stress-dependent epigenome remodeling in skeletal myotubes
Year: 2021 DOI:10.1038/s41419-021-04082-z
Authors: Nadine Hosny El Said, Francesco Della Valle, Peng Liu, Andreu Paytuví-Gallart, Sabir Adroub, Juliette Gimenez & Valerio Orlando
Ago1 controls myogenic differentiation by regulating eRNA-mediated CBP-guided epigenome reprogramming
Year: 2021 DOI:10.1016/j.celrep.2021.110066.
Authors: Fallatah B, Shuaib M, Adroub S, Paytuví-Gallart A, Della Valle F, Nadeef S, Lanzuolo C, Orlando V.
2021 Nov 30;37(9):110066./ doi: 10.1016/j.celrep.2021.110066.

 

Transdifferentiation of Mouse Embryonic Fibroblasts into Dopaminergic Neurons Reactivates LINE-1 Repetitive Elements
Year: 2020 DOI:https://doi.org/10.1016/j.stemcr.2019.12.002
Authors: Francesco Della Valle, Manjula P.Thimma, Massimiliano Caiazzo, Salvatore Pulcrano, MirkoCelii, Sabir A.Adroub, Gregorio Alanis-Lobato, Vania Broccoli, Valerio Orlando
Stem Cell Reports (2019), https://doi.org/10.1016/j.stemcr.2019.12.002
  • LINE-1 elements
  • cell transdifferentiation
  • cell plasticity
Ubiquitin ligases HUWE1 and NEDD4 cooperatively control signal-dependent PRC2-Ezh1α/β-mediated adaptive stress response pathway in skeletal muscle cells
Year: 2019 DOI:10.1186/s13072-019-0322-5
Authors: Peng Liu, Muhammad Shuaib, Huoming Zhang, Seba Nadeef, Valerio Orlando
Epigenetics Chromatin. 2019; 12: 78.
  • HUWE1
  • NEDD4
  • Polycomb
  • Ubiquitination
Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells
Year: 2019 DOI:https://doi.org/10.1016/j.cels.2019.09.005
Authors: Muhammad Shuaib, Krishna MohanParsi, Manjula Thimma, Sabir Abdu Adroub, Hideya Kawaji, Loqmane Seridi, Yanal Ghosheh, Alexandre Fort, Bodor Fallatah, Piero Carninci, Valerio Orlando
Cell Syst. 2019 Nov 27;9(5):446-458.e6. doi: 10.1016/j.cels.2019.09.005. Epub 2019 Oct 16.PMID: 31629687
  • RNAi components
  • nuclear AGO1
  • non-coding RNA
  • enhancers
  • 3D chromatin organization
  • gene expression regulation
Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication Between Clocks
Year: 2018 DOI:10.1016/j.cell.2018.08.042
Authors: Dyar KA, Lutter D, Artati A, Ceglia NJ, Liu Y, Armenta D, Jastroch M, Schneider S, de Mateo S, Cervantes M, Abbondante S, Tognini P, Orozco-Solis R, Kinouchi K, Wang C, Swerdloff R, Nadeef S, Masri S, Magistretti P, Orlando V, Borrelli E, Uhlenhaut NH, Baldi P, Adamski J, Tschöp MH, Eckel-Mahan K, Sassone-Corsi P
Cell. 2018 Sep 6;174(6):1571-1585.e11. doi: 10.1016/j.cell.2018.08.042.PMID: 30193114 
  • CircadiOmics
  • circadian rhythms
  • clock
  • high-fat diet
  • metabolism
  • metabolomics
A Cytosolic Ezh1 Isoform Modulates a PRC2-Ezh1 Epigenetic Adaptive Response in Postmitotic Cells
Year: 2017 DOI:10.1038/nsmb.3392
Authors: Beatrice Bodega, Federica Marasca, Valeria Ranzani, Alessandro Cherubini, Francesco Della Valle, Maria Victoria Neguembor, Michel Wassef, Alessio Zippo, Chiara Lanzuolo, Massimiliano Pagani, Valerio Orlando
Nat Struct Mol Biol. 2017 May;24(5):444-452.
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