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Publications

  1. Lab of environmental epigenetics

 

 

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
 
Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Year: 2021 DOI:10.1038/s41467-021-23542-w
Authors: Alessandro Bonetti # 1 2, Federico Agostini # 3, Ana Maria Suzuki 4 5, Kosuke Hashimoto, Giovanni Pascarella 4, Juliette Gimenez 6, Leonie Roos 7 8, Alex J Nash 7 8, Marco Ghilotti, Christopher J F Cameron 9 10, Matthew Valentine 4, Yulia A Medvedeva 11 12 13, Shuhei Noguchi 4, Eneritz Agirre 14, Kaori Kashi 4, Samudyata 14, Joachim Luginbühl 4, Riccardo Cazzoli, Saumya Agrawal 4, Nicholas M Luscombe 3 16 17, Mathieu Blanchette 9, Takeya Kasukawa, Michiel de Hoon 4, Erik Arner 4, Boris Lenhard 7 8 18, Charles Plessy 4, Gonçalo Castelo-Branco, Valerio Orlando 19 20, Piero Carninci 21
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
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.

 

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
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
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
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.

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 
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
How Polycomb-Mediated Cell Memory Deals With a Changing Environment: Variations in PcG Complexes and Proteins Assortment Convey Plasticity to Epigenetic Regulation as a Response to Environment
Year: 2018 DOI:10.1002/bies.201700137
Authors: Federica Marasca, Beatrice Bodega, Valerio Orlando
Bioessays. 2018 Apr;40(4):e1700137. doi: 10.1002/bies.201700137. Epub 2018 Mar 9
  • PRC2
  • PcG proteins
  • adaptation
  • environmental changes
  • epigenetic memory
  • evolution
  • plasticity
FANTOM5 CAGE profiles of human and mouse samples
Year: 2017 DOI:10.1038/sdata.2017.112
Authors: Shuhei Noguchi, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Naoko Suzuki, Michihira Tagami, Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T,, Edge ASB, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Kawamoto H, Morikawa H, Nakamura Y, Nozaki T, Ogishima S, Ohkura N, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Passier, Patrikakis M, Pombo A, Pradhan-Bhatt S, Qin XY, Rehli M, Rizzu P, Please refer to the link to find the other authors
Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.PMID: 28850106
Gathering by the Red Sea highlights links between environment and epigenetics.
Year: 2017 DOI:10.1038/nsmb.3422
Authors: Mo Li, Emiliana Borrelli, Pierre J Magistretti, Juan Carlos Izpisua Belmonte, Paolo Sassone-Corsi, Valerio Orlando
Nat Struct Mol Biol. 2017 Jun 6;24(6):491-493.
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.
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
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.
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
    •   
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.
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome
Year: 2015 DOI:10.1371/journal.pbio.1002315
Authors: Laurence D Hurst , Avazeh T Ghanbarian, Alistair R R Forrest , FANTOM consortium; Lukasz Huminiecki
  • PMID: 26685068
    •  
  • PMCID: PMC4686125
    •  
  • DOI: 10.1371/journal.pbio.1002315
Comparative Study
 
- 2015 Dec 18;13(12):e1002315.
 doi: 10.1371/journal.pbio.1002315. eCollection 2015 Dec.

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage
Year: 2015 DOI:10.1371/journal.pone.0144176
Authors: Daniel Carbajo , Shigeyuki Magi, Masayoshi Itoh , Hideya Kawaji, Timo Lassmann , Erik Arner, Alistair R R Forrest , Piero Carninci, Yoshihide Hayashizaki , Carsten O Daub, FANTOM consortium; Mariko Okada-Hatakeyama , Jessica C Mar
2015 Dec 14;10(12):e0144176.- doi: 10.1371/journal.pone.0144176. eCollection 2015.
CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes
Year: 2014 DOI:10.1038/srep05228
Authors: Yuki Hasegawa , Dave Tang, Naoko Takahashi 1, Yoshihide Hayashizaki, Alistair R R Forrest
2014 Jun 24;4:5228.-doi: 10.1038/srep05228.
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Year: 2022 DOI:10.1038/s41467-022-28758-y
Authors: Mathys Grapotte # 1 2 3, Manu Saraswat # 1 2, Chloé Bessière # 1 2, Christophe Menichelli, Jordan A Ramilowski , Jessica Severin, Yoshihide Hayashizaki , Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata , Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi , Takeya Kasukawa , Akira Hasegawa , Harukazu Suzuki, Hiromi Nishiyori-Sueki , Martin C Frith , FANTOM consortium;, Clément Chatelain , Piero Carninci , Michiel J L de Hoon, Wyeth W Wasserman , Laurent Bréhélin , Charles-Henri Lecellier
  • PMID: 35232988
    •  
  • PMCID: PMC8888638
    •  
Free PMC article
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Year: 2021 DOI:10.1038/s41467-021-23143-7
Authors: Mathys Grapotte , Manu Saraswat , Chloé Bessière, Christophe Menichelli , Jordan A Ramilowski , Jessica Severin, Yoshihide Hayashizaki , Masayoshi Itoh, Michihira Tagami , Mitsuyoshi Murata , Miki Kojima-Ishiyama, Shohei Noma , Shuhei Noguchi , Takeya Kasukawa, Akira Hasegawa , Harukazu Suzuki, Hiromi Nishiyori-Sueki , Martin C Frith, FANTOM consortium; Clément Chatelain , Piero Carninci, Michiel J L de Hoon , Wyeth W Wasserman, Laurent Bréhélin , Charles-Henri Lecellier
  • PMID: 34078885
    •  
  • PMCID: PMC8172540
The statistical geometry of transcriptome divergence in cell-type evolution and cancer
Year: 2015 DOI:10.1038/ncomms7066
Authors: Cong Liang, FANTOM Consortium; Alistair R R Forrest
  • PMID: 25585899
    •  
  • DOI: 10.1038/ncomms7066
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