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Affiliations

• Bioscience
• Bioengineering

Education Profile

• ​​​​​​​Postdoctoral fellow, Zentrum fuer Molekulare Biologie (ZMBH) University of Heidelberg, Germany,1997
  
• Ph.D. University "La Sapienza", Rome Italy, 1989
  

Research Interests

​The epigenome constitutes the chromosomal molecular interface that allows the genome to interact with the environment. The epigenome enables cells to learn, remember and maintain their functional states throughout life and enable organisms to integrate environmental signals.

Prof. Orlando's lab is interested in investigating the chromatin mediated fundamental mechanisms that control cell identity and plasticity. These include signaling to chromatin regulation and nuclear organization by Polycomb proteins, the role of ncRNA-protein interactions in transcriptional regulation, Epigenomics and how this relates for development, transdifferentiation and adaptation (e.g. Metabolism), in particular in stress conditions.

Furthermore, as part of the mechanistic plastic properties of the genome in response to developmental and environmental cues, Prof. Orlando's lab also investigates the epigenetic regulation of the expression and dynamics of transposable elements and their role in cell differentiation and epigenomic biodiversity.

Selected Publications

• Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkNat Commun. 2022 Mar 1;13(1):1200. doi: 10.1038/s41467-022-28758-y.
• Transcriptomic and Network Analyses Reveal Immune Modulation by Endocannabinoids in Approach/Avoidance TraitsInt J Mol Sci. 2022 Feb 25;23(5):2538. doi: 10.3390/ijms23052538.
• Ago1 controls myogenic differentiation by regulating eRNA-mediated CBP-guided epigenome reprogramming.Cell Rep . 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.Cell Death Dis . 2021 Sep 16;12(10):850. doi: 10.1038/s41419-021-04082-z.
• New insights into the functional role of retrotransposon dynamics in mammalian somatic cells.Cell Mol Life Sci . 2021 Jul;78(13):5245-5256. doi: 10.1007/s00018-021-03851-5. Epub 2021 May 14.
• Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.Nat Commun . 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7.
• Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.Nat Commun . 2021 May 19;12(1):3128. doi: 10.1038/s41467-021-23542-w.
• Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories and Modulates Amygdala Pyramidal Neuron Transcriptome.Int J Mol Sci . 2021 Jan 15;22(2):810. doi: 10.3390/ijms22020810.
• Functional annotation of human long noncoding RNAs via molecular phenotyping.Genome Res . 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27.
• RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.Nat Commun . 2020 Feb 24;11(1):1018. doi: 10.1038/s41467-020-14337-6.
• Transdifferentiation of Mouse Embryonic Fibroblasts into Dopaminergic Neurons Reactivates LINE-1 Repetitive Elements.Stem Cell Reports . 2020 Jan 14;14(1):60-74. doi: 10.1016/j.stemcr.2019.12.002. Epub 2020 Jan 2.
• Ubiquitin ligases HUWE1 and NEDD4 cooperatively control signal-dependent PRC2-Ezh1α/β-mediated adaptive stress response pathway in skeletal muscle cells.Epigenetics Chromatin . 2019 Dec 19;12(1):78. doi: 10.1186/s13072-019-0322-5.
• Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells.Cell Syst . 2019 Nov 27;9(5):446-458.e6. doi: 10.1016/j.cels.2019.09.005. Epub 2019 Oct 16.
• Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks.Cell . 2018 Sep 6;174(6):1571-1585.e11. doi: 10.1016/j.cell.2018.08.042
• 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.Bioessays . 2018 Apr;40(4):e1700137. doi: 10.1002/bies.201700137. Epub 2018 Mar 9.
  
• FANTOM5 CAGE profiles of human and mouse samples.Sci Data . 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112. 
• Gathering by the Red Sea highlights links between environment and epigenetics.Nat Struct Mol Biol .2017 Jun 6;24(6):491-493. doi: 10.1038/nsmb.3422.
• A cytosolic Ezh1 isoform modulates a PRC2-Ezh1 epigenetic adaptive response in postmitotic cells.Nat Struct Mol Biol . 2017 May;24(5):444-452. doi: 10.1038/nsmb.3392. Epub 2017 Mar 27
• Characterization of piRNAs across postnatal development in mouse brain.Sci Rep . 2016 Apr 26;6:25039. doi: 10.1038/srep25039.
• The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.PLoS Biol . 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.PLoS One . 2015 Dec 14;10(12):e0144176. doi: 10.1371/journal.pone.0144176. eCollection 2015.
• Discovery of molecular markers to discriminate corneal endothelial cells in the human body.PLoS One . 2015 Mar 25;10(3):e0117581. doi: 10.1371/journal.pone.0117581. eCollection 2015.
• Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.Science . 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.
• The statistical geometry of transcriptome divergence in cell-type evolution and cancer.Nat Commun . 2015 Jan 14;6:6066. doi: 10.1038/ncomms7066.
• Repetitive elements dynamics in cell identity programming, maintenance and disease.Curr Opin Cell Biol . 2014 Dec;31:67-73. doi: 10.1016/j.ceb.2014.09.002.
• CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.Sci Rep . 2014 Jun 24;4:5228. doi: 10.1038/srep05228.
• Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.Proc Natl Acad Sci U S A . 2014 Apr 8;111(14):5289-94. doi: 10.1073/pnas.1312717110. Epub 2014 Mar 27.
• Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.PLoS One . 2014 Mar 27;9(3):e80274. doi: 10.1371/journal.pone.0080274. eCollection 2014
• A promoter-level mammalian expression atlas.Nature . 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.
• RNA-interference components are dispensable for transcriptional silencing of the drosophila bithorax-complex.PLoS One . 2013 Jun 13;8(6):e65740. doi: 10.1371/journal.pone.0065740. Print 2013.
• PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C.PLoS Genet . 2013;9(2):e1003283. doi: 10.1371/journal.pgen.1003283. Epub 2013 Feb 21.