MONICA BALLARINO

I SEMESTER

MOLECULAR BIOLOGY AND GENOMICS

III year, Bioinformatics

Lessons will start in October 2025 

Timetable: Monday-Wednesday, Ex Officine Ortopediche, Classroom E (CUO35) from 09:00 to 11:00

https://www.uniroma1.it/sites/default/files/PIANTA_LEGENDA_DEF_AGG_040414_1.pdf

Lessons are carried out in presence by taking into account safety distances. 

OPIS CODE AA 2025)) 4KEZFQ91

Type of exam: oral 
Teaching material will be available on the e_learning page of the course 

II SEMESTER

MOLECULAR BIOLOGY 

I year, Physics LM-17

Lessons will start on Thursday, 27 February 2025

Timetable: Tuesday (10:00-12:00) and Thursday (12:00-14:00), Auletta Seminari (CUO26) 

CODICE OPIS AA 2025)) 4WXZ7Q7I

Type of exam: oral 
Teaching material is available on the e_learning page of the course 

GENOMICA

III anno, Scienze biologiche

Le lezioni cominceranno Mercoledì, 26 Febbraio 2025 con il Modulo 2 (1022925_2, docente Ballarino) e proseguiranno con la Prof.ssa Ciapponi (Modulo 1)

Orario delle lezioni: Lunedì e Mercoledì, Aula Serra I (Ed. Genetica, CU022) dalle 11,00 alle 13,00 

CODICE OPIS AA 2025)) 4ISU868C 

Modalità di esame: orale. Interrogazione con entrambe le docenti.

Il materiale didattico è disponibile sulla pagina e_learning del corso (modulo 2, Ballarino)

MONICA BALLARINO
Researcher Identifiers
ORCID ID: 0000-0002-8595-7105
SCOPUS Author ID: 6603725001

Personal Statement
I specialize in RNA research, with a particular focus on how the intrinsic properties of this molecule define the physiological role of non-coding RNAs. My current studies focus on the function of lncRNAs through the development and application of dedicated computational pipelines, microscopy techniques and biochemical approaches. Additionally, my lab has substantial expertise in CRISPR-cas9 methodologies, which have been utilized to generate mouse animal models with targeted mutations in specific non-coding loci. The long-term objective of my laboratory is to unravel how the aberrant regulation of lncRNAs affects muscle function in humans, both directly, as observed in skeletal and cardiac muscle diseases, and indirectly, as seen in neuromuscular disorders. Recently, we have leveraged genomic editing technologies on induced pluripotent stem cells (iPSCs), which we are now differentiating into various cell types, including skeletal muscle fibres, cardiac cells, motor neurons and neuromuscular organoids.

Positions and Scientific Appointments
2024-pres Delegate for institutional relations BBCD-IBPM
2024-pres Responsible Mobility Area (RAM) Erasmus, Facoltà di Farmacia e Medicina, Sapienza University
2023-pres Deputy Coordinator of the PhD in Genetics and Molecular Biology, Sapienza University
2022-pres Member of CIVIS-EU University. Experimental Models in Molecular Biomedicine
2022-pres Referent person E-learning platform, Facoltà di Farmacia e Medicina, Sapienza University of Rome
2021-pres Referent person VQR (2015-2019; 2020-2024), Dept. BBDC, Sapienza University of Rome
2020-pres Member of Centro Ricerca e Servizi sperimentazione preclinica, Sapienza University of Rome
2019-pres Associate Professor, BBCD Department, Sapienza University of Rome.
2019-pres Member of Accademia Medica of Rome https://www.accademiamedicadiroma.it/soci/
2018-pres Member of Società Italiana di Biofisica e Biologia Molecolar - SIBBM https://www.sibbm.org/soci
2017-pres Member of PhD Board in Genetics and Molecular Biology, Sapienza
2016-19 Assistant Professor, BBCD Department, Sapienza University of Rome
2012-15 RTDA researcher, BBCD Department, Sapienza University of Rome
2009-12 Research Associate (Chercheur), Institute de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstanden, Strasbourg, France
2010 Visiting Scientist, Institut de Biologie de l'ENS, Paris, France
2005-09 Post-doctoral training, Sapienza University of Rome
2002-05 Ph.D. fellow, Sapienza University of Rome

Fellowships and Awards:
2025 Women at the Top leadership certification, GSoM POLIMI - Politecnico di Milano
2024 ASN 2023/2025. Habilitation Full Professor, 05/E2 - MOLECULAR BIOLOGY
2024 Best poster IIM Meeting 2024, Assisi. Long noncoding RNAs at the interface between muscles and nerves. Marco Simula, PhD XXXIX cycle (*)
2024 Best poster SIBBM2024, Trento. The nuclear lncRNA Charme plays an evolutionarily conserved role in the epigenetic regulation of muscle differentiation. Giulia Buonaiuto, PhD XXXVI cycle (*)
2022 FSE – Regione Lazio Contributo premiale per ricercatori
2020 Best PhD Thesis in Genetics and Molecular Biology, Sapienza. Investigating the role of Charme:
a chromatin-associated lncRNA supervisor of mammals myogenesis. Fabio Desideri, PhD XXXII cycle (*)
2019 Recognition of "Excellent university teaching", Sapienza University of Rome
2017 FFABR-ANVUR (GU n.297 21-12-2016 Sup Ord n.57), MIUR
2016 Poster Prize XIX CONGRESSO NAZIONALE SIGU, Torino. A new murine long non-coding RNA conserved in human and involved in muscle differentiation. Rossella Tita, PhD XXIX cycle (*)
2015-19 ANVUR-VQR Recognition of 3/4 “Excellent-extremely relevant” 1/4 “Excellent” publications
2015 Best Poster, Telethon XVIII Scientific convention, Riva del Garda. RNA-based gene therapy of DMD
2010 Long-Term Fellowship Espoirs de la Recherche “FRM - Fondation pour la Recherche Medicale”
2009 Best Poster, SIROCCO meeting, Hinxton. New connections between miRNA transcription & processing
2005 Premio di Studio Fondazione Telethon
2004 Long-Term fellowship by Istituto Pasteur-Fondazione Cenci-Bolognetti
2003 Short-Term fellowship by Istituto Pasteur-Fondazione Cenci-Bolognetti
2003 Biologist state assessment (150/150). Università degli Studi della Tuscia, Viterbo, ITALY
2002 Long-Term fellowship by Consiglio Nazionale delle Ricerche (CNR), Bando n. 113.50 BO.2
(*) PhD advisor, Monica Ballarino

Pubblications in peer-reviewed journals (last 10-years):
- Palma A., et al Genome biology of long non-coding RNAs in humans: A virtual karyotype Comput Struct Biotechnol J. (2025) Jan 31;27:575-584. doi: 10.1016/j.csbj.2025.01.026.
- Silvestri B., et al HuD impairs neuromuscular junctions and induces apoptosis in human iPSC and Drosophila ALS models. Nat Commun. (2024) Nov 7;15(1):9618. DOI: 10.1038/s41467-024-54004-8.
- Desideri F., et al CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology. Nucleic Acids Res. 2024 Sep 9;52(16):9936-9952. DOI: 10.1093/nar/gkae590.
- Taliani, V., et al The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart (2023) eLife, 12, art. no. e81360. DOI: 10.7554/elife.81360
- Buonaiuto, G., et al Preparation of Cardiac Extracts from Embryonal Hearts to Capture RNA–protein Interactions by CLIP (2023) Bio-protocol, 13 (20), art. no. e4857. DOI: 10.21769/BioProtoc.4857
- Ballarino, M., et al Exploring the landscape of tools and resources for the analysis of long non-coding RNAs (2023) Computational and Structural Biotechnology Journal, 21, pp.4706-471 DOI:10.1016/j.csbj.2023.09.041
- Desideri, F., et al Advances in endogenous RNA pull-down: A straightforward dextran sulfate-based method enhancing RNA recovery (2022) Frontiers in Molecular Biosciences, 9, art.no.1004746. DOI: 10.3389/fmolb.2022.1004746
- Carvelli, A., et al A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. (2022) EMBO Journal, 41 (13), art. no. e108918. DOI: 10.15252/embj.2021108918
- Macino, M., et al Targeting the expression of long noncoding rnas in murine satellite cells from single myofibers (2021) Bio-protocol, 11 (21), art. no. e4209. DOI: 10.21769/BioProtoc.4209
- Buonaiuto, G., et al Muscle Regeneration and RNA: New Perspectives for Ancient Molecules (2021) Cells, 10 (10), art. no. 2512. DOI: 10.3390/cells10102512
- Cipriano, A., et al Epigenetic regulation of wnt7b expression by the cis-acting long noncoding rna lnc-rewind in muscle stem cells. (2021) eLife, 10, art. no. e54782, pp. 1-25. DOI: 10.7554/ELIFE.54782
- Santini, T., et al Visualization of nuclear and cytoplasmic long noncoding rnas at single-cell level by rna-fish (2021) Methods in Molecular Biology, 2157, pp. 251-280. DOI: 10.1007/978-1-0716-0664-3_15
- Desideri, F., et al Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1 (2020) Cell Reports, 33 (12), art. no. 108548. DOI: 10.1016/j.celrep.2020.108548
- Rea, J., et al HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade. (2020) Cell Death and Disease, 11 (7), art. no. 527. DOI: 10.1038/s41419-020-02738-w ISSN: 20414889
- Martone, J., et al Non-coding RNAs Shaping Muscle (2020) Frontiers in Cell and Developmental Biology, 7, art. no. 394. DOI: 10.3389/fcell.2019.00394
- Pagano, F., et al The noncoding side of cardiac differentiation and regeneration (2020) Current Stem Cell Research and Therapy, 15 (8), pp. 723-738. DOI: 10.2174/1574888X15666200123120249
- Ballarino, M., et al Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice. (2018) EMBO Journal, 37 (18), art. no. e99697.DOI:10.15252/embj.20189969
- Dimartino, D., et al The Long Non-coding RNA lnc-31 Interacts with Rock1 mRNA and Mediates Its YB-1-Dependent Translation. (2018) Cell Reports, 23 (3), pp. 733-740. DOI: 10.1016/j.celrep.2018.03.101
- Cipriano, A., Ballarino, M. The ever-evolving concept of the gene: The use of RNA/Protein experimental techniques to understand genome functions. (2018) Frontiers in Molecular Biosciences, art.no. 20. DOI: 10.3389/fmolb.2018.00020
- Ribeiro, D.M., et al Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. (2018) Nucleic Acids Research, 46 (2), pp. 917-928. DOI: 10.1093/nar/gkx1169
- Rosa, A., et al Divergent lncRNAs take the lead on pluripotent cell differentiation (2016) Stem Cell Investigation, 2016 (SEP), art. no. 47. DOI: 10.21037/sci.2016.09.02
- Ballarino, M., et al Non-coding RNAs in muscle differentiation and musculoskeletal disease (2016) Journal of Clinical Investigation, 126 (6), pp. 2021-2030. DOI: 10.1172/JCI84419
- Rosa, A., Ballarino, M. Long Noncoding RNA Regulation of Pluripotency (2016) Stem Cells International, 2016, art.no. 1797692. DOI: 10.1155/2016/1797692
- Morlando, M., et al Long non-coding RNAs: New players in hematopoiesis and leukemia, (2015) Frontiers in Medicine, 2 (APR), art. no. 23. DOI: 10.3389/fmed.2015.00023
- Ballarino, M., et al Novel long noncoding RNAs (lncRNAs) in Myogenesis: A miR-31 overlapping lncRNA transcript controls myoblast differentiation (2015) Molecular and Cellular Biology, 35 (4), pp. 728-736. DOI: 10.1128/MCB.01394-14

Submitted manuscripts:
- Grandioso A. et al, “A circuit involving the lncRNA MB3 and the driver genes MYC and OTX2 inhibits apoptosis in Group 3 Medulloblastoma by regulating the TGF-β pathway via HMGN5” CDDIS-25-2205 under review
- Palma A. et al, “Transcriptional profiling of human brain cortices identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis” HELIYON-D-24-71208 under review
- Buonaiuto G. et al, “Long noncoding RNA HSCHARME is altered in human cardiomyopathies and promotes stem cells-derived cardiomyocyte maturation by splicing regulation" NCOMMS-24-83523 under review

Invited Presentations
- 2024 Istituti del Polo San Lorenzo, “Lights from the dark matter: noncoding RNAs in neuromuscular physiology and disease”, Rome
- 2023 International Winter School, Genome integrity and genome organization in physiology and Pathology, “Myogenesis and long non-coding RNAs: a chromatin affair”, Sapienza University of Rome
- 2023 EMBO Course FISHing for RNAs: Classical to Single Molecule Approaches, “FISHing for Charme, a lncRNA solution to cell differentiation issue”, EMBL Heidelberg
- 2021 PhD School in Genetics and Molecular Biology, “Methodological issues and challenges for probing the function of long noncoding RNAs”, Sapienza University of Rome
- 2021 EMBO Course FISHing for RNAs: Classical to Single Molecule Approaches, “FISHing for Charme, a long noncoding solution to cell differentiation issues”, EMBL Heidelberg
- 2020 2nd CCP Phenogenomics Conference "A comprehensive glimpse on Charme long noncoding RNA” Vestec, Prague
- 2019 PhD School in Biology and Molecular Medicine, “A noncoding solution to cell differentiation issues: the Charme example”, Sapienza University of Rome
- 2018 SSAS-Scuola Superiore di Studi Avanzati dell’Ateneo “New and improved methodologies to detect RNA/protein interactions with chromatin”, Rome
- 2018 EPIGEN Final Meeting. “Non-coding regulation of myogenic chromatin” San Servolo, Venice,
- 2018 SIBBM “When and where: temporal and spatial regulation of biological processes”, “Non-coding regulation of myogenic chromatin”, Rome
- 2017 Unità di Terapia Intensiva Cardiologica-Ospedale S. Andrea, “Long non coding RNA nella miogenesi e nelle malattie del cuore”, Rome
- 2016 Chromatin, Epigenome, Drug discovery, training-school meeting, “Non-coding answers to differentiation questions”, Naples
- 2015 Joint meeting People Marie Curie, RNA Day, “LncRNPs and control of chromatin structure” Rome
- 2008 Congres de la Sociètè Francaise d’Hematologie, “miRNA and hematopoietic differentiation” Paris, France

Fundings (last 5 years)
2025 ELIXIR x NextGenerationIT: consolidation of the Italian Infrastructure for Omics Data and Bioinformatics, MoMyc
2025 Human Technopole 24-LI-PILOT Call for Access to the National Facilities Ion Imaging in Neuro-Muscular Organoids (iNEMO), Access granted
2022 PRIN PNRR “RNA secondary structures and their relationship with function: application to non-coding RNAs (RNA2Fun)” (P2022FFEWN), 100K€
2022 PRIN “Study of Noncoding RNAs in Organoids for Muscle-Nerve development (NOMeN)”,187K€
2022 PNRR Spoke 3, linea tematica 2. “Studying how lncRNA and circRNA alteration impacts neuromuscular transmission and ALS” CUP B83C22002870006, 160.0 K€
2022 Bando Visiting Professor cat. A, 5.0 K€
2021 Sapienza Ricerca “A muscle perspective into neurodegeneration: dissecting the role of long noncoding RNAs through hiPSC-derived neuromuscular organoids” RM12117A5DE7A45B, 14.8 K€
2020 POR FESR Lazio 2020-T0002E0001 “Soluzione Integrata di Microscopia Brillouin Avanzata” A03752020-36389 (SIMBA), 149.0 K€

Scientific Organization
2025 Co-organiser PhD EMBL-Sapienza lectures “Neurobiology and Epigenetics”, Sapienza, Rome
2025 Co-organiser GLASS- Gender & Leadership in Academia - Sapienza School, SASS Sapienza, Rome
2023 Co-organiser EMBO Practical Course on FISHing for RNAs, EMBL Heidelberg, Germany
2023 Co-organiser PhD EMBL-Sapienza lectures “Neurobiology and Epigenetics”, Sapienza, Rome
2021 Co-organiser PhD Workshop “Cutting-edge molecular technologies: a Sapienza/EMBL joint effort to share complementary expertise”, Sapienza, Rome
2017 Co-organiser 1st EMBL-Sapienza "Chromatin and Epigenetics" PhD meeting, Sapienza, Rome
Associate Editor, Frontiers Molecular Bioscience

Editorial activity
Editor of the BBCD Scientific Report https://bbcd.bio.uniroma1.it/sites/default/files/allegati/2024-08/SCIENT...
Associate Editor, Frontiers Molecular Bioscience
Review Editor, Frontiers in Genetics; Frontiers in Cell and Developmental Biology
Reviewer, Nat. Comm; PLoS ONE; Mol.Cell.Biol.; Mol Cell; FEBS; NAR; ARS (issue on "NON-CODIN RNAs AND EPIGENETICS”)