Human Genome Biology in health and disease
In our lab we are interested in understanding the function of DNA repetitive elements in the epigenetic regulation of the transcriptional response of the cell. In particular, we are asking whether DNA repeats could influence the inter-individual variability between humans in terms of response to environmental cues, adaptation and predisposition to human diseases. DNA repeats cover almost 70% of the human genome, and their function was largely ignored for decades. Nevertheless, there are emerging evidences of the peculiar role of repeats in regulating the epigenome. For instance, DNA repeats are involved in chromosome structural organization, gene regulation, genome integrity, and evolution. Moreover, a plethora of potential functions for expressed repeat regions have been assayed using data generated by the ENCODE and FANTOM consortia. These studies indicate a functional role for repetitive DNA in cell identity by means of repeat- encoded, ncRNA-mediated mechanisms, acting both in cis and in trans. The work of our team may provide important mechanistic information and novel interpretation of how specific non coding DNA functions may directly influence cellular processes, such as differentiation and disease. Ultimate goal that to demonstrate that evolutionary acquisition of such elaborated fine modulation of transcription represent an added value for mammalians, and humans in particular, to react to environment, adapt to stress, and eventually predispose to better or worse outcomes in disease progression. Such an effort in elucidating DNA repeats molecular mechanisms might at the end get genome biology and epigenetics research closer to truly effective forms of personalized medicine.
- Mechanistic insights in TEs (transposable elements) transcriptional and genomic dynamics in human primary CD4+ T cells
- Dissecting satellite function as orchestrators of 3D network of interactions for the timely expression of TUs during cellular differentiation and diseases
|Nome / Name||Ruolo / Role|
|Valeria Di Gioia||Studentfirstname.lastname@example.org|
|Erica Gasparotto||PhD Studentemail@example.com|
|Marco Ghilotti, PhD||Senior Post Docfirstname.lastname@example.org|
|Valentina Menetti, PhD||Post Docemail@example.com|
|Federica Marasca, PhD||Senior Post Doc|| firstname.lastname@example.org
|Maria Luce Negri||Predoctoral Fellowemail@example.com|
|Benedetto Polimeni||Predoctoral Fellow, Bioinformaticianfirstname.lastname@example.org|
|Anna Rita Putiganno||Predoctoral Fellow, Bioinformaticianemail@example.com|
|Valeria Ranzani, PhD||Research Scientist, Bioinformaticianfirstname.lastname@example.org|
|Shruti Sinha, PhD||Post Doc, Bioinformaticianemail@example.com|
|Rebecca Vadalà||PhD Studentfirstname.lastname@example.org|
- Profound Alterations of the Chromatin Architecture at Chromosome 11p15.5 in Cells From Beckwith-Wiedemann and Silver-Russell Syndromes Patients
Rovina D, La Vecchia M, Cortesi A, Fontana L, Pesant M, Maitz S, Tabano S, Bodega B, Miozzo M, Sirchia S
Sci Rep. 2020 May 19;10(1):8275.
- The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease
Marasca F, Gasparotto E, Polimeni B, Vadalà R , Ranzani V, Bodega B.
Int J Mol Sci. 2020 Apr 30;21(9):E3201.
- 3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
Marasca F, Cortesi A, Manganaro L, Bodega B.
J Vis Exp 2020 Jan 25;(155).
- Dysfunctional polycomb transcriptional repression contributes to Lamin A/C dependent muscular dystrophy
Bianchi A, Mozzetta C, Pegoli G, Lucini F, Valsoni S, Rosti V, Petrini C, Cortesi A, Gregoretti F, Antonelli L, Oliva G, De Bardi M, Rizzi R, Bodega B, Pasini D, Ferrari F, Bearzi C, Lanzuolo C
J Clin Invest. 2020;130(5):2408-2421.
- 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in Facioscapulohumeral muscular dystrophy
Cortesi A, Pesant M, Sinha S, Marasca M, Sala E, Gregoretti F, Antonelli L, Oliva G, Chiereghin C, Soldà G, Bodega B*.
Genome Res. 2019 May 16. pii: gr.233288.117. doi: 10.1101/gr.233288.117. [Epub ahead of print]
- 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.
Marasca F, Bodega B, Orlando V.
Bioessays. (2018) 40(4):e1700137
- A cytosolic Ezh1 isoform modulates a PRC2-Ezh1 epigenetic adaptive response in postmitotic cells.
Bodega B, Marasca F, Ranzani V, Cherubini A, Della Valle F, Neguembor MV, Wassef M, Zippo A, Lanzuolo C, Pagani M, Orlando V.
Nat Struct Mol Biol (2017) 24:444-452
- Chromosome Conformation Capture in Primary Human Cells.
Cortesi A, Bodega B.
Methods Mol Biol (2016) 1480:213-21
- Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, et al. , [Fantom_5 Consortium]
Science (2015) 347:1010-4
- Lamin A/C sustains PcG protein architecture, maintaining transcriptional repression at target genes.
Cesarini E, Mozzetta C, Marullo F, Gregoretti F, Gargiulo A, Columbaro M, Cortesi A, Antonelli L, Di Pelino S, Squarzoni S, Palacios D, Zippo A, Bodega B, Oliva G, Lanzuolo C.
J Cell Biol (2015) 211:533-51
- The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.
Ranzani V, Rossetti G, Panzeri I, Arrigoni A, Bonnal RJ, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M.
Nat Immunol (2015) 16:318-325
- Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth.
Zanconato F, Forcato M, Battilana G, Azzolin L, Quaranta E, Bodega B, Rosato A, Bicciato S, Cordenonsi M, Piccolo S.
Nat Cell Biol (2015) 17:1218-27
- Repetitive elements dynamics in cell identity programming, maintenance and disease.
Bodega B, Orlando V.
Curr Opin Cell Biol (2014) 31:67-73
- A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy.
Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D.
Cell (2012) 149:819-31
- Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation.
Bodega B, Ramirez GD, Grasser F, Cheli S, Brunelli S, Mora M, Meneveri R, Marozzi A, Mueller S, Battaglioli E, Ginelli E.
BMC Biol (2009) 7:41
- Evolutionary genomic remodelling of the human 4q subtelomere (4q35.2).
Bodega B, Cardone MF, Muller S, Neusser M, Orzan F, Rossi E, Battaglioli E, Marozzi A, Riva P, Rocchi M, Meneveri R, Ginelli E.
BMC Evol Biol (2007) 7:39
- The boundary of macaque rDNA is constituted by low-copy sequences conserved during evolution.
Bodega B, Cardone MF, Rocchi M, Meneveri R, Marozzi A, Ginelli E.
Genomics (2006) 88:564-71