Molecular Biology, Cytogenetics, Epigenomics Laboratory
Referents:
- Prof. Solomon Nergadze: Epigenomics and Bioinformatics
- Prof. Elena Raimondi: Molecular Cytogenetics
- Prof. Elena Giulotto: Molecular and Cellular Biology
Co-workers:
- Eleonora Cappelletti (post-doc)
- Maria Francesca Piras (collaborator)
- Marialaura Biundo (PhD student)
- Edoardo Rapisarda (PhD student)
RESEARCH LINES
Research projects focus on the molecular mechanisms involved in maintaining mammalian
genome integrity, which play a fundamental role in carcinogenesis and evolution. The main
structures required for preserving the structural and functional integrity of chromosomes are
centromeres and telomeres.
A major strength of the laboratory is the integration of different experimental approaches,
including a wide range of cellular, biomolecular, genomic, cytogenetic, and bioinformatic
techniques.
FUNCTION AND EVOLUTION OF THE CENTROMERE
Centromeres are essential for chromosome segregation during cell division. Unlike other loci,
centromere function is not determined by the DNA sequence itself, but by epigenetic factors. In
particular, centromeric chromatin is characterized by the presence of the histone H3 variant CENP-A and numerous proteins that form the complex known as CCAN (Constitutive
Centromere Associated Network). In addition, centrochromatin is characterized by specific
histone modifications. Mammalian centromeres are typically associated with highly tandemly
repeated DNA (satellite DNA); this type of organization has hindered detailed molecular
analysis of centromeric chromatin. Our research group was the first to demonstrate the natural
existence of stable and functional centromeres lacking satellite DNA. These centromeres are
present in several chromosomes of the genus Equus (horses, donkeys, and zebras); they represent
a unique model system for studying the epigenetic control of centromere function and its role in
genome evolution. More recently, we have demonstrated the presence of satellite-free
centromeres in other mammalian species. The absence of repetitive DNA at the centromere
allows us to investigate the role of DNA methylation, transcription, and histone modifications in
centromere functionality, as well as to analyse the three-dimensional organization of centromeric
chromatin. Thanks to T2T (Telomere-to-Telomere) genome assemblies generated using next-
generation sequencing technologies, it is now also possible to study the molecular organization
of centromeres associated with repetitive DNA and compare it with that of single-sequence
centromeres.
Current knowledge of mammalian centromere biology is derived mainly from studies conducted
in a limited number of model organisms. Our research has highlighted that the centromere
organization observed in these models is not universal but rather represents only one of several
possible molecular structures occurring in nature.
Our aim is therefore to investigate centromere architecture in species belonging to different
mammalian orders and to compare them through genomic and epigenomic analyses in order to
define the mechanisms that have driven karyotype evolution and speciation.
Collaborations:
- Aurora Ruiz-Herrera (Universitat Autonoma de Barcelona, Spain)
- Theodore Kalbfleisch e Ernest Bailey (University of Kentucky)
- Jessica Petersen (University of Nebraska)
- Rebecca Bellone e Carrie Finno (University of California-Davis)
- Nicolas Altemose (Stanford University)
- Terje Raudsepp (Texas A&M University)
- The Horse Genome Project
- The Horse FAANG Project
- The Ruminant T2T Consortium
CENTROMERES IN CANCER
The vast majority of cancers are characterized by alterations in chromosome number caused by
segregation defects, which may result from impaired centromere function. However, centromere
biology in cancer remains poorly investigated. In particular, although deregulation of
centromeric proteins is common and associated with poor prognosis, the genomic and
epigenomic organization of centromeres in tumors is still largely unexplored. The
methodological approaches developed for studying centromere evolution in mammals will be
applied to the investigation of the molecular evolution of centromeres in cancer cell lines and tumor explants characterized by highly rearranged karyotypes. This research is conducted in
close collaboration with the Fondazione IRCCS Policlinico San Matteo.
Collaborations:
- Marco Paulli, Giuseppina Ferrario, Roberta Riboni, Giuseppe Neri (Fondazione IRCCS
Policlinico San Matteo)
TELOMERES
Telomeres are nucleoprotein structures located at the ends of linear chromosomes. In mammals,
telomeric DNA, consisting of tandem repeats of the hexanucleotide TTAGGG, is bound by a
multiprotein complex known as “shelterin.” Telomeres protect chromosome ends from
degradation and fusion with other telomeres. Telomere dysfunction causes chromosomal
rearrangements that may lead to tumorigenesis. Critically short telomeres are indistinguishable
from accidental DNA breaks and result in genomic instability. Our group contributed to
demonstrating that telomeres are transcribed into non-coding RNA molecules known as
TElomeric Repeat-containing RNA (TERRA). We subsequently demonstrated that telomere
transcription is tightly regulated and involved in maintaining telomere integrity. Repeated
sequences identical to telomeric repeats are also located at internal chromosomal sites and are
referred to as interstitial telomeres. Our studies demonstrated that, in mammals, interstitail
telomeres were inserted during evolution through the repair of double-strand breaks by a
mechanism involving telomerase. Recently, we showed that human interstitial telomeres are
transcribed and that these RNAs compose a relevant portion of the TERRA pool. Our aim is to
investigate the evolution and function of telomeres and interstitial telomeres in humans and other
mammals.
Collaborations:
- Claus Azzalin (Instituto de Medicina Molecular João Lobo Antunes, Lisbona)
Recent selected publications:
- Telomere-to-Telomere Horse and Donkey Genomes Reveal Unusual Centromere Evolution
in Equids. Li K, Cappelletti E, Dessaix C, Ciosek J, Robyn E, Johnson L, AbouEl Ela NH, Arias
X, Adelson DL, Raudsepp T, Piras FM, Laird-Smith M, Hudson E, Pickett BD, Koren S,
Walenz BP, Brooks SY, Sison C, Crawford J, Bouffard G, Phillippy AM, Miller D, Antczak DF,
Cullen J, Stroupe S, Davis B, McCue M, Durward-Akhurst S, Petersen JL, Giulotto E,
Kalbfleisch T. 2026, Cell Genomics in press;
- Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free
centromere formation in Perissodactyla. Biundo M, Piras FM, Rapisarda E, Ryder OA,
Nergadze SG, Giulotto E, Cappelletti E. 2026, Commun Biol in press;
- TERRA transcripts and promoters from telomeric and interstitial sites. Santagostino M, Sola
L, Cappelletti E, Piras FM, Gennari N, Biundo M, Nergadze SG, Giulotto E. 2025, RNA.
doi:10.1261/rna.080790.125;
- CENP-A/CENP-B uncoupling in the evolutionary reshuffling of centromeres in equids.
Cappelletti E, Piras FM, Biundo M, Raimondi E, Nergadze SG, Giulotto E. 2025, Genome Biol.
doi: 10.1186/s13059-025-03490-0;
- The localization of centromere protein A is conserved among tissues. Cappelletti E, Piras
FM, Sola L, Santagostino M, Petersen JL, Bellone RR, Finno CJ, Peng S, Kalbfleisch TS,
Bailey E, Nergadze SG, Giulotto E. 2023, Commun Biol. doi: 10.1038/s42003-023-05335-7.