Molecular Biology, Cytogenetics, Epigenomics Laboratory

Biologia Molecolare, Citogenetica, Epigenomica

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 (post-doc)
  • Wasma Amin Abdelgadir Ahmed (PhD student), Lorenzo Sola (PhD student)

 

RESEARCH LINES

Research projects concern the molecular mechanisms involved in maintaining the integrity of the mammalian genome that play a fundamental role in carcinogenesis and evolution. The main structures necessary for maintaining the structural and functional integrity of chromosomes are the centromeres and telomeres.

STUDY METHODS

The complementary skills of the responsible teachers make it possible to address the scientific problems described through different experimental approaches including a wide spectrum of cellular, biomolecular (including Next Generation sequencing techniques), cytogenetics (including the analysis of single chromatin molecules) and bioinformatics methods .

THE CENTROMER AND ITS EPIGENETIC NATURE

Centromeres are essential for the separation of chromosomes during cell division. Contrary to what happens for other loci, the function of the centromeres is not determined by the DNA sequence, but by epigenetic factors. In particular, centromeric chromatin is peculiar for the presence of modified histone H3, CENP-A, and numerous proteins that make up the complex called CCAN (Constitutive Centromere Associated Network). Furthermore, centrochromatin is characterized by histone modifications, the role of which in the function of the centromere is controversial. Mammalian centromeres are typically associated with highly repeating DNA in tandem (satellite DNA); this type of organization has hindered the detailed molecular analysis of centromeric chromatin.

Our research group has demonstrated for the first time the existence in nature of stable and functional centromeres without satellite DNA (Wade et al Science 2009). These centromeres are present in numerous chromosomes of the genus Equus (horses, donkeys and zebras); they constitute a unique model system for the study of the epigenetic control of centromeric function and its role in the evolution of the genome (Piras et al, Cytogenet. Genome Res. 2009; Piras et al, PLoS Genet. 2010; Purgato et al, Chromosoma 2015; Giulotto et al, Prog. Mol. Subcell. Biol. 2017; Nergadze et al, Genome Res. 2018; Cappelletti et al, Sci. Rep. 2019; Roberti et al, Genes 2019; Peng et al. Genes (Basel) 2021; Piras et al. IJMS 2022). It is known that chromosomal segregation alterations are responsible for the onset of chromosomal number abnormalities observed in most cancers. Therefore the Equidae system offers the opportunity to investigate the mechanisms involved in chromosomal instability associated with the development and progression of many forms of cancer.

The absence of DNA repeated at the centromere of many equine chromosomes offers us the opportunity to study the role of DNA methylation, transcription and histone modifications and the three-dimensional organization of centromeric chromatin.

Collaborations:

  • Aurora Ruiz-Herrera (Universitat Autonoma de Barcelona, Spain);
  • Jessica Petersen (University of Nebraska);
  • Rebecca Bellone e Carrie Finno (University of California-Davis);
  • Ernest Bailey e Theodore Kalbfleisch (University of Kentucky),The Horse Genome Project, The Horse FAANG Project.

TELOMERES

Telomeres are nucleoprotein structures located at the ends of linear chromosomes. In mammals, telomeric DNA, consisting of the tandem repetition of the hexanucleotide TTAGGG, is linked by a multiprotein complex called "shelterin". Telomeres protect the termination of chromosomes from degradation and fusion with other telomeres. Telomere malfunction causes chromosomal rearrangements that can lead to tumorigenesis. Too short telomeres are indistinguishable from accidental DNA breaks and cause genomic instability. Our group contributed to the demonstration that telomeres are transcribed in non-coding RNA molecules called Telomeric Repeat-containing RNA (TERRA) (Azzalin et al. Science 2007). Afterwards we demonstrated that telomere transcription is finely regulated (Nergadze et al. RNA 2009) and is probably involved in maintaining telomere integrity. It has been shown that the deregulation of telomeric RNA transcription is deleterious to telomere metabolism and leads to genomic instability. Defects in the regulation of telomeric RNA expression could therefore contribute to carcinogenesis and tumor progression (Vitelli et al Int J Mol Sci. 2018). Our group aims at studying the transcriptional status of telomeres in normal and tumor cells. The analysis of telomere expression in tissues obtained from patients with different types of cancer will allow us to study the link between deregulation of telomeric RNA transcription, carcinogenesis and tumor progression.

Repeated sequences identical to telomeric ones are located in internal sites of the chromosomes and called interstitial telomeres. Our work has shown that, in mammals, interstitial telomeres have been inserted in the course of evolution during the repair of double-stranded breaks through a mechanism that involves telomerase (Nergadze et al Genome Res. 2004; Nergadze et al Genome Biol. 2007, Santagostino et al Int. J. Mol. Sci, 2020, Sola et al Int. J. Mol. Sci. 2021). Our group aims at analyzing the evolution and function of interstitial telomeres using molecular, cytogenetic and bioinformatic methods.

Collaborations:

  • Francesco Lescai (DBB);
  • Claus Azzalin (Instituto de Medicina Molecular João Lobo Antunes, Lisbona)