6 results on '"Andrea Luchetti"'
Search Results
2. Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence
- Author
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Alessandro Formaggioni, Andrea Luchetti, and Federico Plazzi
- Subjects
mitochondrial genome ,mtDNA architecture ,mtDNA structure ,nucleotide composition ,compositional bias ,strand asymmetry ,Science - Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
- Published
- 2021
- Full Text
- View/download PDF
3. Riding the Wave: The SINE-Specific V Highly-Conserved Domain Spread into Mammalian Genomes Exploiting the Replication Burst of the MER6 DNA Transposon
- Author
-
Andrea Luchetti, Mariana Lomiento, and Barbara Mantovani
- Subjects
highly-conserved domains ,mammalia ,tc1/mariner transposon ,short interspersed elements (sines) ,miniature inverted-repeat transposable element (mite) ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals.
- Published
- 2019
- Full Text
- View/download PDF
4. A Perturbed MicroRNA Expression Pattern Characterizes Embryonic Neural Stem Cells Derived from a Severe Mouse Model of Spinal Muscular Atrophy (SMA)
- Author
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Andrea Luchetti, Silvia Anna Ciafrè, Michela Murdocca, Arianna Malgieri, Andrea Masotti, Massimo Sanchez, Maria Giulia Farace, Giuseppe Novelli, and Federica Sangiuolo
- Subjects
survival motor neuron (SMN) ,spinal muscular atrophy (SMA) ,neural stem cells (NSCs) ,motor neurons (MNs) ,microRNAs (miRNAs) ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder and the leading genetic cause of death in infants. Despite the disease-causing gene, survival motor neuron (SMN1), encodes a ubiquitous protein, SMN1 deficiency preferentially affects spinal motor neurons (MNs), leaving the basis of this selective cell damage still unexplained. As neural stem cells (NSCs) are multipotent self-renewing cells that can differentiate into neurons, they represent an in vitro model for elucidating the pathogenetic mechanism of neurodegenerative diseases such as SMA. Here we characterize for the first time neural stem cells (NSCs) derived from embryonic spinal cords of a severe SMNΔ7 SMA mouse model. SMNΔ7 NSCs behave as their wild type (WT) counterparts, when we consider neurosphere formation ability and the expression levels of specific regional and self-renewal markers. However, they show a perturbed cell cycle phase distribution and an increased proliferation rate compared to wild type cells. Moreover, SMNΔ7 NSCs are characterized by the differential expression of a limited number of miRNAs, among which miR-335-5p and miR-100-5p, reduced in SMNΔ7 NSCs compared to WT cells. We suggest that such miRNAs may be related to the proliferation differences characterizing SMNΔ7 NSCs, and may be potentially involved in the molecular mechanisms of SMA.
- Published
- 2015
- Full Text
- View/download PDF
5. Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence
- Author
-
Andrea Luchetti, Federico Plazzi, Alessandro Formaggioni, Formaggioni A., Luchetti A., and Plazzi F.
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Science ,Mitochondrion ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Complete sequence ,Compositional bia ,Gene ,compositional bias ,Ecology, Evolution, Behavior and Systematics ,nucleotide composition ,Paleontology ,Chromosome ,Eukaryota ,mtDNA architecture ,strand asymmetry ,Multipartite ,030104 developmental biology ,Space and Planetary Science ,Evolutionary biology ,mitochondrial genome ,GenBank ,mtDNA expansion ,mtDNA structure - Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans), the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans), the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively), even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases, moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
- Published
- 2021
6. Riding the Wave: The SINE-Specific V Highly-Conserved Domain Spread into Mammalian Genomes Exploiting the Replication Burst of the MER6 DNA Transposon
- Author
-
Mariana Lomiento, Barbara Mantovani, Andrea Luchetti, and A. Luchetti, M. Lomiento, B. Mantovani
- Subjects
0106 biological sciences ,0301 basic medicine ,Transposable element ,tc1/mariner transposon ,Protein domain ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,Catalysis ,highly-conserved domain ,Evolution, Molecular ,Inorganic Chemistry ,lcsh:Chemistry ,03 medical and health sciences ,Animals ,Humans ,DNA transposon ,Sine ,Physical and Theoretical Chemistry ,Molecular Biology ,Gene ,lcsh:QH301-705.5 ,Phylogeny ,Spectroscopy ,Short Interspersed Nucleotide Elements ,Mammals ,highly-conserved domains ,miniature inverted-repeat transposable element (mite) ,Organic Chemistry ,short interspersed elements (sines) ,General Medicine ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Homo sapiens ,Evolutionary biology ,DNA Transposable Elements ,Amniote ,mammalia - Abstract
Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals.
- Published
- 2019
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