Biomedical subjects

Manuela Sironi

Publications and source records attributed to Manuela Sironi.

15 recordsLinked to original sources

PubMed2006

Intron size in mammals: complexity comes to terms with economy.

Different and contrasting models have been proposed to explain intron size evolution in mammals. Here, we demonstrate that intron and intergenic size per se has no adaptive role in gene expression regulation but reflects the need to preserve conserved intronic elements. Although the amount of non-coding functional elements explains the within-genome size variation of intergenic spacers, we show that an additional, additive pressure has been acting on highly expressed introns to reduce the cost of their transcription.

Animals↗

PubMed2006

A region in the dystrophin gene major hot spot harbors a cluster of deletion breakpoints and generates double-strand breaks in yeast.

Deletions within the dystrophin gene (DMD) account for >70% of mutations leading to Duchenne and Becker muscular dystrophies (DMD and BMD). Deletion breakpoints were reported to be scattered within regions that also represent meiotic recombination hot spots. Recent studies indicates that deletion junctions arise from nonhomologous end joining (NHEJ), a major pathway for repairing DNA double-strand breaks (DSBs) in mammals. Here we show that a region in intron 47 (i.e., a major deletion hot spot in the DMD gene) generates DSBs during meiosis in yeast and harbors a cluster of previously sequenced deletion breaks. Mapping of breakpoints in 26 BMD/DMD patients indicated that the frequency of breakpoint occurrence around this region is 3-fold higher than expected by chance. These findings suggest that DSBs mediate deletion formation in intron 47 and possibly account for the high frequency of meiotic recombination in the region. Statistical analysis indicated the presence of at least one other breakpoint cluster in intron 47. Taken together, these results suggest that the primary events in deletion formation occur within discrete regions and that the scattered breakpoint distribution reflects both a variable degree of DSB end processing and the availability of a small (compared to the huge regions involved) deletion junction sample.

Base Sequence↗

PubMed2006

Both conserved and non-conserved regions of Spo11 are essential for meiotic recombination initiation in yeast.

DNA double-strand breaks (DSBs) are the initiators of most meiotic recombination events. In Saccharomyces cerevisiae, at least ten genes are necessary for meiotic DSB formation. However, the molecular roles of these proteins are not clearly understood. The meiosis-specific Spo11 protein, which shows sequence similarity with a subunit of an archaeal topoisomerase, is believed to catalyze the meiotic DSB formation. Spo11 is also required for induction of meiotic DSBs at long inverted repeats and at large trinucleotide repeat tracts. Here we report the isolation and characterization of temperature-sensitive spo11-mutant alleles to better understand how Spo11 functions, and how meiotic DSBs are generated at various recombination hotspots. Analysis of mutation sites of isolated spo11-mutant alleles indicated that both N-terminal and C-terminal non-conserved residues of Spo11 are essential for the protein's function, possibly for interaction with other meiotic DSB enzymes. Several of the mutation sites within the conserved region are predicted to lie on the surface of the protein, suggesting that this region is required for activation of the meiotic initiation complex via protein-protein interaction. In addition to the conditional mutants, we isolated partially recombination-defective mutants; analysis of one of these mutants indicated that Ski8, as observed previously, interacts with Spo11 via the latter's C-terminal residues.

Alleles↗

PubMed2006

Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns.

BACKGROUND: Transposable elements (TEs) represent more than 45% of the human and mouse genomes. Both parasitic and mutualistic features have been shown to apply to the host-TE relationship but a comprehensive scenario of the forces driving TE fixation within mammalian genes is still missing. RESULTS: We show that intronic multispecies conserved sequences (MCSs) have been affecting TE integration frequency over time. We verify that a selective economizing pressure has been acting on TEs to decrease their frequency in highly expressed genes. After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. In addition to developmental regulators and transcription factors, TE-depleted regions encompass loci that might require subtle regulation of transcript levels or precise activation timing, such as growth factors, cytokines, hormones, and genes involved in the immune response. The latter, despite having reduced frequencies of most TE types, are significantly enriched in mammalian-wide interspersed repeats (MIRs). Analysis of orthologous genes indicated that MIR over-representation also occurs in dog and opossum immune response genes, suggesting, given the partially independent origin of MIR sequences in eutheria and metatheria, the evolutionary conservation of a specific function for MIRs located in these loci. Consistently, the core MIR sequence is over-represented in defense response genes compared to the background intronic frequency. CONCLUSION: Our data indicate that gene function, expression level, and sequence conservation influence TE insertion/fixation in mammalian introns. Moreover, we provide the first report showing that a specific TE family is evolutionarily associated with a gene function category.

Animals↗

PubMed2005

Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences.

The non-coding portion of human genome is punctuated by a large number of multispecies conserved sequence (MCS) elements with largely unknown function. We demonstrate that MCSs are unevenly distributed in human introns with the majority of relatively short introns (< 9 kb long) displaying no or a few MCSs and that MCS density reaching up to 10% of total size in longer introns. After correction for intron length, MCSs were found to be enriched within genes involved in development and transcription, whereas depleted in immune response loci. Moreover, many central nervous system tissues show a preferential expression of MCS-rich genes and MCS enrichment significantly correlates with gene functional complexity in terms of distinct protein domains. Analysis of human-mouse orthologous pairs indicated a significant association between intronic MCS density and conservation of protein sequence, promoter regions and untranslated sequences. Moreover, MCS density correlates with the predicted occurrence of human-mouse conserved alternative splicing events. These observations suggest that evolution acts on human genes as integrated units of coding and regulatory capacity and that functional complexity might represent a major source of negative selection on non-coding sequences. To substantiate our result, we also searched previously experimentally identified intronic regulatory elements and indicate that about half of these sequences map to an MCS; in particular, support to the notion whereby mutations in MCSs can result in human genetic diseases is provided, because three previously identified intronic pathological variations were found to occur within MCSs, and human disease and cancer genes were found significantly enriched in MCSs.

Animals↗

PubMed2005

Mutation finding in patients with dysferlin deficiency and role of the dysferlin interacting proteins annexin A1 and A2 in muscular dystrophies.

Mutations in the DYSF gene underlie two main muscle diseases: Limb Girdle Muscular Dystrophy (LGMD) 2B and Miyoshi myopathy (MM). Dysferlin is involved in muscle membrane-repair and is thought to interact with other dysferlin molecules and annexins A1 and A2 at the sarcolemma. We performed genotype/phenotype correlations in a large cohort of dysferlinopathic patients and explored the possible role of annexins as modifier factors in LGMD-2B and MM. In particular, clinical examination, expression of sarcolemmal proteins and genetic analysis were performed on 27 dysferlinopathic subjects. Expression of A1 and A2 annexins was investigated in LGMD-2B/MM subjects and in patients with other muscle disorders. We identified 24 different DYSF mutations, 10 of them being novel. We observed no clear correlation between mutation type and clinical phenotype, but MM patients were found to display muscle symptoms significantly earlier in life than LGMD subjects. Remarkably, dysferlinopathic patients and subjects suffering from other muscular disorders expressed higher levels of both annexins compared to controls; a significant correlation was observed between annexin expression levels and clinical severity scores. Also, annexin amounts paralleled the degree of muscle histopathologic changes. In conclusion, our data indicate that the pathogenesis of different inherited and acquired muscle disorders involves annexin overexpression, probably because these proteins actively participate in the plasmalemma repair process. The positive correlation between annexin A1 and A2 and clinical severity, as well as muscle histopathology, suggests that their level may be a prognostic indicator of disease.

Adolescent↗

PubMed2005

Fixation of conserved sequences shapes human intron size and influences transposon-insertion dynamics.

The basis for intron expansion in humans is largely unexplored. In this article, we demonstrate that intron expansion has primarily been determined by fixation of multispecies conserved sequences (MCSs) over time. The presence of MCSs has shaped intron features: the insertion of transposable elements (TEs) has been constrained as more MCSs were fixed. Analysis of TE and MCS distribution suggested an unprecedented estimate of information requirements for proper splicing of long introns with indication of sequence constraints extending up to >3 kb downstream 5' splice sites.

Alternative Splicing↗

PubMed2004

Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing.

The human transcriptome is constituted of a great majority of intron-containing and a minority of intron-lacking mRNAs; given the different processing these transcripts undergo, they are expected to carry, intermingled with coding properties, very different editing information. Here we applied a computational approach to compare intronless and intron-containing coding sequences. Hexamer composition comparison allowed the definition of over- and under-represented motifs in intronless genes; surprisingly, experimental testing revealed that intron-lacking coding sequences are enriched rather than depleted in elements with splicing enhancement ability. Similarly, we show evidence that intronless transcripts display a significantly higher frequency of both shuttling and non-shuttling SR protein binding sites compared to intron-containing sequences. These observations suggest that SR proteins (and possibly other splicing factors) play a role in cellular processes distinct from splicing.

Base Sequence↗

PubMed2004

Human skin-derived stem cells migrate throughout forebrain and differentiate into astrocytes after injection into adult mouse brain.

Recent evidence indicates that neural stem cell properties can be found among a mammalian skin-derived multipotent population. A major barrier in the further characterization of the human skin-derived neural progenitors is the inability to isolate this population based on expression of cell surface markers. Our work has been devoted to purified human skin-derived stem cells that are capable of neural differentiation, based on the presence or absence of the AC133 cell surface marker. The enriched skin-derived AC133(+) cells express the CD34 and Thy-1 antigens. These cells cultured in a growth medium containing epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) proliferate, forming spheres, and differentiate in vitro into neurons, astrocytes, and rarely into oligodendrocytes. Single cells from sphere cultures initiated from human purified AC133(+) cells were replated as single cells and were able to generate new spheres, demonstrating the self-renewing ability of these stem cell populations. Brain engraftment of cells obtained from human purified AC133(+)-derived spheres generated different neural phenotypes: immature neurons and a most abundant population of well differentiated astrocytes. The AC133-derived astrocytes assumed perivascular locations in the frontal cortex. No donor-derived oligodendrocytes were found in the transplanted mouse brains. Several donor small, rounded cells that expressed endothelial markers were found close to the host vessel and near the subventricular zone. Thus, mammalian skin AC133-derived cells behave as a multipotent population with the capacity to differentiate into neural lineages in vitro and, prevalently, endothelium and astrocytes in vivo, demonstrating the great plasticity of these cells and suggesting potential clinical application.

Adolescent↗

PubMed2004

An intragenic deletion/inversion event in the DMD gene determines a novel exon creation and results in a BMD phenotype.

Duchenne and Becker Muscular Dystrophy (DMD and BMD) are caused, in the majority of cases, by deletions in the dystrophin gene ( DMD). Here we describe the unprecedented case of a BMD patient carrying a large out-of-frame intragenic deletion, together with an inversion in the DMD gene, resulting in the inclusion of a novel exon in the transcript. Multiplex PCR amplification revealed the presence of a 48-52 exon deletion, but transcript analysis identified two unexpected products, neither of them including exon 53. The shorter mRNA derived from the juxtaposition of exons 47-54 (in-frame), while the longer one resulted from the inclusion of a novel 73-bp exon between exons 47 and 54. Sequence analysis revealed that the inserted sequence derived from an inverted portion of intron 53; its inclusion is predicted to determine protein truncation. The presence of a genomic inversion involving exon 53 and flanking regions was confirmed, and inversion/deletion breakpoints were sequenced. The inverted 73-bp sequence displays splicing signals at both ends and thus it is probably recognized as a novel exon when the partially inverted hnRNA is processed. These findings highlight the importance of mRNA analysis on patients that, based on routine DNA screenings, do not follow the reading-frame rule. This is the first reported patient carrying both an intragenic deletion and inversion in the DMD locus. This case might provide further insight into both the mechanisms that determine genomic rearrangements in the DMD locus and the molecular signals that drive exon inclusion.

Adult↗

PubMed2004

Silencer elements as possible inhibitors of pseudoexon splicing.

Human pre-mRNAs contain a definite number of exons and several pseudoexons which are located within intronic regions. We applied a computational approach to address the question of how pseudoexons are neglected in favor of exons and to possibly identify sequence elements preventing pseudoexon splicing. A search for possible splicing silencers was carried out on a pseudoexon selection that resembled exons in terms of splice site strength and exon splicing enhancer (ESE) representation; three motifs were retrieved through hexamer composition comparisons. One of these functions as a powerful silencer in transfection-based splicing assays and matches a previously identified silencer sequence with hnRNP H binding ability. The other two motifs are novel and failed to induce skipping of a constitutive exon, indicating that they might act as weak repressors or in synergy with other unidentified elements. All three motifs are enriched in pseudoexons compared with intronic regions and display higher frequencies in intronless gene-coding sequences compared with exons. We consider that a subpopulation of pseudoexons might rely on negative regulators for splicing repression; this hypothesis, if experimentally verified, might improve our understanding of exonic splicing regulatory sequences and provide the identification of a novel mutation target for human genetic diseases.

Animals↗

PubMed2003

Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature.

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

Amino Acid Sequence↗

PubMed2002

Relevance of sequence and structure elements for deletion events in the dystrophin gene major hot-spot.

Large intragenic deletions within the DMD locus account for about 60% of Duchenne and Becker muscular dystrophy patients. Two deletion hot-spots have been described in the dystrophin gene, but the mechanisms that determine chromosome breaks in these regions are unknown, and the huge dimensions of the gene have hampered the description of a consistent number of breakpoint sequences. A long-distance polymerase chain reaction strategy was used to amplify 20 deletion junctions involving the major hot-spot and to describe breakpoint position at the sequence level. These junctions were analyzed together with previously reported breakpoint locations so as to increase the sample number and possibly provide a comprehensive study. Minisatellite core sequences, chi elements, translin-binding sites, Pur elements, and matrix attachment regions were sought over the whole gene. Sequence-dependent DNA curvature and duplex stability were also calculated throughout the gene, and their cumulative frequency distribution was evaluated. No association with either sequence or structure elements involved in known illegitimate recombination mechanisms was identified. This study highlights the importance of a whole gene approach to rule out the presumptive role of specific features that, when locally analyzed, might suggest involvement in gene rearrangements.

Base Sequence↗

PubMed2002

Comparative analysis of the human dystrophin and utrophin gene structures.

We present analysis of intronic sequences in the human DMD and UTRN genes. In both genes accumulation of repeated elements could account for intron expansion. Out-of-frame rod-domain exons have stronger splice sites and are separated by significantly longer introns as compared to in-frame exons. These features are unique for the two homologs and not shared by other spectrin superfamily genes.

Cytoskeletal Proteins↗

PubMed2002

Alternative sources of neurons and glia from somatic stem cells.

Stem cell populations have been shown to be extremely versatile: they can generate differentiated cells specific to the tissue in which they reside and descendents that are of different germ layer origin. This raises the possibility of obtaining neuronal cells from new biological source of the same adult human subjects. In this study, we found that epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) cooperated to induce the proliferation, self-renewal, and expansion of neural stem cell-like population isolated from several newborn and adult mouse tissues: muscle and hematopoietic tissues. This population, in both primary culture and secondary expanded clones, formed spheres of undifferentiated cells that were induced to differentiate into neurons, astrocytes, and oligodendrocytes. Brain engraftment of the somatic-derived neural stem cells generated neuronal phenotypes, demonstrating the great plasticity of these cells with potential clinical application.

Aging↗