Biology subjects

Giuliani, C.

Publications and source records attributed to Giuliani, C..

4 recordsLinked to original sources

bioRxiv2025

HaploExplore, first software specifically designed for the detection of minor allele (MiA-) Haploblocks

MotivationHaplotype blocks in the genome are informative of evolutionary processes and they play a pivotal role in describing the genomic variability across human populations and susceptibility/resistance to diseases. Several software have been developed for haplotype blocks detection, but they do not distinguish between the impacts of major and minor SNP alleles. In this study, we present a powerful haploblock detection software, specifically designed for identifying haploblocks associated with SNP minor allele haploblocks (MiA-haploblocks). These haploblocks are particularly important as they can significantly influence phenotypic traits, offering a novel approach for studying genetic associations and complex traits. ResultsHaploExplore operates on VCF files containing phased data, exhibiting rapid processing times and generating user-friendly outputs. Its results are convergent for populations starting from 100 individuals. A comparative analysis of HaploExplore against other haploblock detection software revealed its superiority in terms of either simplicity, or flexibility, or speed, with the unique capability to target minor alleles. HaploExplore will be very useful for evolutionary genomics and for GWAS analysis in human diseases, given that the effects of genetic associations may accumulate within a specific haploblock.

genomics↗

bioRxiv2023

Epigenetic features of far northern Yakutian population

Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below -40{degrees}C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. This work reports the first epigenetic study of the Yakutian population using whole blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions.

genetics↗

bioRxiv2020

DLX5/6 GABAergic expression affects social vocalization: implications for human evolution

DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape...) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identify an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.

evolutionary biology↗

bioRxiv2019

Altitude-wise analysis of co-occurrence networks of mitochondrial genome in Asian population

Networks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We have studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mt-DNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects and variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clusteringrevealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral RSRS50 variant 10398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.

systems biology↗