Biology subjects

Vibranovski, M. D.

Publications and source records attributed to Vibranovski, M. D..

7 recordsLinked to original sources

bioRxiv2026

Widespread occurrence of XXY females in Drosophila mojavensis and related species

Bridges first reported that XXY individuals are fertile females in Drosophila melanogaster, arising at low frequency (~1/2000) through errors in chromosome segregation (BRIDGES 1914; BRIDGES 1916). Although widely used in genetic studies, XXY females are seldom found in wild-type strains or natural populations, presumably because natural selection keeps them at very low frequency. Here we show that many wild-type strains of D. mojavensis and its close relatives D. arizonae, D. navojoa, and D. wheeleri carry XXY and XXYY females at frequencies of up to 88%; males from these strains are frequently XYY or XYYY. Although field collections were hampered by population declines and safety concerns, we found one XXY female (out of 87) and one XYY male (out of 36) in a natural population of D. mojavensis, indicating that these genotypes also occur at appreciable frequencies in nature. XXY females are expected to produce XY-bearing and X-bearing eggs in equal proportions; instead, we found a 57:43 ratio. Mathematical modeling shows that this meiotic-drive advantage is sufficient to explain high frequencies of XXY females. It is universally accepted that Y evolution responds exclusively to male selection, yet in XXY-bearing species it also responds to female fitness.

evolutionary biology↗

bioRxiv2024

Meiotic Sex Chromosome Inactivation: conservation across the Drosophila genus

The inherent difference between sex chromosomes in males and females drives conflicts in gene expression, leading to adaptations such as Meiotic Sex Chromosome Inactivation (MSCI). In this study, we explore the evolutionary dynamics of MSCI within the Drosophila genus by analyzing transcriptomes across different stages of spermatogenesis in D. melanogaster and its progressively more distant relatives, D. simulans, D. willistoni, and D. mojavensis. Stage-specific bulk RNA sequencing, showing a strong correlation in spermatogenic gene expression patterns among these species, revealed that MSCI dates back to the early evolution of the Drosophila genus, impacting the regulation of both coding and long non-coding RNAs. Notably, for newly evolved genes, X-linked genes show higher expression levels than autosomal genes during mitosis and meiosis, indicating that MSCI predominantly regulates older genes. In contrast, newly evolved autosomal genes exhibit a gradual increase in expression throughout spermatogenesis, reaching their peak in the post-meiotic phase. During this phase, the expression of X-linked new genes decreases, eventually aligning with that of autosomal genes. This expression pattern suggests that haploid selection plays a crucial role in the regulation of new genes, with monoallelic expression of the X chromosome providing an advantage across all stages of germline development, while autosomal gene expression gains a selective edge primarily in the post-meiotic phase. Together, these findings provide new insights into the evolution of sex chromosomes and highlight the critical role of MSCI in shaping gene expression profiles in Drosophila.

genetics↗

bioRxiv2024

OligoY pipeline for full Y chromosome painting

MotivationThe standard protocol for designing probes used in full chromosome fluorescent labeling experiments does not include repetitive sequences to avoid off-target hybridization. Due to the Y chromosomes highly repetitive nature, most assembly nowadays still have heavily fragmented and incomplete Y sequences. Among these, the remaining non-repetitive sequences are insufficient to design probes and efficiently perform FISH Oligopaint assays, since they do not cover most regions of the chromosome. Ergo, cytogenetic studies with the Y are sparse, and analysis such as its function throughout the cell cycle and insights into its evolutionary history and relationships with other regions of the genome remain poorly studied. ResultsIn this work, we introduce a new pipeline for designing FISH Oligopaint probes for the Y chromosome of any species of interest. OligoY pipeline uses open-source tools, enriches the amount of contigs assigned to the Y chromosome from the draft assembly, and effectively uses repetitive sequences unique to the target chromosome to design probes. Throughout all of its steps, the pipeline guarantees the user the autonomy to choose parameters, thus maximizing overall efficiency of cytogenetic experiments. After extensive in silico and in situ tests and validations with Drosophila melanogaster, we showed for the first time a pipeline for probe design that significantly increases previous Y chromosome staining with no off-target signal. AvailabilityThe pipeline is available at https://github.com/isabela42/OligoY.

bioinformatics↗

bioRxiv2023

Retro-miRs: Novel and functional miRNAs originated from mRNA retrotransposition

BackgroundReverse transcribed gene copies, or retrocopies, have emerged as a major source of evolutionary novelties. MicroRNAs (miRNAs) are small, highly conserved RNAs molecules among species that serve as key post-transcriptional regulators of gene expression. The birth and subsequent evolution of miRNAs have been addressed, but not fully. ResultsIn this study, we carried out a comprehensive investigation of miRNAs origination through retroduplicated mRNA sequences (retrocopies). We identified 17 retroduplicated miRNAs (retro-miRs) that emerged from mRNAs retrocopies. Four of these retro-miRs had de novo origination within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and were duplicated along with their host mRNAs. We found that retro-miRs are primates specific, including 5 retro-miRs conserved among all primates and two human-specific retro-miRs. All of the retro-miRs were expressed and had predicted and experimentally validated target genes, with the exception of miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes, such as metabolic processes, cell signaling and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs have a potential oncogenic role in cancer, targeting key cancer genes and being overexpressed in several cancer types, including Liver Hepatocellular Carcinoma and Stomach Adenocarcinoma. ConclusionOur findings demonstrate that mRNAs retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play roles in cancer.

genomics↗

bioRxiv2020

Dynamic Sex Chromosome Expression in Drosophila Male Germ Cells

Sex chromosome gene content and expression is unusual. In many organisms the X and Y chromosomes are inactivated in spermatocytes, possibly as a defense mechanism against insertions into unpaired chromatin. In addition to current sex chromosomes, Drosophila has a small gene-poor X-chromosome relic (4th) that re-acquired autosomal status. Using single cell RNA-Seq, we demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes. In contrast, genes on the single Y chromosome become maximally active in primary spermatocytes. Reduced X steady-state transcript levels are due to failed activation of RNA-Polymerase-II by phosphorylation of Serine 2 and 5. One Sentence SummarySex chromosome expression during spermatogenesis at the single cell level

developmental biology↗

bioRxiv2020

Natural selection and parallel clinal and seasonal changes in Drosophila melanogaster

Spatial and seasonal variation in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because non-adaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal change. Here, we test whether there is a genome-wide correlation between clinal and seasonal change, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the US, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variation, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation which happens over space and time in D. melanogaster.

evolutionary biology↗

bioRxiv2019

Response to \"Expression reduction of biallelically transcribed X-linked genes during the female human preimplantation development.\"

Reinius and Sandberg (2019) have recently shown that X-linked balletic gene expression decreases during human preimplantation embryonic development, corroborating their previous hypothesis of X dampening as a mechanism of dosage compensation. Here we demonstrate that their analyses are based on biologically false premises, thus not demonstrating the phenomena of X dampening in humans.

genetics↗