Biology subjects

Soshnev, A. A.

Publications and source records attributed to Soshnev, A. A..

6 recordsLinked to original sources

bioRxiv2026

FetchPA: a guided, end-to-end solution for local ATAC-Seq data processing and analyses

Local genome accessibility strongly correlates with activity of cis-regulatory elements, and Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq) has emerged as method of choice to profile chromatin accessibility in both healthy and pathogenic conditions. The introduction of streamlined protocols and manufacturer kits has made this technique accessible to labs of a variety of disciplines, background, and research interests. Many bioinformatics tools have been created for the quality control, mapping, and visualization of ATAC-seq data, however these tools require familiarity with shell scripting, version control, UNIX directory structure, Python and/or R. Several pipelines for the processing of ATAC-seq data have been developed, yet even with these tools, bioinformatic analyses represents a bottleneck between wet-lab protocol execution and graphical representation of differentially accessible regions. To address this problem, we assembled FetchPA, an intuitive pipeline which allows users with virtually no scripting and version control experience to install and manage all software for end-to-end analyses of ATAC-Seq data. FetchPA handles both local and public repository sources of sequencing data, executes standard QC benchmarks, and handles genome assembly and alignment using industry-standard PEPATAC pipeline. Further, it guides the user through the identification of differentially accessible regions and allows basic exploratory analyses via a dialogue interface. FetchPA operates in Windows Subsystem for Linux (WSL) and is installed via a single script that handles all individual tools, as well as their dependencies and updates, reference genome annotations and system resource allocation.

genomics↗

bioRxiv2026

FetchR: an intuitive end-to-end solution for local RNA-Seq analyses

RNA-Seq, analyses of RNA abundance by next-generation sequencing, has become a near-universal tool in modern biology. Availability of streamlined protocols and kits, straightforward ability to multiplex hundreds of samples, low cost of short-read sequencing, and well-established analytical pipelines make RNA-Seq a method of choice when even a few genes need to be analyzed in parallel. While many tools have been developed for quality control, mapping, and visualization of RNA-Seq data, managing all these individually still requires substantial familiarity with shell scripting and R, and remains a bottleneck for laboratories with limited computational background. We assembled FetchR, an intuitive pipeline with built-in, clear explanations of features and outputs, for local analyses of RNA-Seq data from either own .fastq files or data imported from Sequence Read Archive via the ENA Portal API. The pipeline operates in Windows Subsystem for Linux (WSL) and is installed via a single script that handles all individual tools, as well as their dependencies and updates, including the reference genome annotation(s), and system requirements. The outputs include standard quality control checks, data visualization, read summation, differential gene expression analyses, visualization, and exploratory analyses using Gene Ontology and Gene Set Enrichment Analyses, as well as detailed logs of every step for subsequent reproducible reporting.

genomics↗

bioRxiv2026

Ventral tegmental area astrocytes regulate drug-cue associations and drug intake

Cocaine use disorder remains a critical public health concern with limited treatment options. Astrocytes are increasingly recognized as active regulators of neurotransmission and are emerging as important contributors to addiction neurobiology. Here, we examined how chemogenetic activation of astrocytic Gq signaling within the ventral tegmental area (VTA) influences cocaine-associated behaviors in drug-naive and cocaine-experienced rats. Using a subthreshold dose of cocaine in a conditioned place preference (CPP) paradigm, we found that VTA astrocyte Gq activation facilitated the acquisition of cocaine CPP in drug-naive rats but suppressed the development of cocaine CPP in cocaine-experienced rats. Additionally, chemogenetic activation of VTA astrocyte Gq signaling suppressed voluntary cocaine intake in a self-administration paradigm. Together, these findings demonstrate that VTA astrocyte Gq signaling shapes cocaine-associated behaviors in a drug history-dependent manner, highlighting VTA astrocytes as a potential therapeutic target in cocaine use disorder.

neuroscience↗

bioRxiv2025

Juvenile hormone degradation enzymes have shared and unique requirements in Drosophila development

Precise control of hormones is essential for animal development. Hormone bioavailability is regulated by their synthesis, transport, sequestration, natural turnover, and programmed degradation. Here, we use Drosophila melanogaster to investigate developmentally programmed degradation of the retinoid-like juvenile hormones (JHs). JHs promote juvenile growth and timely development by functionally opposing the steroid hormone, ecdysone. Despite well-characterized biochemistry, the developmental requirements for programmed JH degradation are poorly understood due to paralogue expansion. To close this knowledge gap, we generated double and triple knockout animals lacking one of two classes of JH degradation enzymes: JH esterases (JHEs) and JH epoxide hydrolases (JHEHs). We found that while both JHEs and JHEHs restrain JH signaling during Drosophila juvenile development, each has separate requirements in the regulation of developmental timing and growth. Strikingly, loss of all three JHEHs doubled the length of juvenile development, and the resulting pupae were smaller. Through targeted and genome-wide transcriptome analysis, measurements of hormone-producing glands, and rescue experiments, we uncovered both shared and unique dysregulated gene networks, some of which have established roles in the regulation of both body size and developmental timing. Our comparative analysis of both JH degradation pathways demonstrated that loss of JHEH, but not JHE, activates multiple levels of compensatory feedback to maintain homeostasis within JH and ecdysone axes. These data not only suggest that JHEH-mediated degradation is the dominant programmed JH degradation pathway in D. melanogaster development, but they also revealed new JH homeostatic mechanisms more generally. Together, this study provides new genetic tools and insights into programmed hormone degradation. Article summaryHormones control the timing of developmental transitions and growth. As such, multiple mechanisms ensure precise amounts of a hormone are available at the right time and place. Here, we investigated the poorly understood process of developmentally programmed hormone degradation using juvenile hormones (JHs) in Drosophila melanogaster as a model. We generated double and triple knockout strains to disrupt JH degradation and found an unexpected separation of requirements in regulating developmental growth and timing. Through phenotypic and transcriptomic analysis, this study provides insights into the mechanisms and complexities of programmed hormone degradation in animal development.

genetics↗

bioRxiv2025

The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity

Polycomb group proteins maintain gene expression patterns established during early development, with Polycomb Repressive Complex 2 (PRC2) methyltransferase a key regulator of cell differentiation, identity and plasticity. Consequently, extensive somatic mutations in PRC2, including gain- or loss- of function (GOF or LOF), are observed in human cancers. The regulation of chromatin structure by PRC2 is critically dependent on its EZH2 (Enhancer of Zeste Homolog 2) subunit, which catalyzes the methylation of histone H3 lysine 27 (H3K27). Recent structural studies of PRC2 revealed extensive conformational changes in the non-catalytic EZH2 N-terminal SANT-Binding Domain (SBD) during PRC2 activation, though the functional significance remains unclear. Here, we investigate how the SBD regulates PRC2 function. The domain is highly conserved in metazoans, dispensable for PRC2 assembly and chromatin localization, yet required for genome-wide histone H3K27 methylation. Further, we show that an intact SBD is necessary for the proliferation of EZH2- addicted lymphomas, and its deletion in the presence of EZH2 GOF mutations inhibits cancer cell growth. These observations provide new insights to the regulation of PRC2 activity in normal development and malignancy.

genetics↗

bioRxiv2023

Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation

Chromatin is a crucial regulator of gene expression and tightly controls development across species. Mutations in only one copy of multiple histone genes were identified in children with developmental disorders characterized by microcephaly, but their mechanistic roles in development remain unclear. Here we focus on dominant mutations affecting histone H4 lysine 91. These H4K91 mutants form aberrant nuclear puncta at specific heterochromatin regions. Mechanistically, H4K91 mutants demonstrate enhanced binding to the histone variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminishes the mutant localization to chromatin. Our functional studies demonstrate that H4K91 mutant expression increases chromatin accessibility, alters developmental gene expression through accelerating pro-neural differentiation, and causes reduced mouse brain size in vivo, reminiscent of the microcephaly phenotypes of patients. Together, our studies unveil a distinct molecular pathogenic mechanism from other known histone mutants, where H4K91 mutants misregulate cell fate during development through abnormal genomic localization.

molecular biology↗