Biology subjects

Iesmantavicius, V.

Publications and source records attributed to Iesmantavicius, V..

9 recordsLinked to original sources

bioRxiv2024

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin

Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation-mass spectrometry and chromatin immunoprecipitation sequencing. Our study identified protein interactors for half the TFs, with over a quarter potentially forming stable complexes. We discovered DNA binding sites for most TFs across 2,027 unique genomic regions, revealing motifs for 38 TFs and uncovering a complex regulatory network of extensive TF cross- and autoregulation. Characterization of the largest TF family revealed conserved DNA sequence preferences but diverse binding patterns, and identified a repressive heterodimer, Ntu1/Ntu2, linked to perinuclear gene localization. Our TFexplorer webtool makes all data interactively accessible, offering new insights into TF interactions and regulatory mechanisms with broad biological relevance. HIGHLIGHTSO_LIComprehensive strain library of endogenously tagged S. pombe TFs C_LIO_LIExperimentally determined atlas of TF interactions with proteins and chromatin C_LIO_LITFexplorer web application for interactive exploration of TF interactomes C_LIO_LIIdentification of repressive Nattou complex linked to perinuclear gene localization C_LI

molecular biology↗

bioRxiv2024

Ubiquitination mediates protein localization in RNA virus-infected cells

Viruses trigger monocytes proinflammatory and antiviral responses. Ubiquitination, a post-translational modification primarily marking proteins for degradation, regulates cellular responses to virus infection. However, a comprehensive analysis of virus-induced ubiquitination in monocytes is lacking. Here we identified a widespread increase of ubiquitination under viral RNA challenge or influenza infection in monocytes. Systematic proteome studies revealed that influenza infection elicits dynamic ubiquitinome alterations, with a notable transition from early to late stage. Most of this increased ubiquitination is not proteolytic and targets proteins involved in subcellular localization, such as the mitochondrial protein COA7 which, when ubiquitinated during infection, translocates to the nucleus and inhibits stress granules formation and TNF- expression. Blocking ubiquitination halts viral ribonucleoproteins nuclear export, highlighting ubiquitinations importance for protein localization during virus infection.

molecular biology↗

bioRxiv2024

Chromatin-dependent motif syntax defines differentiation trajectories

Transcription factors recognizing short DNA sequences within gene regulatory regions are crucial drivers of cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, NGN2 and MyoD1, which recognize ubiquitous E-box motifs yet instigate distinct cell fates--neurons and muscles, respectively. Following controlled induction in embryonic stem cells, we monitor binding across differentiation trajectories, employing an interpretable machine-learning approach integrating pre-existing DNA accessibility data. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding and predicting genome engagement with high precision. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer-factors, influenced by multi-motifs, rotational spacing, flanking sequences, and specific interaction partners, accounting for subsequent lineage divergence. Extending our methodology to other models demonstrates how such combination of opportunistic-binding and context-specific chromatin opening underpin transcription factor specificity driving differentiation trajectories.

genomics↗

bioRxiv2024

A conserved chronobiological complex times C. elegans development

The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for LIN-42s function in timing rhythmic development. Here, using targeted deletions, we find that the LIN-42 PAS domains are dispensable for the proteins function in timing molts. Instead, we observe arrhythmic molts upon deletion of a distinct sequence element, conserved with PER. We show that this element, designated CK1{delta}-binding domain (CK1BD), mediates stable binding to KIN-20, the C. elegans CK1{delta}/{varepsilon} orthologue. We demonstrate that CK1{delta} phosphorylates LIN-42 and define two conserved helical motifs in the CK1BD, CK1BD-A and CK1BD-B, that have distinct roles in controlling CK1{delta}-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molting timing in vivo, and loss of LIN-42 binding changes KIN-20 subcellular localization. The interactions mirror the central role of a stable circadian PER-CK1 complex in setting a robust [~]24-hour period. Hence, our results establish LIN-42/PER - KIN-20/CK1{delta}/{varepsilon} as a functionally conserved signaling module of two distinct chronobiological systems.

developmental biology↗

bioRxiv2023

Nitrogen signaling factor triggers a respiration-like gene expression program

Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin Nitrogen Signaling Factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program independently of the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.

microbiology↗

bioRxiv2023

einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

We describe einprot, an R package providing easy-to-use reproducible workflows for quality control, statistical analysis and visualization of quantitative proteomics data. einprot is applicable to tabular output from MaxQuant, Proteome Discoverer and FragPipe, and a single function call generates an html report that describes the full analysis pipeline applied to the data and contains static and interactive figures and tables for further exploration. This has the potential to facilitate routine analyses as well as to provide a standardized, yet comprehensive way to communicate results to collaborators and the broader community. The source file underlying the report is also returned, giving the user full flexibility to further modify the workflow according to their needs.

bioinformatics↗

bioRxiv2023

TOBF1 modulates mouse embryonic stem cell fate through co-transcriptional regulation of alternative splicing

Embryonic stem (ES) cells retain the ability to undergo lineage-specific differentiation that can eventually give rise to different cell types that constitute an organism. Although stem cell specific biological networks of transcription factors and epigenetic modifiers are well established, how the ES cell specific transcriptional and alternative splicing (AS) machinery regulate their expression has not been sufficiently explored. In this study, we show that the lncRNA associated protein TOBF1 regulates the co-transcriptional alternative splicing of transcripts necessary for maintaining stem cell identity in mouse ES cells. Overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and alternative splicing upon its disruption unmasked local nuclear territories where these distinct events converge, ultimately leading to the maintenance of mouse ES cell identity.

developmental biology↗

bioRxiv2022

Mouse Nuclear RNAi-defective 2 Promotes Splicing of Weak 5' Splice Sites

Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5 splice site (5SS). In mammals, many introns contain weak 5SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

molecular biology↗

bioRxiv2018

Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation

Mammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking-and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

genomics↗