Biology subjects

Basrai, M. A.

Publications and source records attributed to Basrai, M. A..

6 recordsLinked to original sources

bioRxiv2026

Yra2 regulates proteolysis of Cse4 to prevent its mislocalization to non-centromeric regions for chromosomal stability in budding yeast

Restricting the localization of centromere-specific histone H3 variant Cse4 (CENP-A in humans) to centromeric chromatin is essential for chromosome segregation. Mislocalization of overexpressed Cse4/CENP-A to non-centromeric regions contributes to chromosomal instability (CIN) in model organisms and human cells. CIN is an important hallmark of many cancers and hence defining mechanisms that prevent mislocalization of Cse4 is clinically significant. Here we report a role for YRA2 (Yeast RNA Annealing Protein 2) in ubiquitin mediated proteolysis of Cse4 to prevent its mislocalization for chromosomal stability. YRA2 was identified in a genome-wide screen for gene deletions that exhibit synthetic dosage lethality (SDL) upon overexpression of CSE4 (GALCSE4). We determined that yra2{Delta} strains exhibit increased Cse4 stability, enriched Cse4 chromatin association, reduced Cse4 ubiquitination, Cse4 mislocalization, and CIN. Defects in interaction of E3 ubiquitin ligase Psh1 with Cse4 contributes to stability of Cse4 in yra2{Delta} strains. Consistent with these results, overexpression of PSH1 suppresses GALCSE4 SDL in yra2{Delta} strain. We determined that Yra2 mediated proteolysis of Cse4 is independent of its RNA related functions as strain deleted for the C-terminal ChTOP domain of Yra2 with an intact N-terminal RNA binding domain exhibits GALCSE4 SDL and defects in Cse4 proteolysis. Furthermore, poly(A)+ RNA export mutants in YRA1 (yra1-2) and MEX67 (mex67-5), that interact with Yra2, do not exhibit GALCSE4 SDL and defects in RNA export are not observed in yra2{Delta} cells. In summary, we have defined a key role for Yra2 in preventing mislocalization of Cse4 by facilitating its proteolysis to preserve chromosomal stability. Article summaryAccurate segregation of chromosomes during cell division is essential because segregation errors are linked to cancer and developmental disorders. We investigated how cells prevent mislocalization of centromere-specific histone H3 variant Cse4, which is essential for faithful chromosome segregation. We found that the yeast RNA annealing protein Yra2 prevents Cse4 mislocalization by promoting Psh1 mediated ubiquitination and degradation of Cse4. Cells lacking Yra2 showed increased stability of Cse4, enhanced chromatin enrichment with mislocalization to non-centromeric regions and CIN. These defects were suppressed by induction of Psh1. Our findings reveal a novel role for Yra2 in regulating Cse4 levels for chromosomal stability.

genetics↗

bioRxiv2025

Scm3 interacts with the N-terminal tail of Cse4 to regulate kinetochore assembly in budding yeast

The kinetochore is a multiprotein complex formed at the centromeres and is essential for the faithful chromosome segregation. In most of the organisms the kinetochore is assembled on a specialized centromeric nucleosome where histone H3 is replaced by a variant, named CENP-A. In budding yeast, the CENP-A homolog, Cse4 is recruited to the centromeric nucleosome through an interaction between its C-terminal domain and a specific chaperone, named Scm3. Interestingly, following Cse4 recruitment during S phase, Scm3 persists at the centromeres throughout the cell cycle. Recent in vitro studies have reported that Scm3 also interacts with N-terminal of Cse4 (N-C) that in turn facilitates a better interaction of Ame1-Okp1 (AO) of COMA subcomplex with N-C, which promotes kinetochore assembly. In this work, using genetic and biochemical assays we provide in vivo evidence of the interaction between Scm3 and N-C. Additionally, by artificially tethering Scm3, we show that their association has the potential to stabilize a missegregating chromosome with inactive centromere, perhaps by forming an active kinetochore at an ectopic site. We propose that at the centromeres, Scm3 has two jobs in tandem - Cse4 deposition and stabilization of N-C, which together culminates into proper kinetochore assembly. This work has clinical significance as both CENP-A and its chaperone are known to be upregulated in human cells under disease states which can predispose the cells to aneuploidy due to increased chances of forming ectopic kinetochores.

cell biology↗

bioRxiv2022

Matrin3 regulates cell proliferation and spindle dynamics by regulating CDC14B alternative splicing

Matrin3 is an RNA-binding protein that affects diverse RNA-related processes, including mRNA splicing. While Matrin3 has been intensively studied in neurodegenerative diseases, its function in cancer remains unclear. Here, we discovered Matrin3-mediated regulation of mitotic spindle dynamics in colorectal cancer (CRC) cells. We identified bound and regulated Matrin3-target RNAs transcriptome-wide in CRC cells and found that Matrin3 broadly modulates mRNA splicing patterns. Among the top Matrin3 targets, we focused on CDC14B and found that Matrin3 loss increased inclusion of an exon containing a premature termination codon into the CDC14B transcript and simultaneous down-regulation of the standard CDC14B transcript. Selective knockdown of the CDC14B standard transcript phenocopied Matrin3 knockdown and exhibited reduced proliferation and defects in mitotic spindle formation, suggesting that CDC14B is a key downstream effector of Matrin3. Collectively, these data reveal an important role for the Matrin3/CDC14B axis in control of CRC cell proliferation and mitotic spindle formation.

molecular biology↗

bioRxiv2020

A Budding Yeast Model for Human Disease Mutations in the EXOSC2 Cap Subunit of the RNA Exosome

RNA exosomopathies, a growing family of tissue-specific diseases, are linked to missense mutations in genes encoding the structural subunits of the conserved 10-subunit exoribonuclease complex, the RNA exosome. Such mutations in the cap subunit gene EXOSC2 cause the novel syndrome SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies). In contrast, exosomopathy mutations in the cap subunit gene EXOSC3 cause pontocerebellar hypoplasia type 1b (PCH1b). Though having strikingly different disease pathologies, EXOSC2 and EXOSC3 exosomopathy mutations result in amino acid substitutions in similar, conserved domains of the cap subunits, suggesting that these exosomopathy mutations have distinct consequences for RNA exosome function. We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by introducing the EXOSC2 mutations in the orthologous S. cerevisiae gene RRP4. The resulting rrp4 mutant cells have defects in cell growth and RNA exosome function. We detect significant transcriptomic changes in both coding and non-coding RNAs in the rrp4 variant, rrp4-G226D, which models EXOSC2 p.Gly198Asp. Comparing this rrp4-G226D mutant to the previously studied S. cerevisiae model of EXOSC3 PCH1b mutation, rrp40-W195R, reveals that these mutants have disparate effects on certain RNA targets, providing the first evidence for different mechanistic consequences of these exosomopathy mutations. Congruently, we detect specific negative genetic interactions between RNA exosome cofactor mutants and rrp4-G226D but not rrp40-W195R. These data provide insight into how SHRF mutations could alter the function of the RNA exosome and allow the first direct comparison of exosomopathy mutations that cause distinct pathologies.

genetics↗

bioRxiv2020

Reduced Gene Dosage of Histone H4 Prevents CENP-A Mislocalization in Budding Yeast

Mislocalization of the centromeric histone H3 variant (Cse4 in budding yeast, CID in flies, CENP-A in humans) to non-centromeric regions contributes to chromosomal instability (CIN) in yeast, fly, and human cells. Overexpression and mislocalization of CENP-A has been observed in cancers, however, the mechanisms that facilitate the mislocalization of overexpressed CENP-A have not been fully explored. Defects in ubiquitin-mediated proteolysis of overexpressed Cse4 (GALCSE4) leads to its mislocalization and synthetic dosage lethality (SDL) in mutants for E3 ubiquitin ligases (Psh1, Slx5, SCFMet30, SCFCdc4), Doa1, Hir2, and Cdc7. In contrast, defects in sumoylation of GALcse4K215/216/A/R prevent its mislocalization and do not cause SDL in a psh1{Delta} strain. Here, we used a genome-wide screen to identify factors that facilitate the mislocalization of overexpressed Cse4 by characterizing suppressors of the psh1{Delta} GALCSE4 SDL. Deletions of histone H4 alleles (HHF1 or HHF2), which were among the most prominent suppressors, also suppress slx5{Delta}, cdc4-1, doa1{Delta}, hir2{Delta}, and cdc7-4 GALCSE4 SDL. Reduced dosage of H4 contributes to defects in sumoylation and reduced mislocalization of overexpressed Cse4. We determined that the hhf1-20, cse4-102, and cse4-111 mutants, which are defective in the Cse4-H4 interaction, also exhibit reduced sumoylation of Cse4 and do not display psh1{Delta} GALCSE4 SDL. In summary, we have identified genes that contribute to the mislocalization of overexpressed Cse4 and defined a role for the gene dosage of H4 in facilitating Cse4 sumoylation and mislocalization to non-centromeric regions, contributing to SDL when Cse4 is overexpressed in mutant strains.

genetics↗

bioRxiv2017

Caffeic Acid Phenethyl Ester (CAPE) Inhibits Growth of Chromosomally instable bub1Δ mutant in Saccharomyces cerevisiae

Chromosomal instability (CIN) is a hallmark of cancer cells. Spindle Assembly Checkpoint (SAC) proteins such as Bub1 monitor errors in chromosome segregation and cause cell cycle delay to prevent CIN. Altered expression of BUBl is observed in several tumor samples and cancer cell lines which display CIN. Caffeic Acid Phenethyl Ester (CAPE) which is an active component of propolis obtained from bee hives has anti-inflammatory antioxidant and anticarcinogenic properties. We used budding yeast S. cerevisiae as a model organism to investigate the molecular mechanism by which CAPE can inhibit the growth of cells with high levels of CIN. Here we show that CAPE leads to growth inhibition of bub1{Delta} strains. CAPE treatment suppressed chromosome mis-segregation in bub1{Delta} strain possibly due to apoptosis of chromosomally instable bub1{Delta} cells. We propose that CAPE may serve as a potential therapeutic agent for treatment of BUB1 deficient cancers and other cancers that exhibit CIN.

genetics↗