Biology subjects

Arnaoutov, A.

Publications and source records attributed to Arnaoutov, A..

10 recordsLinked to original sources

bioRxiv2026

TREX2 component PCID2 scaffolds alternative SAC3-based subcomplexes with distinct RNA processing and export function

The TREX2 complex bridges transcription and RNA export. Its subunits show differences in expression, localization, and dynamics, suggesting distinct cellular roles. To understand the roles of individual TREX2 components, we characterized their interactomes. We identified novel, evolutionarily conserved SAC3(PCI-fold)-based subcomplexes with its PCID2 subunit. PCID2 acts as a scaffold for mutually exclusive yet structurally related subcomplexes with GANP, LENG8, and SAC3D1. These subcomplexes have alternative localization at the nuclear envelope, nuclear speckles and cytosol. LENG8 localizes in nuclear speckles and interacts extensively with the mRNA processing factors. LENG8 depletion alters mRNA processing and polyadenylation site usage. LENG8 thus acts upstream of the canonical TREX2 complex, in which PCID2 cooperates with GANP in mRNA export. Together, our findings reveal that TREX2 is not a uniform complex but a modular system, in which TREX2 subunits can assemble into functionally distinct subcomplexes through interacting partners that define their specificity and alternative functions. HIGHLIGHTSO_LITREX2 subunits play distinct roles in RNA retention and exhibit subunit-specific preference for interactions with different protein partners C_LIO_LIPCID2 forms mutually exclusive subcomplexes with GANP, LENG8, and SAC3D1 C_LIO_LIGANP, LENG8, and SAC3D1 alter PCID2 intracellular localization C_LIO_LILENG8 is a nuclear speckle protein that modulates alternative mRNA processing C_LI

molecular biology↗

bioRxiv2026

The gamma-Tubulin Ring Complex promotes mitotic spindle integrity and acts as a microtubule minus-end cap during mitosis

{gamma}-TuRC is the primary microtubule (MT) nucleator in eukaryotic cells. Vertebrate {gamma}-TuRC is composed of {gamma}-tubulin and the {gamma}-Tubulin Complex Proteins (GCPs): GCP2, GCP3, GCP4, GCP5, and GCP6. {gamma}-TuRC localizes to MT-Organizing Centers (MTOCs) and promotes MT nucleation by providing a structural template that mirrors the 13-protofilament symmetry of the MT lattice. To understand the contribution of individual {gamma}-TuRC subunits in mitotic spindle dynamics, we endogenously tagged GCP2, GCP4 or GCP6 with an Auxin-Inducible Degron (AID) tag, enabling precise and rapid depletion of each protein. When depletion occurred before mitotic entry, we observed that cells arrested in prometaphase and that loss of any single subunit resulted in displacement of all {gamma}-TuRC components from spindle poles. In cells with preformed spindles, depletion triggered rapid spindle collapse, demonstrating that {gamma}-TuRC remains essential for the maintenance of spindle integrity. Remarkably, depletion of KIF2A, a MT-depolymerizing kinesin, rescued spindle collapse after {gamma}-TuRC loss, suggesting that KIF2A activity contributes to the spindle instability observed in the absence of {gamma}-TuRC. These findings indicate a dual role of {gamma}-TuRC in mitosis: acting not only as a critical MT nucleation factor for initiation of spindle assembly but also as a stabilizing and capping structure at the minus ends of spindle MTs to preserve spindle integrity.

cell biology↗

bioRxiv2025

Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity

The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. Here, we apply the auxin-inducible degron (AID) system to rapidly deplete each lamin isoform within one cell cycle and reveal the immediate impacts of lamin loss on the nucleus. Surprisingly, neither acute lamin A/C (LA/C), lamin B1 (LB1), nor lamin B2 (LB2) depletion altered nuclear shape or induced nuclear blebbing, indicating that acute lamin loss is not sufficient to alter nuclear morphology. LB1 depletion is immediately followed by LA/C meshwork disorganization due to actin cytoskeletal forces on the lamina, yet neither LA/C nor LB1 depletion induced nuclear rupturing. We found that the abundant inner nuclear membrane protein LAP2{beta} protects nuclear integrity in the absence of LB1, as depletion of both LB1 and LAP2{beta} induced severe LA/C disorganization and frequent nuclear rupturing. Depolymerization of the actin cytoskeleton prevents nuclear rupture in LAP2{beta}- and LB1-depleted nuclei. We conclude that both LB1 and LAP2{beta} resist cytoskeletal force to maintain regular lamin A/C meshwork organization and preserve nuclear integrity.

cell biology↗

bioRxiv2024

Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast, but much less is known about the human complex. Auxin-induced degradation was used to rapidly deplete the scaffold subunit CNOT1, and CNOT4, to characterize the functions of human CCR4-NOT in gene regulation. Depleting CNOT1 increased RNA levels and caused a widespread decrease in RNA decay. In contrast, CNOT4 depletion only modestly changed steady-state RNA levels and, surprisingly, led to a global acceleration in mRNA decay. Further, depleting either subunit resulted in a global increase in RNA synthesis. In contrast to most of the genome, the transcription of KRAB-Zinc-Finger-protein (KZNFs) genes, especially those on chromosome 19, was repressed. KZNFs are transcriptional repressors of retrotransposable elements (rTEs), and consistent with the decreased KZNFs expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. These data establish CCR4-NOT as a global regulator of gene expression and a novel silencer of rTEs.

molecular biology↗

bioRxiv2021

Role of the Topoisomerase IIα Chromatin Tether domain in Nucleosome Binding & Chromosome Segregation

Due to the intrinsic nature of DNA replication, replicated genomes retain catenated genomic loci that must be resolved to ensure faithful segregation of sister chromatids in mitosis. Type II DNA Topoisomerase (TopoII) decatenates the catenated genomic DNA through its unique Strand Passage Reaction (SPR). Loss of SPR activity results in anaphase chromosome bridges and formation of Polo-like Kinase Interacting Checkpoint Helicase (PICH)-coated ultra-fine DNA bridges (UFBs) whose timely resolution is required to prevent micronuclei formation. Vertebrates have two TopoII isoforms- TopoII and TopoII{beta}, that share a conserved catalytic core. However, the essential mitotic function of TopoII cannot be compensated by TopoII{beta}, due to differences in their catalytically inert C-terminal domains (CTDs). Using genome-edited human cells, we show that specific binding of TopoII to methylated histone, tri-methylated H3K27 (H3K27me3), via its Chromatin Tether (ChT) domain within the CTD contributes critically to avoid anaphase UFB formation. Reducing H3K27 methylation prior to mitosis increases UFBs, revealing a requirement for proper establishment of H3K27me3 after DNA replication to facilitate TopoII-ChT dependent UFB prevention. We propose that interaction of the TopoII-ChT with H3K27me3 is a key factor that ensures the complete resolution of catenated loci to permit faithful chromosome segregation in human cells. Summary StatementGenomic catenations originating from the DNA replication process must be resolved by DNA Topoisomerase II (TopoII) to permit sister chromatid disjunction. The results show that specific recognition of methylated histone containing chromatin by TopoII is critical for complete resolution of the genome.

cell biology↗

bioRxiv2020

The Nuclear Pore Complex consists of two independent scaffolds

Macromolecular transport between the nucleus and cytoplasm is mediated through Nuclear Pore Complexes (NPCs), which are built from multiple copies of roughly 34 distinct proteins, called nucleoporins1-3. Models of the NPC depict it as a composite of several sub-domains that have been named the outer rings, inner ring, cytoplasmic fibrils and nuclear basket. While the NPC has been extensively studied, the roles of individual nucleoporins within NPCs and their functional interactions remain poorly understood. Here, we applied a rapid degron system to systematically investigate how individual nucleoporins contribute toward NPC architecture. We find that acute depletion of outer ring components (NUP96 or NUP107) disperses the outer ring and cytoplasmic fibrils without disassembly of inner ring members. Conversely, rapid degradation of the inner ring complex component NUP188 disrupts the inner ring without dislodging outer ring members. We also found that depletion of NUP93 destabilized all NPC domains, indicating that it has a unique role as a lynchpin of NPC structure. Our data highlight the modular nature of NPC organization, suggesting that the outer and inner ring complexes do not extensively rely on each other for structural stability after NPC assembly is complete. This dynamic assessment provides new insights regarding the remarkable structural independence of domains within the NPC.

cell biology↗

bioRxiv2020

PICH translocase activity is required for proper distribution of SUMOylated proteins on mitotic chromosomes

Proper chromosome segregation is essential for faithful cell division and if not maintained results in defective cell function caused by abnormal distribution of genetic information. Polo-like kinase 1 interacting checkpoint helicase (PICH) is a DNA translocase essential in chromosome bridge resolution during mitosis. Its function in resolving chromosome bridges requires both DNA translocase activity and ability to bind chromosomal proteins modified by Small Ubiquitin-like modifier (SUMO). However, it is unclear how these activities are cooperating to resolve chromosome bridges. Here, we show that PICH specifically promotes the organization of SUMOylated proteins like SUMOylated TopoisomeraseIIα (TopoIIα) on mitotic chromosomes. Conditional depletion of PICH using the Auxin Inducible Degron (AID) system resulted in the retention of SUMOylated chromosomal proteins, including TopoIIα, indicating that PICH functions to control proper association of these proteins with chromosomes. Replacement of PICH with its mutants showed that PICH is required for the proper organization of SUMOylated proteins on chromosomes. In vitro assays showed that PICH specifically attenuates SUMOylated TopoIIα activity using its SUMO-binding ability. Taken together, we propose a novel function of PICH in remodeling SUMOylated proteins to ensure faithful chromosome segregation.Summary Statement Polo-like kinase interacting checkpoint helicase (PICH) interacts with SUMOylated proteins to mediate proper chromosome segregation during mitosis. The results demonstrate that PICH controls association of SUMOylated chromosomal proteins, including Topoisomerase IIα, and that function requires PICH translocase activity and SUMO binding ability.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsTopoIIαTopoisomerase IIαPICHPolo-like kinase interacting checkpoint helicaseSPRStrand passage reactionSUMOSmall ubiquitin-like modifierXEEXenopus egg extractCSFCytostatic factordnUbc9dominant negative E2 SUMO-conjugating enzymeSENPSentrin-specific proteasePIASProtein inhibitor of activated STATSIMSUMO-interacting-motifView Full Text

cell biology↗

bioRxiv2019

PICH promotes SUMOylated TopoisomeraseIIα dissociation from mitotic centromeres for proper chromosome segregation

Polo-like kinase interacting checkpoint helicase (PICH) is a SNF2 family DNA translocase and is a Small Ubiquitin-like modifier (SUMO) binding protein. Despite that both translocase activity and SUMO-binding activity are required for proper chromosome segregation, how these two activities function to mediate chromosome segregation remains unknown. Here, we show that PICH specifically promotes dissociation of SUMOylated TopoisomeraseII (TopoII) from mitotic chromosomes. When TopoII is stalled by treatment of cells with a potent TopoII inhibitor, ICRF-193, TopoII becomes SUMOylated, and this promotes its interaction with PICH. Conditional depletion of PICH using the Auxin Inducible Degron (AID) system resulted in retention of SUMOylated TopoII on chromosomes, indicating that PICH removes stalled SUMOylated TopoII from chromosomes. In vitro assays showed that PICH specifically regulates SUMOylated TopoII activity using its SUMO-binding and translocase activities. Taken together, we propose a novel mechanism for how PICH acts on stalled SUMOylated TopoII for proper chromosome segregation.\n\nSummary StatementPolo-like kinase interacting checkpoint helicase (PICH) interacts with SUMOylated proteins to mediate proper chromosome segregation during mitosis. The results demonstrate that PICH promotes dissociation of SUMOylated TopoisomeraseII from chromosomes and that function leads to proper chromosome segregation.

cell biology↗

bioRxiv2019

IRBIT Directs Differentiation of Intestinal Stem Cell Progeny to Maintain Tissue Homeostasis

The maintenance of the intestinal epithelium is ensured by the controlled proliferation of intestinal stem cells (ISCs) and differentiation of their progeny into various cell types, including enterocytes (ECs) that both mediate nutrient absorption and provide a barrier against pathogens. The signals that regulate transition of proliferative ISCs into differentiated ECs are not fully understood. IRBIT is an evolutionarily conserved protein that regulates ribonucleotide reductase (RNR), an enzyme critical for the generation of DNA precursors. Here, we show that IRBIT expression in ISC progeny within the Drosophila midgut epithelium cells is essential for their differentiation via suppression of RNR activity. Disruption of this IRBIT-RNR regulatory circuit causes a rapid, premature loss of intestinal tissue integrity as flies age. This age-related dysplasia can be reversed by suppression of RNR activity in ISC progeny. Collectively, our findings demonstrate an unexpected and novel role of the IRBIT-RNR pathway in gut homeostasis.

developmental biology↗

bioRxiv2019

Distinct Basket Nucleoporins roles in Nuclear Pore Function and Gene Expression: Tpr is an integral component of the TREX-2 mRNA export pathway

Nuclear pore complexes (NPCs) are important for many processes beyond nucleocytoplasmic trafficking, including protein modification, chromatin remodeling, transcription, mRNA processing and mRNA export. The multi-faceted nature of NPCs and the slow turnover of their components has made it difficult to understand the role of basket nucleoporins (Nup153, Nup50 and Tpr) in these diverse processes. To address this question, we used an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins: Loss of individual nucleoporins caused distinct alteration in patterns of nucleocytoplasmic trafficking and gene expression. Importantly, Tpr elimination caused rapid and pronounced changes in transcriptomic profiles within two hours of auxin addition. These changes were dissimilar to shifts observed after loss of Nup153 or Nup50, but closely related to changes after depletion of mRNA export receptor NXF1 or the GANP subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex. Moreover, GANP association to NPCs was specifically disrupted upon TPR depletion. Together, our findings demonstrate a unique and pivotal role of Tpr in regulating gene expression through GANP- and/or NXF1-dependent mRNA nuclear export.

cell biology↗