Biology subjects

Yunusova, A.

Publications and source records attributed to Yunusova, A..

4 recordsLinked to original sources

bioRxiv2025

A novel role for the CNTN6 locus in lumenization and radial glial cell fate determination during early human cortical development revealed in cerebral organoids

Neurodevelopmental disorders are a class of heterogeneous diseases with a significant genetic contribution, including pathologies resulting from copy number variations (CNVs). Recent advancements in genetic diagnostic technologies have led to the identification of new genes associated with neurodevelopmental disorders through CNVs. One such gene is CNTN6, whose variants and CNVs are associated with intellectual disability and autism spectrum disorders. Cntn6 encodes a neural cell adhesion molecule involved in rodents in axon and dendrite guidance, synapse formation, and oligodendrocyte differentiation, playing a critical role in brain development. However, in humans, the specific molecular and cellular pathogenetic mechanisms remain elusive. Using various techniques to model human brain development pathologies, such as somatic cell reprogramming, cerebral organoids, and genome editing, we established that the CNTN6 locus is involved in the lumenization and cell identity of radial glial cells, as well as in regulating their proliferation. Furthermore, we found that the CNTN6 locus is involved in the nuclear-cytoplasmic translocation of PAX6 protein, a key regulator of forebrain development. Molecular studies revealed that CNTN6 partially functions through the Notch signaling pathway during the early stages of human brain development. Our findings unveil a novel role of the CNTN6 locus in the early stages of human cortical development.

developmental biology↗

bioRxiv2025

Condensins-mediated mitotic folding persists as a structural echo in interphase chromatin

The Structural Maintenance of Chromosomes (SMC) protein complexes, cohesin and condensins, orchestrate cell cycle-dependent transitions in chromosome folding: from the relatively decondensed interphase chromatin, organized into dynamic DNA loops by cohesin, to the highly condensed arrays of DNA loops in mitotic chromosomes formed by condensins. Here, using Hi-C data from mouse embryonic stem cell lines with auxin-inducible degron-tagged subunits of SMC complexes, we clarify the role of condensins in shaping chromatin contacts within the interphase nucleus. We found that depletion of condensin I leads to weakened segregation of chromatin into A and B compartments. We also show that the contact patterns established by condensins during mitosis are preserved in interphase, suggesting a structural memory of mitotic chromosome folding. Condensins influence chromocenter organization: in the absence of condensin II during mitosis, centromeres tend to cluster, forming hyperclusters of pericentric heterochromatin. In contrast, depletion of condensin I reduces the number of heterochromatin clusters, consistent with enhanced chromosome territoriality. By combining a cohesin-degron system with Mcph1 knockout, we established an artificial model in which condensin II becomes the major driver of chromatin folding in interphase nuclei following cohesin depletion. Unlike extrusive cohesin, condensin II does not stall at sequence-specific sites and forms large, randomly positioned loops on interphase chromatin. Moreover, condensin II activity during interphase does not interfere with cohesin-dependent structures such as TADs and chromatin loops. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/669285v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1926857org.highwire.dtl.DTLVardef@100640eorg.highwire.dtl.DTLVardef@a903dcorg.highwire.dtl.DTLVardef@3c6a16_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

Evaluation of the OsTIR1 and AtAFB2 AID systems for chromatin protein degradation in mammalian cells

Auxin-inducible degron (AID) system is a promising tool for dynamic protein degradation. In mammalian cells, this approach has become indispensable to study fundamental molecular functions, such as replication, chromatin dynamics or transcription, that are otherwise difficult to dissect. We present evaluation of the two prominent AID systems based on OsTIR1 and AtAFB2 auxin receptor F-box proteins (AFBs). We analyzed degradation dynamics of cohesin/condensin complexes subunits in mouse embryonic stem cells (mRad21, mSMC2, mCapH, mCapH2) and human haploid HAP1 line (hRad21, hSMC2). Double antibiotic selection helped to achieve high homozygous AID targeting efficiency for all genes, ranging from 11 to 77%. We found that the main challenge for successful protein degradation is obtaining cell clones with high and stable AFB expression levels due to mosaic expression of AFBs, which also tends to decline with passages in the absence of constant puromycin selection, even at the AAVS1 safe-harbor locus. Comparing two AFBs, we found that OsTIR1 system showed weak dynamics of protein degradation. At the same time, AtAFB2 approach was very efficient even in random integration. Other factors such as degradation dynamics and low basal depletion were also in favor of AtAFB2 system. Our main conclusion is that repeated addition of puromycin to culture medium prevents AtAFB2 silencing and restores auxin sensitivity, facilitating robust protein degradation. We hope that our report will be useful for researchers that plan to establish AID method in their lab.

molecular biology↗

bioRxiv2019

DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote

Mechanisms that ensure repair of double-stranded DNA breaks play a key role in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found in the form of concatemer consisting of multiple co-integrated transgene copies. Here we investigated contribution of various DSB repair pathways to the concatemer formation. We injected a pool of linear DNA molecules carrying unique barcodes at both ends into mouse zygotes and obtained 10 transgenic embryos with transgene copy number ranging from 1 to 300 copies. Sequencing of the barcodes allowed us to assign relative positions to the copies in concatemers and to detect recombination events that happened during integration. Cumulative analysis of approximately 1000 integrated copies revealed that more than 80% of copies underwent recombination when their linear ends were processed by SDSA or DSBR. We also observed evidence of double Holliday junction (dHJ) formation and crossing-over during the formation of concatemers. Additionally, sequencing of indels between copies showed that at least 10% of the DNA molecules introduced into the zygote are ligated by non-homologous end joining (NHEJ). Our barcoding approach documents high activity of homologous recombination after exogenous DNA injection in mouse zygote.

molecular biology↗