Maternal Smc3 protects the integrity of the zygotic genome through DNA replication and mitosis

Studies on the regulation of E3 ubiquitin ligase APC3 and its interacting proteins on the tetraspore formation and release in Gracilariopsis lemaneiformis (Rhodophyta)

E3 ubiquitin ligases play significant roles in development of high plants and animals. We recently found that E3 ubiquitin ligase APC3, the subunit of the anaphase promoting complex/cyclosome, was involved in tetraspore formation and release in Gracilariopsis lemaneiformis, an economically important red alga. GlAPC3 showed opposite expression pattern in low-fertility cultivar 981 and high-fertility strain WLP during the process of tetraspore formation and release, up-regulated in 981 and down-regulated in WLP. Five proteins related to chromosome segregation, SMC3, NUF2, APC2, APC8 and APC10, were detected to interact with APC3, which were all located in the nucleus. NUF2 and CDC20 were the substrates of APC3, combined with Lysine-11, Lysine-48 and Lysine-63 of ubiquitin chains containing two or four ubiquitin. The key amino acids for ubiquitination of APC3 covered 474th Aspartate, 502nd tyrosine and 506th leucine, any mutation of which resulted in a loss of ubiquitination. During the process of tetraspore formation and release, SMC3 was significantly up-regulated only in 981, low number of tetraspore release. NUF2 and APC2 were significantly down-regulated only in WLP, with high frequency and large amount of tetraspores release. The data provided that APC3, SMC3 and NUF2 might be the key gene affecting the fertility of Gp. lemaneiformis. The study helps to explore the regulation mechanism of APC3 with SMC3 and NUF2 by the process of chromatids segregation in regulating tetraspore formation and release of Gp. lemaneiformis.

Species-specific satellite DNA composition dictates PRC1-mediated pericentric heterochromatin

Pericentromeres are heterochromatic regions adjacent to centromeres that ensure accurate chromosome segregation. Despite their conserved function, they are composed of rapidly evolving A/T-rich satellite DNA. This paradoxical observation is partially resolved by epigenetic mechanisms that maintain H3K9me3-based heterochromatin, independent of specific DNA sequences. However, these mechanisms can function only after H3K9me3 has already been established, and this mark is absent from paternal chromatin in the mouse zygote. It is unknown how variation in satellite DNA sequence impacts alternative forms of heterochromatin at this earliest stage of life. Here we show functional consequences of satellite DNA variation for pericentric heterochromatin formation, recruitment of the Chromosome Passenger Complex (CPC), and interactions with the mitotic spindle. The AT-hook of Polycomb Repressive Complex 1 (PRC1) directly recognizes A/T-rich satellite DNA and packages it in H2AK119ub1 heterochromatin. By fertilizing M. musculus eggs with sperm from other mouse species, we show that divergent satellite sequences differ in their ability to bind PRC1, resulting in differences in H2AK119ub1 heterochromatin formation on mitotic chromosomes. Furthermore, we find that satellites that robustly form H2AK119ub1 inhibit molecular pathways that recruit the CPC to pericentromeres, increasing microtubule forces on kinetochores during mitosis. Our results provide a direct link between satellite DNA composition and pericentromere function and highlight early embryogenesis as a critical point in development that is sensitive to satellite DNA evolution.

Analysis and identification of potential biomarkers for dysfunctional uterine bleeding

Clinical evidence increasingly suggests that traditional treatments for dysfunctional uterine bleeding (DUB) have limited success. In this study, blood samples from 10 DUB patients and 10 healthy controls were collected for transcriptome sequencing. Then, the differentially expressed genes (DEGs) were screened and crossed with the DUB-related module genes to obtain the target genes. These target genes were analyzed for functional enrichment. Further, the biomarkers were screened by protein-protein interaction (PPI) analysis and analyzed by the gene set enrichment analysis (GSEA) and ingenuity pathway analysis (IPA). To explore the pathogenesis of DUB, immune microenvironment analyses were also performed. Potential drugs targeting these biomarkers were predicted for clinical treatment. The expression of these biomarkers was validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that, a total of 754 target genes were found to be related to cell proliferation and senescence. Five biomarkers-CENPE, KIF11, PIK3R1, SMC3, and SMC4-were identified, all of which were down-regulated in the DUB group, and most of these findings were confirmed by qRT-PCR. Notably, CENPE expression showed a negative association with activated NK cells and a positive association with resting NK cells. In addition, 44 potential drugs were predicted for DUB treatment. In conclusion, five DUB biomarkers were identified, enhancing understanding of gene regulation in DUB and providing a theoretical foundation for clinical diagnosis and treatment.

ZNF521 promotes acute myeloid leukemogenesis by suppressing the expression and acetylation of SMC3

Zinc finger protein 521 (ZNF521) participates in the self-renewal of hematopoietic stem cells, and its abnormal expression has been implicated to promote leukemia. However, the specific role of ZNF521 in leukemia has not been fully understood. In this study, we aimed to further elucidate its role. Using acute leukemia cell line THP-1, we demonstrated that knocking down ZNF521 inhibited leukemia cell proliferation, promoted apoptosis, and induced cell arrest in G2/M phase. Interestingly, we also observed the upregulation of SMC3 expression and acetylation, as well as the downregulation of histone deacetylases 8 (HDAC8), CDK2, and CDK6. The proliferation inhibition was reversed by knocking down SMC3, suggesting the key role of SMC3 reduction in ZNF521 elevated proliferation. Conversely, ZNF521 overexpression in HL-60 cells resulted in enhanced proliferation and inhibited apoptosis. Furthermore, we discovered that ZNF521 can interact with HDAC8, which deacetylates SMC3, and the interaction promotes proliferation and suppresses apoptosis. Notably, when HDAC8 was knocked down or its activity was inhibited by a HDAC8 inhibitor, the previous observed trend was reversed. Consequently, ZNF521 plays a critical role in acute myeloid leukemogenesis by reducing the expression and acetylation of SMC3. Overall, this study sheds light on the potential for targeted treatment in highly ZNF521 expressed acute myeloid leukemia, providing a valuable clue for precise and effective therapeutic approaches.

Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.

Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.

Chronic exposure to (2 R,6 R)-hydroxynorketamine induces developmental neurotoxicity in hESC-derived cerebral organoids

(R,S)-ketamine (ketamine) has been increasingly used recreationally and medicinally worldwide; however, it cannot be removed by conventional wastewater treatment plants. Both ketamine and its metabolite norketamine have been frequently detected to a significant degree in effluents, aquatic, and even atmospheric environments, which may pose risks to organisms and humans via drinking water and aerosols. Ketamine has been shown to affect the brain development of unborn babies, while it is still elusive whether (2 R,6 R)-hydroxynorketamine (HNK) induces similar neurotoxicity. Here, we investigated the neurotoxic effect of (2 R,6 R)-HNK exposure at the early stages of gestation by applying human cerebral organoids derived from human embryonic stem cells (hESCs). Short-term (2 R,6 R)-HNK exposure did not significantly affect the development of cerebral organoids, but chronic high-concentration (2 R,6 R)-HNK exposure at day 16 inhibited the expansion of organoids by suppressing the proliferation and augmentation of neural precursor cells (NPCs). Notably, the division mode of apical radial glia was unexpectedly switched from vertical to horizontal division planes following chronic (2 R,6 R)-HNK exposure in cerebral organoids. Chronic (2 R,6 R)-HNK exposure at day 44 mainly inhibited the differentiation but not the proliferation of NPCs. Overall, our findings indicate that (2 R,6 R)-HNK administration leads to the abnormal development of cortical organoids, which may be mediated by inhibiting HDAC2. Future clinical studies are needed to explore the neurotoxic effects of (2 R,6 R)-HNK on the early development of the human brain.

Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis

Persistence of unrepaired DNA damage in oocytes is detrimental and may cause genetic aberrations, miscarriage, and infertility. RPA, an ssDNA-binding complex, is essential for various DNA-related processes. Here we report that RPA plays a novel role in DNA damage repair during postnatal oocyte development after meiotic recombination. To investigate the role of RPA during oogenesis, we inactivated RPA1 (replication protein A1), the largest subunit of the heterotrimeric RPA complex, specifically in oocytes using two germline-specific Cre drivers (Ddx4-Cre and Zp3-Cre). We find that depletion of RPA1 leads to the disassembly of the RPA complex, as evidenced by the absence of RPA2 and RPA3 in RPA1-deficient oocytes. Strikingly, severe DNA damage occurs in RPA1-deficient GV-stage oocytes. Loss of RPA in oocytes triggered the canonical DNA damage response mechanisms and pathways, such as activation of ATM, ATR, DNA-PK, and p53. In addition, the RPA deficiency causes chromosome misalignment at metaphase I and metaphase II stages of oocytes, which is consistent with altered transcript levels of genes involved in cytoskeleton organization in RPA1-deficient oocytes. Absence of the RPA complex in oocytes severely impairs folliculogenesis and leads to a significant reduction in oocyte number and female infertility. Our results demonstrate that RPA plays an unexpected role in DNA damage repair during mammalian folliculogenesis.

Cohesin is required for meiotic spindle assembly independent of its role in cohesion in C. elegans

Accurate chromosome segregation requires a cohesin-mediated physical attachment between chromosomes that are to be segregated apart, and a bipolar spindle with microtubule plus ends emanating from exactly two poles toward the paired chromosomes. We asked whether the striking bipolar structure of C. elegans meiotic chromosomes is required for bipolarity of acentriolar female meiotic spindles by time-lapse imaging of mutants that lack cohesion between chromosomes. Both a spo-11 rec-8 coh-4 coh-3 quadruple mutant and a spo-11 rec-8 double mutant entered M phase with separated sister chromatids lacking any cohesion. However, the quadruple mutant formed an apolar spindle whereas the double mutant formed a bipolar spindle that segregated chromatids into two roughly equal masses. Residual non-cohesive COH-3/4-dependent cohesin on separated sister chromatids of the double mutant was sufficient to recruit haspin-dependent Aurora B kinase, which mediated bipolar spindle assembly in the apparent absence of chromosomal bipolarity. We hypothesized that cohesin-dependent Aurora B might activate or inhibit spindle assembly factors in a manner that would affect their localization on chromosomes and found that the chromosomal localization patterns of KLP-7 and CLS-2 correlated with Aurora B loading on chromosomes. These results demonstrate that cohesin is essential for spindle assembly and chromosome segregation independent of its role in sister chromatid cohesion.