Sex Chromosomes Research Articles

In forensic genetics, Y-chromosomal short tandem repeats (Y-STRs) are widely used in male lineage tracing, kinship analysis, and mixture interpretation. Conventional genotyping of Y-STRs relies on length-based detection via capillary electrophoresis (CE). However, massively parallel sequencing (MPS) enables simultaneous determination of both length and sequence genotypes, thereby increasing the information obtained per assay. While developing and validating an MPS panel, we made an unexpected observation: the DYS572 locus exhibited heterozygous genotypes in both male and female samples. This could misidentify a single-source sample as a mixed sample. Reference sequence alignment revealed that the DYS572 region on the Y chromosome (GRCh38, chrY: 3,811,419-3,811,858) shares 98.41% sequence identity (432/439bp) with a homologous region on the X chromosome (GRCh38, chrX: 90,242,118-90242557). The corresponding X-chromosomal region harbors seven single nucleotide variants (SNVs) distinguishing it from the Y sequence: four upstream of the repeat region at positions - 183 (rs1031074259), - 62 (rs34553462), - 56 (rs3959844), and - 47 (rs36022122), and three downstream at positions + 6 (rs35114058), + 96 (rs2752369), and + 194 (rs2752370). In practical applications, if primer design or bioinformatic filtering is suboptimal, amplification products of DYS572 may originate from the X chromosome. This study provides a thorough characterization of the DYS572 locus on the sex chromosomes, along with the genotyping patterns observed in males and females. This information will be valuable for future forensic applications.

Background: Klinefelter syndrome (KS), the most common sex chromosome aneuploidy in males (47,XXY), is generally associated with hypogonadism, gynecomastia, and infertility. Nevertheless, its association with thrombotic risk remains insufficiently recognized, despite accumulating evidence indicating a predisposition to venous thromboembolism (VTE) comparable to that observed in classical, inherited thrombophilias. Description of Case: We present the case of a 33-year-old South Asian male who exhibited unilateral lower limb swelling and pain persisting for one month. Doppler ultrasonography revealed chronic deep vein thrombosis (DVT) affecting the left common femoral and deep femoral veins. The patient lacked identifiable risk factors for thrombosis, such as recent surgery, trauma, malignancy, or immobilization. Physical examination revealed signs of hypogonadism and gynecomastia. Hormonal assays indicated elevated gonadotropin levels with low serum testosterone levels, while karyotype analysis confirmed a 47,XXY genotype, consistent with KS. Further evaluations, including screening for acquired thrombophilias (antiphospholipid antibodies) and genetic mutations (Factor V Leiden, Prothrombin G20210A, and MTHFR C677T), yielded negative results. The patient was successfully managed with heparin, transitioned to long-term anticoagulation with warfarin, and demonstrated clinical improvement upon follow-up. Discussion: This case highlights the significant yet often overlooked association between KS and thrombotic events. The pathophysiological mechanisms remain unclear but are hypothesized to be multifactorial, involving increased expression of X-linked coagulation factors (e.g., Factor VIII), endothelial dysfunction, and a higher prevalence of comorbidities. Notably, in our case, the absence of conventional or inherited prothrombotic factors underscores KS as a potential primary contributor to the hypercoagulable state. Conclusion: Clinicians are advised to maintain a heightened level of suspicion for KS in male patients who present with unexplained thrombotic events, particularly when these events are accompanied by symptoms indicative of hypogonadism. The early identification and management of thrombotic risk in individuals with KS are crucial to mitigating morbidity. Further research is necessary to elucidate the mechanisms that link KS with thrombophilia, as this may inform screening strategies and therapeutic interventions.

This article investigates the theoretical detection rate of non-invasive prenatal screening (NIPS) and the residual risk of copy-number variations (CNVs) after normal NIPS results, for fetuses with isolated mild increased nuchal translucency (ImiNT), compared to chromosomal microarray analysis (CMA). A retrospective analysis was conducted on CMA results in a cohort with ImiNT (2.5mm or 95th percentile ≤ NT < 3.5mm). Theoretical detection rates and residual risk values were calculated for four NIPS panels-Basic NIPS-3, Basic NIPS-5, Expanded NIPS (ExpNIPS), and Genome-Wide (GW) NIPS-for common chromosomal aneuploidies and clinically significant CNVs. In a cohort of 936 fetuses with ImiNT, 44 cases had clinically significant CMA results. Basic NIPS-3 could detect 10 cases (9 trisomy 21 and 1 trisomy 18), leaving a residual risk of 3.63% (1/28). Basic NIPS-5 detected 17 cases, including 7 sex chromosome abnormalities, reducing the residual risk to 2.88% (1/35). ExpNIPS identified 18 cases, adding one microdeletion compared to Basic NIPS-5, with a residual risk of 2.78% (1/36). GW NIPS detected 22 cases, finding 5 additional CNVs > 10Mb compared to Basic NIPS-5, lowering the residual risk to 2.35% (1/43). Using NIPS as a substitute for invasive prenatal diagnosis in cases of ImiNT should still be approached with caution. Couples must be ensured to understand the advantages and limitations of both methods. They should also be informed about the residual risk, ranging from 2.35 (1/43) to 3.63% (1/28), even after normal NIPS results. This understanding will help couples make informed decisions.

We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 megabases and hap 2 spanning 2,633 megabases. Contig N50 and scaffold N50 lengths are in the range of 31-41 Mb and 66-69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus; contig N50 46-48 Mb, scaffold N50 67-71 Mb, BUSCO 95.4% - 98.0%) and a comparison with previously published genome assemblies of reindeer.

TFOS DEWS III: Digest.

Invasive prenatal diagnostic tests have higher detection rates (DR) than screening tests. Cell-free (cf)DNA screening has higher detection than Combined testing (CT). We estimated cost per cytogenetic abnormality diagnosed for prenatal testing and screening methods (USA data). We compared seven strategies: universal diagnosis with microarray; with karyotype; cfDNA screening with four methodologies (DANSR, MPSS, SNPs and RCA); and CT. Five abnormality groupings were considered: common autosomal trisomies (21,18,13); sex chromosome aneusomies; triploidy; clinically significant sub-chromosome changes; and CNVs. Prevalence, detection, false-positive rates, and unit costs (literature) were obtained. DR was aggregated across groups as were costs, including diagnostic tests following positive screening results. All six high detection strategies had greater cost per abnormality diagnosed than CT ($19,600). Costliest was cfDNA using MPSS ($96,100), followed by universal karyotyping ($95,900), cfDNA using SNPs, DANSR ($94,800 - $92,800), universal microarray ($56,600) and cfDNA with RCA ($32,200). The additional cost per extra abnormality diagnosed compared to CT ('marginal' cost) was lowest for universal microarray ($62,100); others were considerably higher ($170,900-$238,300). Preferred prenatal strategies vary among stakeholders. As monopolies (large systems and Accountable Care Organizations) now control many American healthcare decisions, lowest cost cfDNA screening will likely prevail in decision making.

Disorder of sexual development (DSD) is defined as a diverse group of congenital conditions in which the development of chromosomal, gonadal and anatomic sex is different or incongruent. It has replaced older terminology like intersex, pseudo hermaphroditism or ambiguous genitalia. These conditions, affecting approximately 1 in 4500 newborns, arise from variations in the complex genetic and hormonal pathways that govern sexual development. The exact data on the incidence or prevalence of DSD in Bangladesh is limited. Bangladesh Medical University (BMU) is the largest tertiary care hospital in Bangladesh, which is considered as the ultimate referral center for such complex cases as DSD. The DSD cases that are commonly encountered in the department of Endocrinology, BMU, include congenital adrenal hyperplasia (CAH), complete androgen insensitivity syndrome (CAIS), gonadal dysgenesis, Leydig cell hypoplasia, etc. However, there are no adequately designed studies to observe the frequency or pattern of DSD at our institute. In this scientific paper, we try to enumerate the approach to a patient with DSD presented at our institute and the common barriers that we encounter. We envision an internationally concerted collaboration among the endocrinologists and biochemists/pathologists involved in this field of patient management at home and abroad in the upcoming days. [J Assoc Clin Endocrinol Diabetol Bangladesh, 2025;4(Suppl 1): S17]

Tetrasomy X (48, XXXX) is an exceptionally rare sex chromosome aneuploidy, with fewer than a few hundred cases documented worldwide. Clinical features vary widely, from mild developmental delay to pronounced dysmorphism, gonadal dysfunction, and tall stature. We report a young female who presented with menstrual irregularities and delayed pubertal development. On physical examination, she was unusually tall (height 182 cm, arm span 194 cm) with a low upper-to-lower segment ratio (0.91), consistent with eunuchoid body proportions. Tanner staging revealed discordant pubertal progression, with breast development at stage B4 but pubic hair at stage P1. Laboratory evaluation demonstrated hypergonadotropic hypogonadism, evidenced by elevated follicle-stimulating hormone (37.93 mIU/ml), elevated luteinizing hormone (16.61 mIU/ml), and low estradiol (17.21 pg/ml). Other biochemical and systemic evaluations, including thyroid, renal, hepatic, and cardiac assessments, were within normal limits. Karyotyping confirmed 48, XXXX, establishing the diagnosis of tetrasomy X. This case emphasizes the diagnostic challenge posed by such rare aneuploidies, particularly in individuals presenting with tall stature and reproductive dysfunction but without overt dysmorphic features. Early recognition is crucial for initiating hormonal replacement, addressing fertility concerns, and ensuring multidisciplinary long-term care. [J Assoc Clin Endocrinol Diabetol Bangladesh, 2025;4(Suppl 1): S60]

Multilocus pathogenic variation—when multiple genetic disorders coexist in a single individual—remains rare but is increasingly recognized in the era of genomic medicine. Reporting such cases is essential for improving diagnostic accuracy, refining clinical management, and informing genetic counseling. We describe a pediatric case with a complex phenotype resulting from the coexistence of two distinct genetic diagnoses—cerebrotendinous xanthomatosis (CTX), a rare autosomal recessive lipid storage disorder caused by biallelic mutations in the CYP27A1 gene and Klinefelter syndrome a common sex chromosome aneuploidy occurring in approximately 1 in 600 males, characterized by hypogonadism, gynecomastia, pubertal delay, infertility, micrognathia, and neurodevelopmental challenges—and an additional incidental finding with clinical relevance. The patient was born to consanguineous parents, presented with neurological symptoms, gastrointestinal dysfunction, endocrine abnormalities, and dysmorphic features. Trio-based exome sequencing identified a homozygous pathogenic variant in CYP27A1 consistent with CTX, while conventional G-banded karyotyping revealed a 47,XXY chromosomal pattern, confirming Klinefelter syndrome. Additionally, a heterozygous pathogenic variant in BRCA2 was incidentally detected, associated with hereditary cancer predisposition. The overlapping manifestations of CTX and Klinefelter syndrome produced a non-classical presentation that delayed diagnosis. Although the BRCA2 variant did not contribute to the current phenotype, it has important implications for future cancer surveillance and family risk assessment. This case underscores the importance of combining classical cytogenetic and modern genomic methods to elucidate complex phenotypes, particularly in consanguineous populations, and highlights the need for the multidisciplinary management of patients with multilocus or incidental findings.

Although female (XX) and male (XY) placentas generally function the same, it is evident that there are sex-specific postnatal health outcomes following placental dysfunction and pregnancy complications. Although the underlying causes for these sex differences are unclear, it is postulated that differences in XX and XY placental function are involved due to sex chromosomes and/or sex steroids. Studies in breast and prostate cancer cells demonstrated a role for the citrullination enzyme peptidylarginine deiminase 2 (PAD2) in post-translational regulation of estrogen (ESR) and androgen receptor (AR) signaling. The goal of this study is to determine if PAD2 is present in mouse placentas and if XX versus XY differences exist in the relative level of PAD2. Fetuses and placentas were collected from three pregnant mice (C57BL6) at 14 days of gestation. Total RNA and protein were isolated from XX and XY placentas, and relative mRNA and protein were analyzed by real-time PCR and Western blot. AR and PAD2 levels were significantly higher in XY than in XX placentas. This study is the first to demonstrate XX and XY differences in PAD2 and AR in the placenta. It suggests a role for PAD2 regulation of androgen receptor signaling in the XY placenta.

Disorders of sex development (DSD) represent a spectrum of congenital conditions where discrepancies exist between chromosomal, gonadal, or anatomical sex. Recent advances in genomic diagnostics and gene-editing technologies have enabled significant progress in the identification of pathogenic variants and the exploration of targeted therapeutic strategies. This review systematically examines the roles of key sex-determining genes—including SRY, SOX9, NR5A1, WT1, FOXL2, and AR—in various DSD subtypes. It further elaborates on gene therapy strategies targeting these loci through the use of CRISPR/Cas9, TALENs, ZFNs, and viral vector-mediated delivery systems. Notably, CRISPR/Cas9 has been utilized to correct or epigenetically activate gene expression in vitro , such as SRY promoter demethylation in embryonic stem cells, and targeted disruption of SOX9 enhancers to model 46, XX testicular DSD in mice. Additionally, lentiviral vectors have enabled stable overexpression of transcriptional regulators (e.g., SOX9, NR5A1) in hiPSCs, inducing differentiation into Sertoli- and Leydig-like cells, with partial restoration of testicular function in vitro . Complementarily, AAV-based vectors—including AAV8 and synthetic AAVDJ—have demonstrated effective delivery of genes like Lhcgr into testicular interstitial tissues, restoring testosterone synthesis and fertility in mouse models. Despite this progress, current gene therapy approaches still face considerable technical challenges, such as off-target effects, immunogenicity of viral vectors or editing enzymes, and long-term transgene expression instability. Germline editing, while theoretically advantageous for early-onset DSD phenotypes, introduces profound ethical dilemmas due to its heritable nature. These include concerns regarding informed consent in minors, gender identity autonomy, and societal consequences of altering reproductive cells. Current international bioethics frameworks urge caution and recommend limiting clinical applications to somatic cells under stringent regulatory oversight. In conclusion, gene therapy offers a transformative potential for the diagnosis and treatment of DSD. Future directions should prioritize enhanced safety, precision delivery systems, and an ethically guided clinical translation pathway to ensure long-term efficacy and societal acceptability.

The biological mechanisms underlying the increased prevalence of Alzheimer’s disease (AD) in women remain undefined. While previous case/control studies have identified sex-biased molecular pathways, the sex-specific relationships between gene expression and AD endophenotypes, particularly involving sex chromosomes, are underexplored. With bulk transcriptomic data across 3 brain regions from 767 decedents, we investigated sex-specific associations between gene expression and post-mortem β-amyloid and tau, as well as antemortem longitudinal cognition. Among 23,118 significant gene associations, 10% were sex-specific, with 73% of these identified in females and primarily associated with tau tangles and longitudinal cognition (90%). Notably, four X-linked genes, MCF2, HDAC8, FTX, and SLC10A3, demonstrated significant sex differences in their associations with AD endophenotypes (i.e., significant sex x gene interaction). Our results also uncovered sex-specific biological pathways, including a female-specific role of neuroinflammation and neuronal development, underscoring the importance of sex-aware analyses to advance precision medicine approaches in AD.

Induced pluripotent stem (iPS) cells share key features with embryonic stem (ES) cells, including similar limitations such as the accumulation of (epi)genetic and genomic alterations. However, sex chromosome instability in mouse iPS cells remains poorly understood. This retrospective study aims to investigate this phenomenon by analyzing mouse iPS cell clones. Specifically, we examine whether factors such as passage number, cell sex, founder cell type, or reprogramming method influence the presence or absence of sex chromosome abnormalities. Sex chromosome stability was evaluated in 26 independent male and female mouse iPS cell clones using standard karyotyping techniques. Additionally, we analyzed an artificially generated XXY iPS cell model, in which an extra X chromosome was introduced into a normal XY cell line. Statistical analyses were conducted on the karyotyping results and correlated with both continuous variables (e.g., passage number) and categorical variables (e.g., cell sex, founder cell type, and reprogramming method). Female iPS cell clones displayed significantly higher levels of sex chromosome instability compared to their male counterparts, regardless of the founder cell type or reprogramming strategy. A similar pattern of X chromosome instability was also observed in the XXY iPS cell model. Our findings demonstrate that sex chromosome instability occurs in mouse iPS cells, as previously reported in mouse ES cells, suggesting a conserved phenomenon across pluripotent stem cell types. Importantly, the presence of multiple X chromosomes in the pluripotent state appears to contribute to this instability. Further studies are required to elucidate the underlying molecular mechanisms.

Mechanisms of X chromosome dosage compensation have been studied in model organisms with distinct sex chromosome ancestry. However, the diversity of mechanisms as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, where dosage compensation is accomplished by an X chromosome specific condensin that belongs to the family of structural maintenance of chromosomes (SMC) complexes. By combining a phylogenetic analyses of the C. elegans dosage compensation complex with a comparative analysis of its epigenetic signatures, such as X-specific topologically associating domains (TADs) and enrichment of H4K20me1, we show that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis following an SMC-4 duplication. Unexpectedly, we found an independent duplication of SMC-4 in Pristionchus pacificus along with X-specific TADs and H4K20me1 enrichment, which suggests that condensin-mediated dosage compensation evolved more than once in nematodes. Differential expression analysis between sexes in several nematode species indicates that dosage compensation itself precedes the evolution of X-specific condensins. In Rhabditina, X-specific condensins may have evolved in the presence of an existing mechanism linked to H4K20 methylation as Oscheius tipulae X chromosomes are enriched for H4K20me1 without SMC-4 duplication or TADs. In contrast, Steinernema hermaphroditum lacks H4K20me1 enrichment, SMC-4 duplication, and TADs. Together, our results indicate that dosage compensation mechanisms continue to evolve in species with shared X chromosome ancestry, and SMC complexes may have been co-opted at least twice in nematodes, suggesting that the process of evolving chromosome wide gene regulatory mechanisms are constrained.

A lack of recombination in the heterogametic sex between parts or all of newly evolving sex chromosomes results in the gradual accumulation of deleterious mutations on proto-Y or proto-W chromosomes. This "genetic degeneration" is caused by several population genetic mechanisms. It can eventually lead to the loss of functionality and deletions of Y- or W-linked genes in species with male or female heterogamety, respectively, reducing the fitness of heterozygous XY males or ZW females. This creates selection to compensate for such degeneration. Contemporary studies of degeneration and dosage compensation are built on classical genetic work by HJ Muller, with molecular analyses of genomes and gene expression now revealing new details. We review these studies, integrating ideas about how degeneration and compensation evolve. We discuss whether these two processes evolve together, whether the initial changes involved in compensation occurred in individual sex-linked genes ("piecemeal"), and whether they were sex-specific. We also discuss the idea that control of expression across larger chromosome regions reflects later changes, after increased expression of X- or Z-linked genes in both sexes favoured reduced X expression in females (or Z expression in males with female heterogamety). We summarise the currently available empirical evidence, and discuss difficulties involved in documenting the evolutionary changes that lead to the different types of dosage compensation, as well as limitations of the data for testing evolutionary hypotheses.

Abstract Disclosure: M.G. Meirelles: None. R.D. Scalco: None. J.M. Moreira: None. S. Domenice: None. R.L. Batista: None. J. Mesia: None. N. Scalissi: None. J.P. Batatinha: None. J.V. Junior: None. C.B. Bueno: None. A. Narciso: None. A. Reis: None. A. Latronico: None. I.J. Arnhold: None. B.B. Mendonca: None. The luteinizing hormone/choriogonadotropin receptor (LHCGR) is essential for gonadal steroidogenesis and sexual differentiation. Loss-of-function variants in LHCGR lead to a spectrum of 46,XY disorders of sex development (DSD), with phenotypic variability depending on chromosomal sex and mutation type. We report two 46,XY sisters, from a consanguineous family, presenting with primary amenorrhea and absent secondary sexual characteristics. Both, aged 31 and 27, showed tall stature (184 cm and 188 cm; target height: 173 cm), and the elder sister also had obesity and metabolic comorbidities. Hormonal evaluation showed elevated gonadotropins (LH: 49–60 IU/L; FSH: 46–50.7 IU/L), low testosterone (&amp;lt;10 ng/dL), and undetectable estradiol (&amp;lt;17 pg/mL). Pelvic ultrasound and MRI confirmed absence of uterus and presence of bilateral intra-abdominal testes (3.5–4.0 cm AP). Histopathological analysis revealed Leydig cell hypoplasia and severe seminiferous tubule hyalinization. Genetic testing identified a novel homozygous LHCGR splice-site variant (c.384-2A&amp;gt;G; NM_000233.4), classified as pathogenic by ACMG guidelines (PM2, PVS1, PP4). In silico prediction tools indicated complete loss of the canonical AG acceptor site at intron 4. SpliceAI showed high probability of splice site loss (Δ score: 0.99), and MaxEntScan indicated a collapse in splice strength, suggesting exon skipping or intron retention. RNA secondary structure modeling (ViennaRNA Fold) revealed reduced thermodynamic stability (ΔG: –30.05 vs. –32.62 kcal/mol), lower frequency of the minimum free energy structure (0.60% vs. 1.96%), and increased structural diversity (35.3 vs. 23), supporting impaired splicing efficiency. This variant likely disrupts LHCGR expression through aberrant splicing and RNA instability, leading to Leydig cell hypoplasia and testosterone deficiency. The disproportionately high FSH in subject with LHCGR loss-of-function longstanding Sertoli cell damage due to undescended testes. These findings expand the mutational and phenotypic spectrum of LHCGR-related DSD and emphasize the relevance of considering LHCGR defects in 46,XY individuals with hypergonadotropic hypogonadism and female phenotype. Keywords:LHCGR variant, Leydig cell hypoplasia, 46,XY DSD, hypergonadotropic hypogonadism, LH resistance. Presentation: Sunday, July 13, 2025

Abstract Disclosure: R.T. Dallago: None. R.L. Batista: None. S. Domenice: None. V.D. Nunes-Nogueira: None. B.B. Mendonca: None. Introduction: Differences of sex development (DSD) are congenital conditions characterized by atypical development of chromosomal, gonadal, and anatomical sex. Nuclear receptor subfamily 5 group A member 1 (NR5A1) plays a crucial role in transcriptional regulation of genes involved in steroidogenesis, adrenal and gonadal development. NR5A1 emerged to be causative of 10 to 20% of 46,XY dysgenetic DSD.Objective: This study aimed to perform a systematic review evaluating the association between phenotype and genotype in patients with NR5A1 defects and 46,XY DSD looking for outcomes of spontaneous puberty, gender change and social sex.Method: The systematic review was conducted in accordance with the Joanna Briggs Institute methodology for systematic reviews. We included studies with pathogenic, likely pathogenic and variants of uncertain significance (VUS) in the NR5A1 gene in patients with 46,XY disorders of DSD. Embase, Medline and HGMD were our databases. Proportional meta-analyses were performed to calculate the overall frequencies.Results: Ninety-eight studies were included, encompassing 311 patients with 46,XY DSD due to NR5A1 defects. Due to the imprecision of meta-analyses involving two or fewer patients, our primary analyses focused on those with three or more patients. The overall frequency of female sex-assignment was 54% (186 patients from 33 studies patients; 95% confidence interval (CI), 42-66%) and male was 46% (95% CI, 34-58%). The frequency of the missense variants was 54% (235 patients from 35 studies; 95% CI, 42-66%); for other variants such as nonsense, splicing, small indel and copy number variation, the frequency was 46% (95% CI, 34-58%). The frequency of the atypical genitalia was 85% (from 35 studies of 235 patients; 95% CI, 75-91%); and the female genitalia was 15% (95% CI, 09-25%); The frequency of spontaneous puberty was 74% (56 patients from 12 studies; 95% CI, 38-93%); and hypergonadotropic hypogonadism was 8% (95% CI, 03-17%); there were 10% of prepubertal gonadectomy (95% CI, 01-50%); The correlation between genotype/phenotype and phenotype/gender change was accessed using odds-ratios as a measure of effects, with no statistical difference (OR = 1.25; CI 95%, 0.56-2.77%) and (OR = 0.46; CI 95%, 0.08-2.73%), respectively. It's important to note that all gender changes were from female to male. The limited sample size, particularly in subgroup analyses, was a major limitation and may have impacted the statistical power of the findings.Conclusion: Patients with NR5A1 variants exhibit significant phenotypic variability. The high frequency of spontaneous puberty highlights the need for caution in irreversible interventions during childhood, emphasizing individualized and multidisciplinary approaches to guide clinical management and gender assignment. Part of this study was support by FAPESP 2019/26780-9. Presentation: Sunday, July 13, 2025

A key event in meiosis is the conversion of a small subset of double strand breaks into interhomolog crossovers. In this study, we demonstrate that Caenorhabditis elegans male spermatogenesis has less robust mechanisms than hermaphrodite oogenesis in regulating crossover numbers. This is not a consequence of differences in meiotic prophase timing, sex chromosome genotype, or the presence or absence of germline apoptosis. Using the cyclin-like crossover marker COSA-1, we show that males are less efficient in both converting double strand breaks into crossover designated events and limiting their number, suggesting weakened crossover homeostasis. Surprisingly, we discovered that significant numbers of COSA-1 foci form at the very end of meiotic prophase in the absence of SPO-11 during spermatogenesis. These COSA-1-marked sites are also independent of homologous recombination, and Topoisomerases I and II. We find that the synaptonemal complex, which holds homologs in proximity, differently modulates COSA-1 enrichment to chromosomes in the absence of SPO-11 in males and hermaphrodites. Together, these findings suggest that males have less robust crossover control and that there are previously unrecognized lesions or structures at the end of meiotic prophase in spermatocytes that can accumulate crossover markers.

Disclosure: A. Hattori: None. A. Seki: None. Y. Naiki: None. A. Nakamura: None. T. Michigami: None. Y. Katoh-Fukui: None. T. Ogata: None. M. Kagami: None. M. Fukami: None.Introduction: Male-specific growth genes, alongside gonadal sex steroids, have been proposed as contributors to sex differences in height; however, no such gene has been identified. SHOX, a key growth gene located in the pseudoautosomal region on the short arm (PAR1) of the sex chromosomes, influences height in a dose-dependent manner. Conventionally, genes on PAR1, including SHOX, were thought to escape X-chromosome inactivation (XCI), thus being expressed equally in men and women. In 2017, Tukiainen et al. reported that most genes on PAR1 are expressed in a male-dominant manner. Nevertheless, sex differences in SHOX expression remain largely unexplored due to its highly tissue-specific expression. Objective: To explore the role of SHOX in sex differences in height. Methods: We compared male and female cartilage and/or chondrocyte samples using the following methods: (i) microarray analysis for X chromosome gene expression (n = 16), (ii) RT-qPCR for SHOX expression (n = 36), (iii) reduced representation bisulfite sequencing (RRBS) for X chromosome DNA methylation (n = 4), and (iv) pyrosequencing for DNA methylation of SHOX-flanking regions (n = 22). Furthermore, we established fibroblast clones derived from a boy and a girl with polydactyly, which enabled us to compare DNA methylation patterns around SHOX among the active and inactive X chromosomes and the Y chromosome using long-read sequencing. Results: Microarray analysis showed male-dominant expression of PAR1 genes, including SHOX. RT-qPCR confirmed male-dominant SHOX expression. RRBS revealed that the X chromosome exhibited female-dominant DNA methylation, which was pronounced in the X-specific region and mild in PAR1. RRBS also showed that SHOX-flanking regions exhibited sexually dimorphic DNA methylation. Specifically, male-dominant DNA methylation was observed in a region upstream of SHOX and a region spanning intron 5-exon 6a, whereas female-dominant DNA methylation was detected in intron 2. These findings were confirmed by pyrosequencing. In silico analysis suggested that the region with female-dominant DNA methylation in intron 2 functions as an enhancer of SHOX. Long-read sequencing of fibroblast clones revealed hypomethylation of intron 2 in the active X and Y chromosomes and hypermethylation in the inactive X chromosome. Discussion: Male-dominant SHOX expression in cartilage tissue indicates a role of SHOX in sex differences in height. Sexually dimorphic DNA methylation around SHOX implies that XCI represses SHOX expression in women. In particular, allele-specific DNA methylation in intron 2 (hypomethylation of the active X and hypermethylation of the inactive X) suggests that this region functions as an enhancer involved in the repression of SHOX expression due to XCI. Conclusion: Male-dominant SHOX expression, driven by the spreading of XCI to SHOX, likely contributes to sex differences in height.Presentation: Saturday, July 12, 2025

We present a genome assembly from an individual male Taleporia tubulosa (Brown Bagworm; Arthropoda; Insecta; Lepidoptera; Psychidae). The assembly contains two haplotypes with total lengths of 394.58 megabases and 397.58 megabases. Most of haplotype 1 (99.89%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.11 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.