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1.
Mol Cell ; 79(4): 689-701.e10, 2020 08 20.
Article in English | MEDLINE | ID: mdl-32610038

ABSTRACT

Meiotic recombination proceeds via binding of RPA, RAD51, and DMC1 to single-stranded DNA (ssDNA) substrates created after formation of programmed DNA double-strand breaks. Here we report high-resolution in vivo maps of RPA and RAD51 in meiosis, mapping their binding locations and lifespans to individual homologous chromosomes using a genetically engineered hybrid mouse. Together with high-resolution microscopy and DMC1 binding maps, we show that DMC1 and RAD51 have distinct spatial localization on ssDNA: DMC1 binds near the break site, and RAD51 binds away from it. We characterize inter-homolog recombination intermediates bound by RPA in vivo, with properties expected for the critical displacement loop (D-loop) intermediates. These data support the hypothesis that DMC1, not RAD51, performs strand exchange in mammalian meiosis. RPA-bound D-loops can be resolved as crossovers or non-crossovers, but crossover-destined D-loops may have longer lifespans. D-loops resemble crossover gene conversions in size, but their extent is similar in both repair pathways.


Subject(s)
Cell Cycle Proteins/metabolism , Homologous Recombination , Meiosis , Phosphate-Binding Proteins/metabolism , Rad51 Recombinase/metabolism , Replication Protein A/metabolism , Animals , Cell Cycle Proteins/genetics , Chromosomes/genetics , Chromosomes/metabolism , Crossing Over, Genetic , DNA, Single-Stranded/metabolism , Genome , Male , Mice, Inbred C57BL , Mice, Inbred DBA , Phosphate-Binding Proteins/genetics , Rad51 Recombinase/genetics , Replication Protein A/genetics , Testis
2.
Mol Cell ; 73(3): 547-561.e6, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30735655

ABSTRACT

Chromatin organization undergoes drastic reconfiguration during gametogenesis. However, the molecular reprogramming of three-dimensional chromatin structure in this process remains poorly understood for mammals, including primates. Here, we examined three-dimensional chromatin architecture during spermatogenesis in rhesus monkey using low-input Hi-C. Interestingly, we found that topologically associating domains (TADs) undergo dissolution and reestablishment in spermatogenesis. Strikingly, pachytene spermatocytes, where synapsis occurs, are strongly depleted for TADs despite their active transcription state but uniquely show highly refined local compartments that alternate between transcribing and non-transcribing regions (refined-A/B). Importantly, such chromatin organization is conserved in mouse, where it remains largely intact upon transcription inhibition. Instead, it is attenuated in mutant spermatocytes, where the synaptonemal complex failed to be established. Intriguingly, this is accompanied by the restoration of TADs, suggesting that the synaptonemal complex may restrict TADs and promote local compartments. Thus, these data revealed extensive reprogramming of higher-order meiotic chromatin architecture during mammalian gametogenesis.


Subject(s)
Cellular Reprogramming , Chromatin Assembly and Disassembly , Chromatin/metabolism , Meiosis , Spermatogenesis , Spermatozoa/metabolism , Animals , Chromatin/chemistry , Chromatin/genetics , Gene Expression Regulation, Developmental , HCT116 Cells , Humans , Macaca mulatta , Male , Mice, Inbred C57BL , Mice, Knockout , Nucleic Acid Conformation , Pachytene Stage , Protein Conformation , Structure-Activity Relationship , Time Factors , Transcription, Genetic , X Chromosome Inactivation
3.
EMBO Rep ; 24(2): e55778, 2023 02 06.
Article in English | MEDLINE | ID: mdl-36440627

ABSTRACT

Following meiotic recombination, each pair of homologous chromosomes acquires at least one crossover, which ensures accurate chromosome segregation and allows reciprocal exchange of genetic information. Recombination failure often leads to meiotic arrest, impairing fertility, but the molecular basis of recombination remains elusive. Here, we report a homozygous M1AP splicing mutation (c.1074 + 2T > C) in patients with severe oligozoospermia owing to meiotic metaphase I arrest. The mutation abolishes M1AP foci on the chromosome axes, resulting in decreased recombination intermediates and crossovers in male mouse models. M1AP interacts with the mammalian ZZS (an acronym for yeast proteins Zip2-Zip4-Spo16) complex components, SHOC1, TEX11, and SPO16. M1AP localizes to chromosomal axes in a SPO16-dependent manner and colocalizes with TEX11. Ablation of M1AP does not alter SHOC1 localization but reduces the recruitment of TEX11 to recombination intermediates. M1AP shows cytoplasmic localization in fetal oocytes and is dispensable for fertility and crossover formation in female mice. Our study provides the first evidence that M1AP acts as a copartner of the ZZS complex to promote crossover formation and meiotic progression in males.


Subject(s)
Meiosis , Multiprotein Complexes , Animals , Female , Male , Mice , Meiosis/genetics , Microtubule-Associated Proteins/metabolism , DNA-Binding Proteins/metabolism , Cell Cycle Proteins/metabolism , Multiprotein Complexes/metabolism
4.
J Cell Mol Med ; 28(7): e18215, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38509755

ABSTRACT

Oligoasthenoteratospermia (OAT), characterized by abnormally low sperm count, poor sperm motility, and abnormally high number of deformed spermatozoa, is an important cause of male infertility. Its genetic basis in many affected individuals remains unknown. Here, we found that CCDC157 variants are associated with OAT. In two cohorts, a 21-bp (g.30768132_30768152del21) and/or 24-bp (g.30772543_30772566del24) deletion of CCDC157 were identified in five sporadic OAT patients, and 2 cases within one pedigree. In a mouse model, loss of Ccdc157 led to male sterility with OAT-like phenotypes. Electron microscopy revealed misstructured acrosome and abnormal head-tail coupling apparatus in the sperm of Ccdc157-null mice. Comparative transcriptome analysis showed that the Ccdc157 mutation alters the expressions of genes involved in cell migration/motility and Golgi components. Abnormal Golgi apparatus and decreased expressions of genes involved in acrosome formation and lipid metabolism were detected in Ccdc157-deprived mouse germ cells. Interestingly, we attempted to treat infertile patients and Ccdc157 mutant mice with a Chinese medicine, Huangjin Zanyu, which improved the fertility in one patient and most mice that carried the heterozygous mutation in CCDC157. Healthy offspring were produced. Our study reveals CCDC157 is essential for sperm maturation and may serve as a marker for diagnosis of OAT.


Subject(s)
Asthenozoospermia , Infertility, Male , Membrane Proteins , Oligospermia , Animals , Humans , Male , Mice , Asthenozoospermia/genetics , Asthenozoospermia/metabolism , Infertility, Male/genetics , Infertility, Male/metabolism , Mice, Knockout , Mutation/genetics , Oligospermia/genetics , Oligospermia/metabolism , Semen/metabolism , Sperm Motility/genetics , Spermatozoa/metabolism , Membrane Proteins/metabolism
5.
Dev Biol ; 496: 15-23, 2023 04.
Article in English | MEDLINE | ID: mdl-36657507

ABSTRACT

BACKGROUND: Cornichon is a functionally conserved transmembrane protein family that generally acts as a cargo-sorting receptor and cycles between the ER and the Golgi. Four Cornichon family members (CNIH1-4) have been identified. The key residues responsible for CNIH1-3 to bind to AMPA receptors are not conserved in CNIH4. Additionally, the function of CNIH1-3 in GPCR signaling is less established, while more established in case of CNIH4 protein that interact with GPCR and control their exportation. Many GPCRs are known for their essential roles in male and female gonad development. But whether CNIH4 plays a role in gametogenesis remains unknown. DESIGN: Mice carrying the Cnih4 knockout allele (Cnih4tm1a-/-) were generated by insertion of a LacZ reporter and a polyadenylation site after exon 1. Western blot, Immunofluorescence, computer-aided sperm analysis and other methods were used in the functional analysis. RESULTS: We identified that both Cnih4tm1a-/- male and female mice have normal fertility. Though, the sperm count, morphology, and motility of Cnih4tm1a-/- mice were slightly impaired compared to those of wild-type mice, the testes to body weight ratio and testicular histology were similar to those in control mice. Histological examination of Cnih4tm1a-/- ovaries detected follicles from primordial to antral stages and the numbers of follicles at each stage were also comparable to wild-type controls. Normal fertility was noticed after six-month fertility tests. That was likely due to the compensatory role of Chin3, which significantly upregulated in the Cnih4tm1a-/- mice to preserve the fertility role. CONCLUSION: Despite CNIH4 showing enriched expression in mouse germ cells, our genetic knockout studies demonstrated that CNIH4 is not essential for gametogenesis and fertility in mice although with a slight reduction in count, motility and morphology of sperm in male mice.


Subject(s)
Fertility , Semen , Male , Female , Animals , Mice , Fertility/genetics , Testis/metabolism , Spermatozoa/metabolism , Gametogenesis , Spermatogenesis/genetics , Mice, Knockout
6.
Plant J ; 113(3): 536-545, 2023 02.
Article in English | MEDLINE | ID: mdl-36534091

ABSTRACT

Polyploidy is a common mode of evolution in flowering plants. Both the natural tetraploid Thinopyrum elongatum and the diploid one from the same population show a diploid-like pairing in meiosis. However, debate on the chromosome composition and origin of the tetraploid Th. elongatum is ongoing. In the present study, we obtained the induced tetraploid Th. elongatum and found that the induced and natural tetraploids are morphologically close, except for slower development and lower seed setting. Using probes developed from single chromosome microdissection and a Fosmid library, obvious differentiations were discovered between two chromosome sets (E1 and E2 ) of the natural tetraploid Th. elongatum but not the induced one. Interestingly, hybrid F1 derived from the two different wheat-tetraploid Th. elongatum amphiploids 8802 and 8803 produced seeds well. More importantly, analysis of meiosis in F2 individuals revealed that chromosomes from E1 and E2 could pair well on the durum wheat background with the presence of Ph1. No chromosome set differentiation on the FISH level was discovered from the S1 to S4 generations in the induced one. In metaphase of the meiosis first division in the natural tetraploid, more pairings were bivalents and fewer quadrivalents with ratio of 13.94 II + 0.03 IV (n = 31). Chromosome pairing configuration in the induced tetraploid is 13.05 II + 0.47 IV (n = 19), with the quadrivalent ratio being only slightly higher than the ratio in the natural tetraploid. Therefore, the natural tetraploid Th. elongatum is of autoploid origin and the induced tetraploid Th. elongatum evolutionarily underwent rapid diploidization in the low generation.


Subject(s)
Chromosomes, Plant , Tetraploidy , Chromosomes, Plant/genetics , Poaceae/genetics , Triticum/genetics , Meiosis/genetics , Chromosome Pairing/genetics
7.
Plant J ; 115(5): 1298-1315, 2023 09.
Article in English | MEDLINE | ID: mdl-37246611

ABSTRACT

Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.


Subject(s)
Cell Nucleolus , Triticum , Triticum/genetics , Cell Nucleolus/genetics , Cell Nucleolus/metabolism , Nucleolus Organizer Region , DNA, Ribosomal/metabolism , DNA Methylation/genetics
8.
Plant J ; 114(6): 1475-1489, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36919201

ABSTRACT

Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most destructive diseases of wheat (Triticum aestivum) around the world. FHB causes significant yield losses and reduces grain quality. The lack of resistance resources is a major bottleneck for wheat FHB resistance breeding. As a wheat relative, Thinopyrum elongatum contains many genes that can be used for wheat improvement. Although the novel gene Fhb-7EL was mapped on chromosome 7EL of Th. elongatum, successful transfer of the FHB resistance gene into commercial wheat varieties has not been reported. In this study, we developed 836 wheat-Th. elongatum translocation lines of various types by irradiating the pollen of the wheat-Th. elongatum addition line CS-7EL at the flowering stage, among which 81 were identified as resistant to FHB. By backcrossing the FHB-resistant lines with the main cultivar Jimai 22, three wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, were successfully applied in wheat breeding without yield penalty. Combining karyotype and phenotype analyses, we mapped the Fhb-7EL gene to the distal end of chromosome 7EL. Five molecular markers linked with the FHB resistance interval were developed, which facilitates molecular marker-assisted breeding. Altogether, we successfully applied alien chromatin with FHB resistance from Th. elongatum in wheat breeding without yield penalty. These newly developed FHB-resistant wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, can be used as novel resistance resources for wheat breeding.


Subject(s)
Fusarium , Triticum , Triticum/genetics , Plant Breeding , Genetic Markers , Poaceae/genetics , Plant Diseases/genetics , Disease Resistance/genetics
9.
Am J Hum Genet ; 108(2): 324-336, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33508233

ABSTRACT

Human infertility is a multifactorial disease that affects 8%-12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive azoospermia (NOA) and one female diagnosed with premature ovarian insufficiency (POI) as well as a nonsense mutation (c.958G>T [p.Glu320∗]) and a splicing mutation (c.1180-3C>G) in two unrelated Chinese men (individual P3907 and individual P6032, respectively) with meiotic arrest. Mutations in C14orf39 resulted in truncated proteins that retained SYCE1 binding but exhibited impaired polycomplex formation between C14ORF39 and SYCE1. Further cytological analyses of meiosis in germ cells revealed that the affected familial males with the C14orf39 frameshift mutation displayed complete asynapsis between homologous chromosomes, while the affected Chinese men carrying the nonsense or splicing mutation showed incomplete synapsis. The phenotypes of NOA and POI in affected individuals were well recapitulated by Six6os1 mutant mice carrying an analogous mutation. Collectively, our findings in humans and mice highlight the conserved role of C14ORF39/SIX6OS1 in SC assembly and indicate that the homozygous mutations in C14orf39/SIX6OS1 described here are responsible for infertility of these affected individuals, thus expanding our understanding of the genetic basis of human infertility.


Subject(s)
Azoospermia/genetics , Mutation , Primary Ovarian Insufficiency/genetics , Adult , Azoospermia/physiopathology , Chromosome Pairing , Codon, Nonsense , DNA-Binding Proteins/metabolism , Female , Homozygote , Humans , Male , Meiosis , Middle Aged , Nuclear Proteins/metabolism , Pedigree , Primary Ovarian Insufficiency/physiopathology , Spermatocytes/metabolism , Spermatocytes/physiology , Synaptonemal Complex/genetics , Synaptonemal Complex/metabolism , Whole Genome Sequencing
10.
Am J Hum Genet ; 108(2): 309-323, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33472045

ABSTRACT

Asthenoteratozoospermia characterized by multiple morphological abnormalities of the flagella (MMAF) has been identified as a sub-type of male infertility. Recent progress has identified several MMAF-associated genes with an autosomal recessive inheritance in human affected individuals, but the etiology in approximately 40% of affected individuals remains unknown. Here, we conducted whole-exome sequencing (WES) and identified hemizygous missense variants in the X-linked CFAP47 in three unrelated Chinese individuals with MMAF. These three CFAP47 variants were absent in human control population genome databases and were predicted to be deleterious by multiple bioinformatic tools. CFAP47 encodes a cilia- and flagella-associated protein that is highly expressed in testis. Immunoblotting and immunofluorescence assays revealed obviously reduced levels of CFAP47 in spermatozoa from all three men harboring deleterious missense variants of CFAP47. Furthermore, WES data from an additional cohort of severe asthenoteratozoospermic men originating from Australia permitted the identification of a hemizygous Xp21.1 deletion removing the entire CFAP47 gene. All men harboring hemizygous CFAP47 variants displayed typical MMAF phenotypes. We also generated a Cfap47-mutated mouse model, the adult males of which were sterile and presented with reduced sperm motility and abnormal flagellar morphology and movement. However, fertility could be rescued by the use of intra-cytoplasmic sperm injections (ICSIs). Altogether, our experimental observations in humans and mice demonstrate that hemizygous mutations in CFAP47 can induce X-linked MMAF and asthenoteratozoospermia, for which good ICSI prognosis is suggested. These findings will provide important guidance for genetic counseling and assisted reproduction treatments.


Subject(s)
Asthenozoospermia/genetics , Infertility, Male/genetics , Animals , Asthenozoospermia/pathology , Asthenozoospermia/physiopathology , Cohort Studies , Female , Gene Deletion , Genes, X-Linked , Hemizygote , Humans , Infertility, Male/metabolism , Infertility, Male/pathology , Infertility, Male/physiopathology , Male , Mice, Inbred C57BL , Mutation , Mutation, Missense , Pedigree , Phenotype , Sperm Injections, Intracytoplasmic , Sperm Motility , Sperm Tail/ultrastructure , Spermatozoa/pathology , Spermatozoa/physiology , Spermatozoa/ultrastructure , Exome Sequencing
11.
Chromosome Res ; 32(1): 1, 2023 12 18.
Article in English | MEDLINE | ID: mdl-38108925

ABSTRACT

Polyploidization is a process which is related to species hybridization and whole genome duplication. It is widespread among angiosperm evolution and is essential for speciation and diversification. Allopolyploidization is mainly derived from interspecific hybridization and is believed to pose chromosome imbalances and genome instability caused by meiotic irregularity. However, the self-compatible allopolyploid in wild nature is cytogenetically and genetically stable. Whether this stabilization form was achieved in initial generation or a consequence of long term of evolution was largely unknown. Here, we synthesized a series of nascent allotetraploid wheat derived from three diploid genomes of A, S*, and D. The chromosome numbers of the majority of the progeny derived from these newly formed allotetraploid wheat plants were found to be relatively consistent, with each genome containing 14 chromosomes. In meiosis, bivalent was the majority of the chromosome configuration in metaphase I which supports the stable chromosome number inheritance in the nascent allotetraploid. These findings suggest that diploidization occurred in the newly formed synthetic allotetraploid wheat. However, we still detected aneuploids in a proportion of newly formed allotetraploid wheat, and meiosis of these materials present more irregular chromosome behavior than the euploid. We found that centromere pairing and centromere clustering in meiosis was affected in the aneuploids, which suggest that aneuploidy may trigger the irregular interactions of centromere in early meiosis which may take participate in promoting meiosis stabilization in newly formed allotetraploid wheat.


Subject(s)
Diploidy , Triticum , Triticum/genetics , Poaceae , Meiosis/genetics , Aneuploidy
12.
PLoS Genet ; 17(8): e1009753, 2021 08.
Article in English | MEDLINE | ID: mdl-34388164

ABSTRACT

Meiosis is essential for the generation of gametes and sexual reproduction, yet the factors and underlying mechanisms regulating meiotic progression remain largely unknown. Here, we showed that MTL5 translocates into nuclei of spermatocytes during zygotene-pachytene transition and ensures meiosis advances beyond pachytene stage. MTL5 shows strong interactions with MuvB core complex components, a well-known transcriptional complex regulating mitotic progression, and the zygotene-pachytene transition of MTL5 is mediated by its direct interaction with the component LIN9, through MTL5 C-terminal 443-475 residues. Male Mtl5c-mu/c-mu mice expressing the truncated MTL5 (p.Ser445Arg fs*3) that lacks the interaction with LIN9 and is detained in cytoplasm showed male infertility and spermatogenic arrest at pachytene stage, same as that of Mtl5 knockout mice, indicating that the interaction with LIN9 is essential for the nuclear translocation and function of MTL5 during meiosis. Our data demonstrated MTL5 translocates into nuclei during the zygotene-pachytene transition to initiate its function along with the MuvB core complex in pachytene spermatocytes, highlighting a new mechanism regulating the progression of male meiosis.


Subject(s)
Meiosis/physiology , Metallothionein/metabolism , Tumor Suppressor Proteins/metabolism , Active Transport, Cell Nucleus/physiology , Animals , Cell Cycle Proteins/metabolism , Chromosome Pairing/genetics , Cytoplasm , DNA-Binding Proteins , Fertility/genetics , Fertility/physiology , Infertility, Male/genetics , Infertility, Male/metabolism , Male , Meiotic Prophase I/physiology , Metallothionein/genetics , Mice , Mice, Inbred C57BL , Pachytene Stage/genetics , Spermatocytes/physiology , Spermatogenesis/physiology , Testis , Tumor Suppressor Proteins/physiology
13.
J Assist Reprod Genet ; 41(1): 109-120, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37831349

ABSTRACT

PURPOSE: Asthenozoospermia is an important cause of male infertility, and the most serious type is characterized by multiple morphological abnormalities of the sperm flagella (MMAF). However, the precise etiology of MMAF remains unknown. In the current study, we recruited a consanguineous Pakistani family with two infertile brothers suffering from primary infertility due to MMAF without obvious signs of PCD. METHODS: We performed whole-exome sequencing on DNAs of the patients, their parents, and a fertile brother and identified the homozygous missense variant (c.1490C > G (p.P497R) in NPHP4 as the candidate mutation for male infertility in this family. RESULTS: Sanger sequencing confirmed that this mutation recessively co-segregated with the MMAF in this family. In silico analysis revealed that the mutation site is conserved across different species, and the identified mutation also causes abnormalities in the structure and hydrophobic interactions of the NPHP4 protein. Different bioinformatics tools predict that NPHP4p.P497R mutation is pathogenic. Furthermore, Papanicolaou staining and scanning electron microscopy of sperm revealed that affected individuals displayed typical MMAF phenotype with a high percentage of coiled, bent, short, absent, and/or irregular flagella. Transmission electron microscopy images of the patient's spermatozoa revealed significant anomalies in the sperm flagella with the absence of a central pair of microtubules (9 + 0) in every section scored. CONCLUSIONS: Taken together, these results show that the homozygous missense mutation in NPHP4 is associated with MMAF.


Subject(s)
Infertility, Male , Siblings , Humans , Male , Flagella/genetics , Infertility, Male/genetics , Infertility, Male/pathology , Mutation , Mutation, Missense/genetics , Proteins/genetics , Semen , Sperm Tail/pathology , Spermatozoa/pathology
14.
Int J Mol Sci ; 25(11)2024 May 28.
Article in English | MEDLINE | ID: mdl-38892039

ABSTRACT

High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, we identified 11 members of the HMGB family in tomato using BLAST. We employed genome-wide identification, gene structure analysis, domain conservation analysis, cis-acting element analysis, collinearity analysis, and qRT-PCR-based expression analysis to study these 11 genes. These genes were categorized into four groups based on their unique protein domain structures. Despite their structural diversity, all members contain the HMG-box domain, a characteristic feature of the HMG superfamily. Syntenic analysis suggested that tomato SlHMGBs have close evolutionary relationships with their homologs in other dicots. The promoter regions of SlHMGBs are enriched with numerous cis-elements related to plant growth and development, phytohormone responsiveness, and stress responsiveness. Furthermore, SlHMGB members exhibited distinct tissue-specific expression profiles, suggesting their potential roles in regulating various aspects of plant growth and development. Most SlHMGB genes respond to a variety of abiotic stresses, including salt, drought, heat, and cold. For instance, SlHMGB2 and SlHMGB4 showed positive responses to salt, drought, and cold stresses. SlHMGB1, SlHMGB3, and SlHMGB8 were involved in responses to two types of stress: SlHMGB1 responded to drought and heat, while SlHMGB3 and SlHMGB8 responded to salt and heat. SlHMGB6 and SlHMGB11 were solely regulated by drought and heat stress, respectively. Under various treatment conditions, the number of up-regulated genes significantly outnumbered the down-regulated genes, implying that the SlHMGB family may play a crucial role in mitigating abiotic stress in tomato. These findings lay a foundation for further dissecting the precise roles of SlHMGB genes.


Subject(s)
Gene Expression Regulation, Plant , Multigene Family , Plant Proteins , Solanum lycopersicum , Stress, Physiological , Solanum lycopersicum/genetics , Solanum lycopersicum/metabolism , Stress, Physiological/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Phylogeny , Genome, Plant , Gene Expression Profiling , Promoter Regions, Genetic/genetics
15.
Hum Mol Genet ; 30(21): 1977-1984, 2021 10 13.
Article in English | MEDLINE | ID: mdl-34155512

ABSTRACT

Serine/threonine kinases domain-containing proteins are known to play important functions in sperm flagella and male fertility. However, the roles of these proteins in human reproduction remain poorly understood and whether their variants are associated with human asthenozoospermia have not been reported. Here, we recruited a Pakistani family having four infertile patients diagnosed with idiopathic asthenozoospermia without any ciliary-related symptoms. Whole-exome sequencing identified a novel homozygous frameshift mutation (c.1235del, p.T412Kfs*14) in serine/threonine kinase 33 (STK33), which displays a highly conserved and predominant expression in testis in humans. This variant led to a dramatic reduction of STK33 messenger RNA (mRNA) in the patients. Patients homozygous for the STK33 variant presented reduced sperm motility, frequent morphological abnormalities of sperm flagella and completely disorganized flagellar ultrastructures, which are typical for multiple morphological abnormalities of the flagella (MMAF) phenotypes. Overall, these findings present evidence establishing that STK33 is an MMAF-related gene and provide new insights for understanding the role of serine/threonine kinases domain-containing proteins in human male reproduction.


Subject(s)
Asthenozoospermia/diagnosis , Asthenozoospermia/genetics , Frameshift Mutation , Genetic Predisposition to Disease , Protein Serine-Threonine Kinases/genetics , Sperm Tail/metabolism , Adult , Genetic Association Studies , Homozygote , Humans , Male , Pedigree , Phenotype , Semen Analysis , Sperm Tail/pathology , Sperm Tail/ultrastructure
16.
Brief Bioinform ; 22(3)2021 05 20.
Article in English | MEDLINE | ID: mdl-32393981

ABSTRACT

With the advances of next-generation sequencing technology, the field of disease research has been revolutionized. However, pinpointing the disease-causing variants from millions of revealed variants is still a tough task. Here, we have reviewed the existing linkage analysis tools and presented PedMiner, a web-based application designed to narrow down candidate variants from family based whole-exome sequencing (WES) data through linkage analysis. PedMiner integrates linkage analysis, variant annotation and prioritization in one automated pipeline. It provides graphical visualization of the linked regions along with comprehensive annotation of variants and genes within these linked regions. This efficient and comprehensive application will be helpful for the scientific community working on Mendelian inherited disorders using family based WES data.


Subject(s)
Exome Sequencing/methods , Family , Genetic Diseases, Inborn/genetics , Genetic Linkage , Algorithms , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Male , Pedigree
17.
Clin Genet ; 104(5): 564-570, 2023 11.
Article in English | MEDLINE | ID: mdl-37286336

ABSTRACT

Male infertility affects more than 20 million men worldwide and is a major public health concern. Male infertility has a strong genetic basis, particularly for those unexplained cases. Here, through genetic analysis of three Pakistani families having eight infertile men with normal parameters in routine semen analysis, we identified a novel ACTL7A variant (c.149_150del, p.E50Afs*6), recessively co-segregating with infertility in these three families. This variant leads to the loss of ACTL7A proteins in spermatozoa from patients. Transmission EM analyses revealed acrosome detachment from nuclei in 98.9% spermatozoa of patients. Interestingly, this ACTL7A variant was frequently detected in our sequenced Pakistani Pashtuns with a minor allele frequency of ~0.021 and all the carriers shared a common haplotype of about 240 kb flanking ACTL7A, indicating that it is likely originated from a single founder. Our findings reveal that a founder ACTL7A pathogenic variant confers a high genetic susceptibility for male infertility with normal routine semen parameters but acrosomal ultrastructural defects in Pakistani Pashtun descendants, and highlight that variants not rare should also be considered when trying to identify disease-causing variants in ethnic groups with the tradition of intra-ethnic marriages.


Subject(s)
Acrosome , Infertility, Male , Humans , Male , Infertility, Male/genetics , Pakistan , Semen , Spermatozoa/metabolism
18.
FASEB J ; 36(12): e22634, 2022 12.
Article in English | MEDLINE | ID: mdl-36331537

ABSTRACT

Testis-specifically expressed genes are important for male reproduction according to their unique expression patterns. However, the functions of most of these genes in reproduction are unclear. Here, we showed that mouse 4930590J08Rik was a testis-specifically expressed gene. 4930590J08Rik knockout mice exhibited a delay in the first wave of spermatogenesis and a reduction of cauda epididymal sperm. Furthermore, knockout spermatozoa exhibited defective acrosome reactions and decreased progressive motility, which led to impaired in vivo fertilization. Transcriptome analysis of testes revealed that most of the differentially expressed genes in knockout testes were associated with metabolic processes. 4930590J08Rik knockout sperm exhibited oxidative phosphorylation deficiency and were highly dependent on increased anaerobic glycolysis to compensate for ATP demands. Taken together, the 4930590J08Rik-disrupted mouse partially mimics the phenotypes of human asthenospermia and oligozoospermia, which provides a new model for further understanding the pathogenesis of idiopathic male infertility.


Subject(s)
Infertility, Male , Semen , Humans , Male , Mice , Animals , Semen/metabolism , Spermatozoa/metabolism , Fertility/genetics , Infertility, Male/metabolism , Testis/metabolism , Spermatogenesis/genetics , Mice, Knockout , Energy Metabolism/genetics , Sperm Motility/genetics
19.
Sensors (Basel) ; 23(6)2023 Mar 20.
Article in English | MEDLINE | ID: mdl-36991972

ABSTRACT

In the distributed information fusion of wireless sensor networks (WSNs), the filtering accuracy is commonly negatively correlated with energy consumption. Therefore, a class of distributed consensus Kalman filters was designed to balance the contradiction between them in this paper. Firstly, an event-triggered schedule was designed based on historical data within a timeliness window. Furthermore, considering the relationship between energy consumption and communication distance, a topological transformation schedule with energy-saving is proposed. The energy-saving distributed consensus Kalman filter with a dual event-driven (or event-triggered) strategy is proposed by combining the above two schedules. The sufficient condition of stability for the filter is given by the second Lyapunov stability theory. Finally, the effectiveness of the proposed filter was verified by a simulation.

20.
Sensors (Basel) ; 23(4)2023 Feb 08.
Article in English | MEDLINE | ID: mdl-36850516

ABSTRACT

The low absolute positioning accuracy of industrial robots is one of the bottlenecks preventing industrial robots from precision applications. Kinematic calibration is the main way to improve the absolute positioning accuracy of industrial robots, which greatly relies on three-dimensional (3D) measurement instruments, including laser trackers and pull rope mechanisms. These instruments are costly, and their required intervisibility space is large. In this paper, a precision 3D measurement instrument integrating multiple laser range sensors is designed, which fuses the information of multiple redundant laser range sensors to obtain the coordinates of a 3D position. An identification model of laser beam position and orientation parameters based on redundant distance information and standard spherical constraint is then developed to reduce the requirement for the assembly accuracy of laser range sensors. A hybrid identification algorithm of PSO-LM (particle swarm optimization Levenberg Marquardt) is designed to solve the high-order nonlinear problem of the identification model, where PSO is used for initial value identification, and LM is used for final value identification. Experiments of identification of position and orientation, verifications of the measuring accuracy, and the calibration of industrial robots are conducted, which show the effectiveness of the proposed 3D measurement instrument and identification methods. Moreover, the proposed instrument is small in size and can be used in narrow industrial sites.

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