Genes & genetic systems最新文献

Ectodermal dysplasia (ED), which exhibits a wide range of clinical symptoms, may be classified into three major types: hypohidrotic, anhidrotic, and hidrotic. A male child (proband) showing anhidrotic dysplasia was used as the subject of this study. The biopsy of the big toe revealed that the male child had no sweat glands. Genetic analysis of the patient revealed a mutation caused by a homozygous nucleotide substitution in the EDAR-associated death domain (EDARADD) (rs114632254) gene c.439G>A (p.Gly147Arg). Phenotypically, his teeth were sharp, but eight teeth were missing (oligodontia). The patient had normal nails with dry skin, sparse hair, everted lower lip vermilion, hyperpigmented eyelids, and abnormal nasal bridge morphology around the eyes. There is also a homozygous dominant (healthy) female and a heterozygous male in this family, who are cousins (aunt children) to the heterozygous parents. The daughter of the patient was also heterozygous. This mutation represents homozygous recessive inheritance, which we describe for the first time. Furthermore, we demonstrated that this genetic disorder can be readily diagnosed using the restriction fragment length polymorphism (RFLP) method after digestion with MnII restriction endonuclease.

Polyglutamine (polyQ) diseases are rare autosomal-dominant neurodegenerative diseases associated with the expansion of glutamine-encoding triplet repeats in certain genes. To investigate the functional influence of repeat expansion on disease mechanisms, we applied a biallelic genome-engineering platform that we recently established, called Universal Knock-in System or UKiS, to develop a human cell trio, a set of three isogenic cell lines that are homozygous for two different numbers of repeats (first and second lines) or heterozygous for the two repeat numbers (third line). As an example of a polyQ disease, we chose spinocerebellar ataxia type 2 (SCA2). In a pseudodiploid human cell line, both alleles of the glutamine-encoding triplet repeat in the SCA2-causing gene, ataxin 2 or ATXN2, were first knocked in with a donor sequence encoding both thymidine kinase and either puromycin or blasticidin resistance proteins under dual drug selection. The knocked-in donor alleles were then substituted with a payload having either 22 or 76 triplet repeats in ATXN2 by ganciclovir negative selection. The two-step substitution and subsequent SNP typing and genomic sequencing confirmed that the SCA2-modeling isogenic cell trio was obtained: three clones of 22-repeat homozygotes, two clones of 22/76-repeat heterozygotes and two clones of 76-repeat homozygotes. Finally, RT-PCR and immunoblotting using the obtained clones showed that, consistent with previous observations, glutamine tract expansion reduced transcriptional and translational expression of ATXN2. The cell clones with homozygous long-repeat alleles, which are rarely obtained from patients with SCA2, showed more drastic reduction of ATXN2 expression than the heterozygous clones. This study thus demonstrates the potential of UKiS, which is a beneficial platform for the efficient development of cell models not only for polyQ diseases but also for any other genetic diseases, which may accelerate our deeper understanding of disease mechanisms and cell-based screening for therapeutic drugs.

N6-methyladenosine (m6A) modifications are the most abundant internal modifications of mRNA and have a significant role in various cancers; however, the m6A methylome profile of oral squamous cell carcinoma (OSCC) in the mRNA-wide remains unknown. In this study, we examined the relationship between m6A and OSCC. Four pairs of OSCC and adjacent normal tissues were compared by Methylated RNA immunoprecipitation sequencing (MeRIP-seq). Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Ingenuity Pathway Analysis (IPA) analyses were used to further analyze the MeRIP-seq data. A total of 2,348 different m6A peaks were identified in the OSCC group, including 85 m6A upregulated peaks and 2,263 m6A downregulated peaks. Differentially methylated m6A binding sites were enriched in the coding sequence in proximity to the stop codon of both groups. KEGG analysis revealed genes with upregulated m6A-modified sites in the OSCC group, which were prominently associated with the forkhead box O (FOXO) signaling pathway. Genes containing downregulated m6A-modified sites were significantly correlated with the PI3K/Akt signaling pathway, spliceosome, protein processing in the endoplasmic reticulum, and endocytosis. IPA analysis indicated that several genes with differential methylation peaks form networks with m6A regulators. Overall, this study established the mRNA-wide m6A map for human OSCC and indicated the potential links between OSCC and N6-methyladenosine modification.

Many organisms with heteromorphic sex chromosomes possess a mechanism of dosage compensation (DC) in which X-linked genes are upregulated in males to mitigate the dosage imbalance between sexes and between chromosomes. However, how quickly the DC is established during evolution remains unknown. In this study, by irradiating Drosophila miranda male flies, which carry young sex chromosomes (the so-called neo-sex chromosomes), with heavy-ion beams, we induced deletions in the neo-Y chromosome to mimic the condition of Y-chromosome degeneration, in which functional neo-Y-linked genes are nonfunctionalized; furthermore, we tested whether their neo-X-linked gametologs were immediately upregulated. Because the males that received 2-Gy iron-ion beam irradiation exhibited lower fertility, we sequenced the genomes and transcriptomes of six F₁ males derived from these males. Our pipeline identified 82 neo-Y-linked genes in which deletions were predicted in the F₁ males. Only three of them showed a one-to-one gametologous relationship with the neo-X-linked genes. The candidate deletions in these three genes occurred in UTRs and did not seriously affect their expression levels. These observations indirectly suggest that DC was unlikely to have operated on the neo-X-linked genes immediately after the pseudogenization of their neo-Y-linked gametologs in D. miranda. Therefore, the dosage imbalance caused by deletions in the neo-Y-linked genes without paralogs may not have effectively been compensated, and individuals with such deletions could have exhibited lethality. Future studies on sex chromosomes at different ages will further reveal the relationship between the age of sex chromosomes and the stringency of DC.

Eukaryotic cells contain multiple types of duplicated sequences. Typical examples are tandem repeat sequences including telomeres, centromeres, rDNA genes and transposable elements. Most of these sequences are unstable; thus, their copy numbers or sequences change rapidly in the course of evolution. In this review, I will describe roles of subtelomere regions, which are located adjacent to telomeres at chromosome ends, and recent discoveries about their sequence variation.

Organisms have evolved elaborate mechanisms that maintain genome stability. Deficiencies in these mechanisms result in changes to the nucleotide sequence as well as copy number and structural variations in the genome. Genome instability has been implicated in numerous human diseases. However, genomic alterations can also be beneficial as they are an essential part of the evolutionary process. Organisms sometimes program genomic changes that drive genetic and phenotypic diversity. Therefore, genome alterations can have both positive and negative impacts on cellular growth and functions, which underscores the need to control the processes that restrict or induce such changes to the genome. The ribosomal RNA gene (rDNA) is highly abundant in eukaryotic genomes, forming a cluster where numerous rDNA copies are tandemly arrayed. Budding yeast can alter the stability of its rDNA cluster by changing the rDNA copy number within the cluster or by producing extrachromosomal rDNA circles. Here, we review the mechanisms that regulate the stability of the budding yeast rDNA cluster during repair of DNA double-strand breaks that are formed in response to programmed DNA replication fork arrest.

Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.

We analyzed 196 haplotype sequences from a gene-rich region (250 kb) that includes Mc1r, a gene involved in coat color regulation, to gain insight into the evolution of coat color variation in subspecies of the house mouse Mus musculus. Phylogenetic networks revealed haplotype groups from the major subspecies of M. m. castaneus (CAS), M. m. domesticus (DOM), and M. m. musculus (MUS). Using haplotype sequences assigned to each of CAS and MUS through phylogenetic analysis, we proposed migration routes associated with prehistoric humans from west to east across Eurasia. Comparing nucleotide diversity among subspecies-specific haplotypes in different geographic areas showed a marked reduction during migration, particularly in MUS-derived haplotypes from Korea and Japan, suggesting intensive population bottlenecks during migration. We found that a C>T polymorphism at site 302 (c.302C>T) in the Mc1r coding region correlated with a darkening of dorsal fur color in both CAS and MUS. However, C/C homozygous mice in MUS showed marked variation in lightness, indicating the possibility of another genetic determinant that affects the lightness of dorsal fur color. Detailed sequence comparisons of haplotypes revealed that short fragments assigned to DOM were embedded in CAS-assigned fragments, indicating ancient introgression between subspecies. The estimated age of c.302C>T also supports the hypothesis that genetic interaction between subspecies occurred in ancient times. This suggests that the genome of M. musculus evolved through gene flow between subspecies over an extended period before the movement of the species in conjunction with prehistoric humans.

Many sex-determining genes (SDGs) were generated as neofunctionalized genes through duplication and/or mutation of gonadal formation-related genes. We previously identified dm-W as an SDG in the African clawed frog Xenopus laevis and found that a partial duplication of the masculinization gene dmrt1 created the neofunctionalized dm-W after allotetraploidization by interspecific hybridization. The allotetraploid Xenopus species have two dmrt1 genes, dmrt1.L and dmrt1.S. Xenopus laevis dm-W has four exons: two dmrt1.S-derived exons (exons 2 and 3) and two other exons (noncoding exon 1 and exon 4). Our recent work revealed that exon 4 originated from a DNA transposon, hAT-10. Here, to clarify when and how the noncoding exon 1 and its coexisting promoter evolved during the establishment of dm-W after allotetraploidization, we newly determined nucleotide sequences of the dm-W promoter region from two other allotetraploid species, X. largeni and X. petersii, and performed an evolutionary analysis. We found that dm-W acquired a new exon 1 and TATA-type promoter in the common ancestor of the three allotetraploid Xenopus species, resulting in the deletion of the dmrt1.S-derived TATA-less promoter. In addition, we demonstrated that the TATA box contributes to dm-W promoter activity in cultured cells. Collectively, these findings suggest that this novel TATA-type promoter was important for the establishment of dm-W as a sex-determining gene, followed by the degeneration of the preexisting promoter.