Next-generation sequencing (NGS) has been used to determine the reference sequences of model organisms. This allows us to identify mutations by the chromosome number and sequence position where the base sequence has been altered, independent of any phenotypic alteration. Because the re-sequencing method by NGS covers all of the genome, it enables detection of the small number of spontaneous de novo germline mutations that occur in the reproductive lineage. The spontaneous mutation rate varies depending on the environment; for example, it increases when 8-oxoguanine accumulates. If the mutation rate (per replication) is greater than 1/genome size (2n), at least one mutation would generally occur in each cell division on average, producing cells with a different genome from the parent cell. Organisms with larger genomes and more divisions by cells in the reproductive lineage are expected to show higher mutation rates per generation, if the mutation rate per replication is constant among species. The accumulation of mutations that arose in the genome of ancestor cells has resulted in heterogeneity and diversity among extant species. In this sense, the ability to produce mutations in cells of the reproductive lineage can be considered as a key feature of organisms, even if mutations also present an unavoidable risk.

Germline mutations are the origin of genetic variation and are widely considered to be the driving force of genome evolution. The rates and spectra of de novo mutations (DNMs) directly affect evolutionary speed and direction and thereby establish species-specific genomic futures in the long term. This has resulted in a keen interest in understanding the origin of germline mutations in mammals. Accumulating evidence from next-generation sequencing and family-based analysis indicates that the frequency of human DNMs varies according to sex, age and local genomic context. Thus, it is likely that there are multiple causes and drivers of mutagenesis, including spontaneous DNA lesions, DNA repair status and DNA polymerase errors. In this review, recent studies of human and mouse germline DNMs are discussed, and the rates and spectra of spontaneous germline DNMs in the mouse mutator lines Pold1^exo/exo and TOY-KO (Mth1^−/−/Ogg1^−/−/Mutyh^−/− triple knockout) are summarized in the context of endogenous causes and mechanisms.

MicroRNA (miRNA) is associated with the development and pathology of atrial fibrillation (AF). In this study, we performed miRNA profiling of left and right atrium samples from individuals with AF-associated rheumatic mitral valve disease (RMVD) to identify miRNAs that are differentially expressed between RMVD patients with AF and RMVD with sinus rhythm (SR) as controls, as well as between left and right atrium samples from RMVD with AF patients. We performed hematoxylin and eosin staining as well as scanning and transmission electron microscopy to examine in detail any morphological and physiological changes in cardiomyocytes from RMVD patients with AF or SR. Raman spectroscopy was performed to identify molecular and structural information of left and right atrium samples from RMVD with AF and SR. We also performed miRNA array profiling to separately profile miRNA expression patterns of right and left atrium samples from three independent RMVD patients with AF and in a mixed pool of 10 RMVD patients with SR. Morphological and physiological analysis showed distinct shapes and structures of cardiomyocytes from the left and right atria of RMVD patients with AF or SR. The intensity of Raman spectroscopy of atrial tissues from RMVD patients with AF and with SR was different. miRNA profiling showed differential miRNA expression between RMVD patients with AF or SR, and between the left and right atria of RMVD patients with AF. Importantly, miRNAs showed consistent expression changes among all three patients, suggesting that these miRNAs have potential as markers for AF pathology. Our results revealed potential biomarker miRNAs for atrial fibrillation pathology in patients with RMVD. Meanwhile, our data suggested that miR-10b and miR-138-2, which were both significantly increased in the left atrium, are responsible for morphological and physiological phenotype differences between the left and right atria.

We investigated the genetic diversity of the core collection of hexaploid wheat accessions in the Japanese wheat gene bank, NBRP-Wheat, with a focus on grain morphology. We scanned images of grains in the core collection, which consists of 189 accessions of Triticum aestivum, T. spelta, T. compactum, T. sphaerococcum, T. macha and T. vavilovii. From the scanned images, we recorded six metric characters (area size, perimeter length, grain length, grain width, length to width ratio and circularity) using the software package SmartGrain ver. 1.2. Statistical analyses of the collected data along with hundred-grain weight revealed that T. aestivum has the largest diversity in grain morphology. Principal component analysis of these seven characters demonstrated that two principal components (PC_core1 and PC_core2) explain more than 96% of the variation in the core collection accessions. The correlation coefficients between the principal components and characters indicate that PC_core1 is related to grain size and PC_core2 to grain shape. From a genome-wide association study, we found a total of 15 significant marker-trait associations (MTAs) for grain morphological characters. More interestingly, we found mutually exclusive MTAs for PC_core1 and PC_core2 on 18 and 13 chromosomes, respectively. The results suggest that grain morphology in hexaploid wheat is determined by two factors, grain size and grain shape, which are under the control of multiple genetic loci.

Transcription factor II D (TFIID), a multiprotein complex consisting of TATA-binding protein (TBP) and 13–14 TBP-associated factors (Tafs), plays a central role in transcription and regulates nearly all class II genes. The N-terminal domain of Taf1p (TAND) can be divided into two subdomains, TAND1 and TAND2, which bind to the concave and convex surfaces of TBP, respectively. The interaction between TAND and TBP is thought to be regulated by TFIIA, activators and/or DNA during transcriptional activation, as the TAND1-bound form of TBP cannot bind to the TATA box. We previously demonstrated that Drosophila TAND1 binds to TBP with a much stronger affinity than yeast TAND1 and that the expression levels of full-length chimeric Taf1p, whose TAND1 is replaced with the Drosophila counterpart, can be varied in vivo by substituting several methionine residues downstream of TAND2 with alanine residues in various combinations. In this study, we examined the transcriptional activation of the GAL1-lacZ reporter or endogenous genes such as RNR3 or GAL1 in yeast cells expressing various levels of full-length chimeric Taf1p. The results showed that the substitution of TAND1 with the Drosophila counterpart in yeast TFIID weakened the transcriptional activation of GAL1-lacZ and RNR3 but not that of GAL1. These findings strongly support a model in which TBP must be released efficiently from TAND1 within TFIID upon transcriptional activation.