Biology subjects

Onami, S.

Publications and source records attributed to Onami, S..

24 records · Page 2Linked to original sources

bioRxiv2021

The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans

The RNA polymerase II-associated factor 1 complex (PAF1C) is a protein complex that consists of LEO1, RTF1, PAF1, CDC73, and CTR9, and has been shown to be involved in Pol II-mediated transcriptional and chromatin regulation. Although it has been shown to regulate a variety of biological processes, the precise role of the PAF1C during germ line development has not been clarified. In this study, we found that reduction in the function of the PAF1C components, LEO-1, RTFO-1, PAFO-1, CDC-73, and CTR-9, in Caenorhabditis elegans affects cell volume expansion of oocytes. Defects in oogenesis were also confirmed using an oocyte maturation marker, OMA-1::GFP. While four to five OMA-1::GFP-positive oocytes were observed in wild-type animals, their numbers were significantly decreased in pafo-1 mutant and leo-1(RNAi), cdc-73(RNAi), and pafo-1(RNAi) animals. Expression of a functional PAFO-1::mCherry transgene in the germline significantly rescued the oogenesis-defective phenotype of the pafo-1 mutants, suggesting that expression of the PAF1C in germ cells is required for oogenesis. Notably, overexpression of OMA-1::GFP partially rescued the oogenesis defect in the pafo-1 mutants. Based on our findings, we propose that the PAF1C promotes oogenesis in a cell-autonomous manner by positively regulating the expression of genes involved in oocyte maturation.

developmental biology↗

bioRxiv2020

Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos

Recent advances in bioimage informatics techniques have yielded quantitative data on multicellular dynamics from microscopy images of animal development. Several such data collections have been created for Caenorhabditis elegans embryos under various gene silencing conditions. However, because of the limited depth of the datasets, it is impractical to apply standard statistical methods to these collections. Here, we created a deep collection of quantitative data on nuclear division dynamics during the first three rounds of cell division in C. elegans embryos, in which 263 essential embryonic genes were silenced individually by RNA-mediated interference. The collection consists of datasets from 33 wild-type and 1142 RNAi-treated embryos, including five or more datasets for 189 genes. Application of a two-sample t-test identified 8660 reproducible RNAi-induced phenotypes for 421 phenotypic characters. Clustering analysis suggested 24 functional processes essential for early embryogenesis. Our collection is a rich resource for understanding animal development mechanisms. In BriefKyoda et al. used bioimage informatics techniques to create a deep collection of quantitative data on nuclear division dynamics in RNAi-treated C. elegans embryos for 263 essential embryonic genes. Statistical analysis identified 8660 reproducible RNAi phenotypes for 421 phenotypic characters. The collection is a rich resource for understanding animal development. HighlightsO_LIBioimage informatics quantified nuclear division dynamics in C. elegans embryos C_LIO_LIFrom RNAi-silenced embryos we collected 1142 data sets on 263 essential genes C_LIO_LIStatistical analysis identified 8660 reproducible RNAi phenotypes C_LIO_LIClustering analysis suggested 24 functional processes in C. elegans embryogenesis C_LI

developmental biology↗

bioRxiv2020

Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes

BackgroundOocyte quality decreases with aging, thereby increasing errors in fertilization, chromosome segregation, and embryonic cleavage. Oocyte appearance also changes with aging, suggesting a functional relationship between oocyte quality and appearance. However, no methods are available to objectively quantify age-associated changes in oocyte appearance. ResultsWe show that statistical image processing of Nomarski differential interference contrast microscopy images can be used to quantify age-associated changes in Caenorhabditis elegans oocyte appearance. Max-min Value (mean difference between the maximum and minimum intensities within each moving window) quantitatively characterized the difference in oocyte cytoplasmic texture between 1- and 3-day-old adults (Day 1 and Day 3 oocytes, respectively). With an appropriate parameter set, the gray level co-occurrence matrix (GLCM)-based texture feature Correlation (COR) more sensitively characterized this difference than the Max-min Value. Manipulating the smoothness of and/or adding irregular structures to the cytoplasmic texture of Day 1 oocyte images reproduced the difference in Max-min Value but not in COR between Day 1 and Day 3 oocytes. Increasing the size of granules in synthetic images recapitulated the age-associated changes in COR. Manual measurements validated that the cytoplasmic granules in oocytes become larger with aging. ConclusionsThe Max-min Value and COR objectively quantify age-related changes in C. elegans oocyte in Nomarski DIC microscopy images. Our methods provide new opportunities for understanding the mechanism underlying oocyte aging.

bioinformatics↗

bioRxiv2020

BD5: an open HDF5-based data format to represent quantitative biological dynamics data

BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML(Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML- based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics.

bioinformatics↗

bioRxiv2019

Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization

The 1-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in 3-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the micro-scale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose, to our knowledge, a new microrheology for Hi-C data to analyze the compliance property as a barometer of rigidness and flexibility of genomic regions along with the time evolution. Our method allows conversion of a Hi-C matrix into the spectrum of the rheological property along the genomic coordinate of a single chromosome. To demonstrate the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD region. The spectrum clearly shows the rheological property of the dynamic chromatin domain formations at an individual time scale. Furthermore, we characterized the appearance of synchronous and liquid-like inter-compartment interactions in differentiated cells. Together, our microrheology provides physical insights revealing the dynamic 3D genome organization from Hi-C data.\n\nSIGNIFICANCEGenomic DNA is hierarchically packed inside the eukaryotic cell nucleus, and the genome organization in 3D contributes to proper genome functions at the multiscale chromatin domains. Although thermal fluctuations inevitably drive movements of the genome molecules in the micro-scale cell environment, there is no method, as yet, to quantify such dynamic 3D genome organization of hierarchical and structural chromatin units. Here, we describe a method to calculate rheological properties as barometers of flexibility and liquid-like behavior of genomic regions. We show that biologically relevant boundaries between chromatin domains are more rigid than the inside at a particular time scale. Our method allows interpretation of static and population-averaged genome conformation data as dynamic and hierarchical 3D genome picture.

biophysics↗

bioRxiv2019

PHi-C: deciphering Hi-C data into polymer dynamics

Computational modelling methods for Hi-C data have revealed averaged and static features of the 3D genome in cell nuclei. Here, we describe a 4D simulation method, PHi-C (Polymer dynamics deciphered from Hi-C data), that depicts dynamic 3D genome features through polymer modelling. This method allows for demonstrations of dynamic characteristics of genomic loci and chromosomes, as observed in live-cell imaging experiments, and provides physical insights into Hi-C data.

bioinformatics↗