Dataset Information

Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution.

ABSTRACT: Measurements of nuclear organization in asymmetric nuclei in 2D images have traditionally been manual. This is exemplified by attempts to measure chromosome position in sperm samples, typically by dividing the nucleus into zones, and manually scoring which zone a fluorescence in-situ hybridisation (FISH) signal lies in. This is time consuming, limiting the number of nuclei that can be analyzed, and prone to subjectivity. We have developed a new approach for automated mapping of FISH signals in asymmetric nuclei, integrated into an existing image analysis tool for nuclear morphology. Automatic landmark detection defines equivalent structural regions in each nucleus, then dynamic warping of the FISH images to a common shape allows us to generate a composite of the signal within the entire cell population. Using this approach, we mapped the positions of the sex chromosomes and two autosomes in three mouse lineages (Mus musculus domesticus, Mus musculus musculus and Mus spretus). We found that in all three, chromosomes 11 and 19 tend to interact with each other, but are shielded from interactions with the sex chromosomes. This organization is conserved across 2 million years of mouse evolution.

SUBMITTER: Skinner BM

PROVIDER: S-EPMC6409866 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution.

Skinner Benjamin Matthew BM Bacon Joanne J Rathje Claudia Cattoni CC Larson Erica Lee EL Kopania Emily Emiko Konishi EEK Good Jeffrey Martin JM Affara Nabeel Ahmed NA Ellis Peter James Ivor PJI

Genes 20190201 2

Measurements of nuclear organization in asymmetric nuclei in 2D images have traditionally been manual. This is exemplified by attempts to measure chromosome position in sperm samples, typically by dividing the nucleus into zones, and manually scoring which zone a fluorescence in-situ hybridisation (FISH) signal lies in. This is time consuming, limiting the number of nuclei that can be analyzed, and prone to subjectivity. We have developed a new approach for automated mapping of FISH signals in a ...[more]

PMID: 30717218

Similar Datasets

Project description:Spermatogenesis is driven by dramatic temporal and spatial changes in chromatin regulation, gene transcription, and protein expression. To assess the mechanistic bases for these developmental changes, we utilized multiomic single-cell/single-nuclear RNA-sequencing (sc/snRNA-seq) and transposase-accessible chromatin (snATAC-seq) to identify chromatin changes associated with transcription along with cellular indexing of transcriptomes and epitopes (CITE-seq) to assess post-transcriptional control of expression in adult mouse and rat testes. We characterized similarities and variations between the transcriptomes of both species, including a difference in the expression of Id4 in spermatogonial stem cells. In both mice and rats, promoter accessibility and gene expression showed the greatest association during meiosis. We mapped cross-species conservation in putative regulatory regions for key spermatogenic genes, including Sdc4, Sycp3 and Spam1, and we found that the correlation between Cd9 chromatin states and CD9 protein abundance allowed for the isolation of distinct germ cell types with improved resolution. Using a gene regulatory network (GRN) model, we identified 40 key regulons conserved between mouse and rat germ cells, highlighting the relevance of chromatin-related factors in regulating the transcription and translation of key genes across spermatogenesis. (iPSCs) into primordial germ cell-like cells that self-organize within xenogeneic reconstituted testes (xrTestes) generated from mouse fetal testicular cells. Subsequent transplant of xrTestes into immunodeficient mice resulted in efficient generation of undifferentiated and differentiated spermatogonia as well as preleptotene spermatocytes with striking similarities to their in vivo counterparts. As the fertilization competency of human iPSC-generated germ cells cannot be evaluated due to ethical constraints, we utilized a similar strategy to differentiate rhesus iPSCs through all fetal germ cell stages into spermatogonia-like cells. Together, these newly identified models of human gametogenesis will allow further mechanistic assessment of both germ cell development and genetic causes of infertility.

Dataset Information

Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution.

Publications

Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets