Biology subjects

Fredrickson, J.

Publications and source records attributed to Fredrickson, J..

4 recordsLinked to original sources

bioRxiv2024

Haploid Asexual Blastocyst Fitness Varies Across Mouse Strains Related to Efficiency of Exit From Totipotency

In vitro activation, both sexually and asexually, facilitates assessing the reproductive mode and fitness of mammalian oocytes. Herein, we present evidence of the enhancement of asexual haploid blastocyst fitness in one selectively-inbred Mus musculus population. We tracked sexually and asexually activated-oocytes as they exited totipotency and self-organized into blastocyst-stage embryos. We examined haploid and diploid parthenogenetic potential of activated-oocytes. Unexpectedly, [~]90% of selectively-inbred mouse oocytes that were asexually activated successfully generated haploid blastocysts, contrasting with [~]90% failure in randomly-outbred mice. Furthermore, by closely tracking the timeline of exit from totipotency, we propose a novel self-correcting totipotency clock, crucial for timely exit from totipotency and successful embryogenesis across mammals. Insufficiency in this self-correcting prerequisite, will alter the fitness landscape in different reproductive modes. Collectively, this work provides a quantitative framework to investigate the unknown disruptive evolutionary trajectories of reproductive modes and fitness of females in anisogamous species. HighlightsO_LISerendipitious discovery of disruptive evolution of haploid asexual reproductive mode and preimplantation embryogenetic fitness in FVB strain of mice. C_LIO_LINovel self-correcting totipotency clock regulates blastulation potential in mammals including humans and limits haploid asexual embryogenesis C_LIO_LIEvolution of haploid asexual reproductive mode and preimplantation embryogenetic fitness in FVB mouse is linked to a superior self-correcting totipotency clock lacking in other animals. C_LI Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/608531v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@12b9f77org.highwire.dtl.DTLVardef@f2759forg.highwire.dtl.DTLVardef@84029org.highwire.dtl.DTLVardef@1ac7f42_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

Multi-tissue landscape of somatic mtDNA mutations indicates tissue specific accumulation and removal in aging

Accumulation of somatic mutations in the mitochondrial genome (mtDNA) during aging has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G[->]A/C[->]T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G[->]T/C[->]A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age indicates a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.

genomics↗

bioRxiv2021

A mutational gradient drives somatic mutation accumulation in mitochondrial DNA and influences germline polymorphisms and genome composition

BackgroundMutations in the mitochondrial genome (mtDNA) can cause devastating maternally inherited diseases, while the accumulation of somatic mtDNA mutations is linked to common diseases of aging. Although mtDNA mutations impact human health, the process(es) that give rise to these mutations are unclear and are under considerable debate. We analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing to provide clues to the mechanism by which de novo mutations arise as well as how the genome is replicated. ResultsWe observe two distinct mutational gradients in G[->]A and T[->]C transitions, but not their complements, that are delimited by the light-strand origin and the control region (CR). The gradients increase with age and are lost in the absence of DNA polymerase {gamma} proofreading activity. A nearly identical pattern is present in human mtDNA somatic mutations. The distribution of mtDNA single nucleotide polymorphisms (SNPs) in the human population and genome base composition across >3,000 vertebrate species mirror this gradient pattern, pointing to evolutionary conservation of this phenomenon. Lastly, high-resolution analysis of the mtDNA control region highlights mutational hotspots and cold-spots that strongly align with important regulatory regions. ConclusionsCollectively, these patterns support an asymmetric strand-displacement mechanism with key regulatory structures in the CR and argue against alternative replication models. The mutational gradient is a fundamental consequence of mtDNA replication that drives somatic mutation accumulation and influences inherited polymorphisms and, over evolutionary timescales, genome composition.

genomics↗

bioRxiv2019

Telomere-to-telomere assembly of a complete human X chromosome

After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist 1,2. The remaining gaps include ribosomal rDNA arrays, large near-identical segmental duplications, and satellite DNA arrays. These regions harbor largely unexplored variation of unknown consequence, and their absence from the current reference genome can lead to experimental artifacts and hide true variants when re-sequencing additional human genomes. Here we present a de novo human genome assembly that surpasses the continuity of GRCh38 2, along with the first gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome 3, we reconstructed the [~]2.8 megabase centromeric satellite DNA array and closed all 29 remaining gaps in the current reference, including new sequence from the human pseudoautosomal regions and cancer-testis ampliconic gene families (CT-X and GAGE). This complete chromosome X, combined with the ultra-long nanopore data, also allowed us to map methylation patterns across complex tandem repeats and satellite arrays for the first time. These results demonstrate that finishing the human genome is now within reach and will enable ongoing efforts to complete the remaining human chromosomes.

bioinformatics↗