bioRxiv ScienceSearch

Biology subjects

Press, M. O.

Publications and source records attributed to Press, M. O..

3 recordsLinked to original sources

HSP90 buffers newly induced mutations in massively mutated plant lines

Robustness to both genetic and environmental change is an emergent feature of living systems. Loss of phenotypic robustness can be associated with increased penetrance of genetic variation. In model organisms and in humans, the phenotypic consequences of standing genetic variation can be buffered by the molecular chaperone HSP90. However, it has been argued that HSP90 has the opposite effect on newly introduced genetic variation. To test the buffering effect of HSP90 on new mutations, we introduced vast numbers of mutations into wild-type and HSP90-reduced plants and assessed embryonic lethality and early seedling phenotypes for thousands of offspring. Although the levels of newly introduced mutations were similar in the two backgrounds, the HSP90-reduced plants showed a significantly greater frequency of embryonic lethality and severe phenotypic abnormalities, consistent with higher penetrance and expressivity of newly introduced genetic variation. We further demonstrate that some mutant phenotypes were heritable in an HSP90-dependent manner, and we map candidate HSP90-dependent polymorphisms. Moreover, both sequence and phenotypic analyses of wild-type and HSP90-reduced plants suggest that the HSP90-dependent phenotypes are largely due the newly introduced mutations rather than to an increased mutation rate in HSP90-reduced plants. Taken together, our results support a model in which HSP90 buffers newly introduced mutations, and the phenotypic consequences of such mutations outweigh those of mutations arising de novo in response to HSP90 perturbation.

genetics

Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions.

The assembly of high-quality genomes from mixed microbial samples is a long-standing challenge in genomics and metagenomics. Here, we describe the application of ProxiMeta, a Hi-C-based metagenomic deconvolution method, to deconvolve a human fecal metagenome. This method uses the intra-cellular proximity signal captured by Hi-C as a direct indicator of which sequences originated in the same cell, enabling culture-free de novo deconvolution of mixed genomes without any reliance on a priori information. We show that ProxiMeta deconvolution provides results of markedly high accuracy and sensitivity, yielding 50 near-complete microbial genomes (many of which are novel) from a single fecal sample, out of 252 total genome clusters. ProxiMeta outperforms traditional contig binning at high-quality genome reconstruction. ProxiMeta shows particularly good performance in constructing high-quality genomes for diverse but poorly-characterized members of the human gut. We further use ProxiMeta to reconstruct genome plasmid content and sharing of plasmids among genomes--tasks that traditional binning methods usually fail to accomplish. Our findings suggest that Hi-C-based deconvolution can be useful to a variety of applications in genomics and metagenomics.

genomics

Short tandem repeats with massive variation and functional consequences across strains of Arabidopsis thaliana

Short tandem repeat (STR) mutations may be responsible for more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assess the scope of this contribution across a collection of 96 strains of Arabidopsis thaliana by massively parallel STR genotyping. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR in these strains. Modest STR expansions are found in most strains, some of which have evident functional effects. For instance, three of six intronic STR expansions are associated with intron retention. Coding STRs are depleted of variation relative to non-coding STRs, consistent with the action of purifying selection, and some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detect dozens of novel STR-phenotype associations that could not be detected with SNPs alone, validating several with follow-up experiments. Our results demonstrate that STRs comprise a large, unascertained reservoir of functionally relevant genomic variation.

genomics