Biology subjects

Tack, D.

Publications and source records attributed to Tack, D..

3 recordsLinked to original sources

bioRxiv2019

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

RNA structures are influenced by their physico-chemical environment. Few studies have assessed genome-wide impacts of abiotic stresses on in vivo RNA structure, however, and none have investigated tissue-specificity. We applied our Structure-seq method to assess in vivo mRNA secondary structure in Arabidopsis shoots and roots under control and salt stress conditions. Structure-seq utilizes dimethyl sulfate (DMS) for in vivo transcriptome-wide covalent modification of accessible As and Cs, i.e. those lacking base pairing and protection. Tissue type was a strong determinant of DMS reactivity, indicating tissue-specificity of RNA structuromes. Both tissues exhibited a significant inverse correlation between salt stress-induced changes in transcript reactivity and changes in transcript abundance, implicating changes in RNA structure and accessibility in transcriptome regulation. In mRNAs wherein the 5UTR, CDS and 3UTR concertedly increased or decreased in mean reactivity under salinity, this inverse correlation was more pronounced, suggesting that concordant structural changes across the mRNA have the greatest impact on abundance. Transcripts with the greatest and least salt stress-induced changes in DMS reactivity were enriched in genes encoding stress-related functions and included housekeeping functions, respectively. We conclude that secondary structure regulates mRNA abundance, thereby contributing to tissue specificity of the transcriptome and its dynamic adjustment under stress.\n\nOne Sentence Summary: Transcriptome-wide methods reveal dynamic tissue-specific and salt stress-dependent modulation of mRNA accessibility and structure, and correlated mRNA abundance changes.

plant biology↗

bioRxiv2017

Evolving Bacterial Fitness with an Expanded Genetic Code

Evolution has for the most part used the canonical 20 amino acids of the natural genetic code to construct proteins. While several theories regarding the evolution of the genetic code have been proposed, experimental exploration of these theories has largely been restricted to phylogenetic and computational modeling. The development of orthogonal translation systems has allowed noncanonical amino acids to be inserted at will into proteins. We have taken advantage of these advances to evolve bacteria to accommodate a 21 amino acid genetic code in which the amber codon ambiguously encodes either 3-nitro-L-tyrosine or stop. Such an ambiguous encoding strategy recapitulates numerous models for genetic code expansion, and we find that evolved lineages first accommodate the unnatural amino acid, and then begin to evolve on a neutral landscape where stop codons begin to appear within genes. The resultant lines represent transitional intermediates on the way to the fixation of a functional 21 amino acid code.

evolutionary biology↗

bioRxiv2017

How Well Do You Know Your Mutation? Complex Effects Of Genetic Background On Expressivity, Complementation, And Ordering Of Allelic Effects

For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and variation across alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.

genetics↗