Despite its central role in RNA polymerase II transcription, the composition and function of the TFIID general transcription factor can vary across tissues and developmental stages. Such variability may provide a substrate for evolutionary innovation and contribute to human-specific regulatory functions. Here, we identify a human-specific short isoform of TAF8 (TAF8s), a scaffold subunit of TFIID, generated through the use of an intronic polyadenylation site (iPAS). Comparative genomic analyses reveal that the genomic substrate for this isoform originated with the insertion of a FLAM-C Alu element into intron 5 in the common ancestor of anthropoid primates (Simiiformes), whereas subsequent small sequence changes at the Alu-associated iPAS coincide with the emergence of TAF8s expression in the human lineage. TAF8s lacks nearly half of the canonical TAF8 coding sequence, is widely expressed across human tissues, and accounts for a substantial fraction of TAF8 transcripts. It encodes a truncated protein lacking the canonical nuclear-localization signal and localizes predominantly to the cytoplasm. Despite retaining interactions with its histone-fold partner TAF10 and other core TFIID subunits, TAF8s loses interaction with TAF2, providing a molecular basis for alternative TFIID sub-complex formation. Together, our findings identify a recently evolved human-specific regulatory innovation at the TAF8 locus that diversifies the composition of a conserved general transcription factor. This example illustrates how evolution of transcript isoforms can generate new protein interactions and molecular complexity in essential cellular machineries, with potential implications for the functional diversification of TAF-containing complexes and the genetic basis of TAF-related developmental disorders.
This organism-independent theoretical study examines genomic evaluation of open-pollinated progeny from partially selfing species when the fitted genetic covariance contains only an additive genomic relationship matrix. Open-pollinated families contain selfed-selfed, selfed-outcrossed, and outcrossed-outcrossed sibling pairs, so their covariance must be averaged using joint pair probabilities rather than probabilities assigned to individual offspring. An offspring-level shortcut overestimates expected additive covariance whenever selfing and outcrossing coexist. Extending the pair calculation to the covariance between additive effects and dominance deviations in homozygotes gives a balanced-reference projection coefficient equal to twice the selfing rate under mating-system equilibrium and random unrelated outcrossing. When the solution is interior, this coefficient represents the exact restricted maximum-likelihood projection for balanced families with exchangeable covariance blocks. An independent Mendelian simulation with biallelic quantitative trait loci recovered the classical pair-specific coefficients without supplying them to the data-generating model and closely reproduced the theoretical coefficient, with a coefficient of determination of 0.9998 and mean absolute error of 0.0073. The additive genomic relationship matrix was constructed in a separate controlled marker simulation by VanRaden scaling, and additive-only restricted maximum-likelihood estimates closely followed the balanced-reference prediction, with a coefficient of determination of 0.9900 and mean absolute departure of 0.0107. The resulting dimensionless index and scale conversion are therefore sensitivity diagnostics rather than universal corrections for genomic evaluation designs.
The field of plant genetic engineering has advanced considerably since the development of the first transgenic crop plants, and even though transgenic varieties of various crops are now commercially available, consumer reluctance and environmental concerns over transgene escape pose limits on their expansion. Gene editing offers the opportunity to selectively and precisely alter DNA sequences without reliance on stably integrated transgenes, assuaging both concerns. Considerable progress has been made with the advent of programmable nucleases such as Cas9 and its derivatives. The transgenes encoding the gene editing components can be expressed transiently without integration in the plant's genome or removed from the genome via outcrossing or haploid induction to result in gene-edited plants that are no longer considered transgenic. Nonetheless, gene editing systems remain challenging to implement in some plant species, notably those that have long generation times or are vegetatively propagated, precluding the removal of editing tools through crosses. In these cases, a transgene-free method for introduction of all components needed to enable gene editing will bring the promise of modern breeding tools within reach. Transgene-free genome editing can be accomplished through the delivery of editing components as DNA, RNA, or ribonucleoproteins with delivery via Agrobacterium, microprojectiles, nanocarriers, DNA and RNA viruses, and grafting. Between technical constraints and scientific goals, it can be challenging to determine an appropriate transgene-free genome editing method. Following a review of the literature, a decision tree is provided to help select an appropriate method for a given plant species and to show how emerging tools, including smaller editors, can advance the field.
Abstract We produce a working hypothesis for the steps by which the canonical genetic code might have been constructed. We assume amino acids were added in the order inferred from their enrichment or depletion in ancestrally reconstructed sequences dating back to the Last Universal Common Ancestor (LUCA) relative to that in ancient but post-LUCA controls. To convert this ordering into a time series of 64-codon genetic codes, we followed the “2-1-3 rule” that information appeared first at the middle codon position, then mostly at the first before the third, with purine vs pyrimidine distinctions tending to precede distinctions between purines or between pyrimidines. Two notable deviations from the 2-1-3 rule suggest an ancestral promiscuity between valine/isoleucine/methionine, and between alanine/threonine, to produce “statistical proteins.” The same promiscuities enable amino acids to be added in order of appearance at successive nodes in the cladograms of Class I and Class II aminoacyl-tRNA synthetase catalytic domains. Trifonov's previous amino acid ordering did not produce this consilience, with both a worse fit to the 2-1-3 rule, and discordance of synthetase trees with the order. More support for late resolution of hydrophobic promiscuity comes from post-LUCA differentiation between the synthetases of valine and isoleucine, in a manner dependent on 2 conserved tryptophans. The observed promiscuous activities of synthetases, and deep mutational scanning data on which amino acid substitutions are best tolerated, also align well with our reconstructed time series of genetic codes. As a working hypothesis, this series can guide research on random peptides, urzymes, and substitution models.
Abstract Spatiotemporal organization of biological molecules is a key driver of cellular processes, including many post-transcriptional epigenetic processes. The germline-specific germ granules are biomolecular condensates that act as hubs for mRNA and small RNA processing and are core regulators of germline gene expression programming. Germ granules have been studied extensively in Caenorhabditis elegans, and recent developments have led to many subdivisions of the germ granule into specialized compartments. Rapid advancements in microscopy and protein-protein interaction (PPI) screening techniques have produced a large amount of data towards characterizing the localization of proteins to specific granules. However, common methods used to probe PPIs are limited in their ability to robustly detect valid interactions, especially the multivalent and sometimes transient ones observed in granule environments. Here we perform a meta-analysis of granule protein interaction screens. While these experiments generally enrich for proteins matching the profile of granule-associated proteins, we find that when considering screens individually, reproducibility is surprisingly low, highlighting not only the variability inherent in these methods but also the dynamic nature of the PPI networks present in granules. We developed an algorithm to provide a measure of each protein’s association with specific granules across various experiments (a “granule association metric” or GAM). By further clustering and investigation of the GAM matrix, we demonstrate the power of this holistic approach to provide deeper insights into germ granule organization, highlight novel candidates, and act as a resource to inform future investigations into granules and their constituent proteins.
