The Coding Loci of Evolution and Domestication: Current Knowledge and Implications for Bio-Inspired Genome Editing

International audienceOne promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations, or species). To get a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually-curated database compiling published data about the genes responsible for evolutionary and domesticated changes across Eukaryotes, and examined the >1,200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often due to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared to intraspecific (27%) and interspecific evolution (11%). While this trend may be subject to detection, publication, and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing

The differential view of genotype–phenotype relationships

International audienceAn integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype–phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes

Psychological and Neural Mechanisms of Subjective Time Dilation

For a given physical duration, certain events can be experienced as subjectively longer in duration than others. Try this for yourself: take a quick glance at the second hand of a clock. Immediately, the tick will pause momentarily and appear to be longer than the subsequent ticks. Yet, they all last exactly 1 s. By and large, a deviant or an unexpected stimulus in a series of similar events (same duration, same features) can elicit a relative overestimation of subjective time (or “time dilation”) but, as is shown here, this is not always the case. We conducted an event-related functional magnetic neuroimaging study on the time dilation effect. Participants were presented with a series of five visual discs, all static and of equal duration (standards) except for the fourth one, a looming or a receding target. The duration of the target was systematically varied and participants judged whether it was shorter or longer than all other standards in the sequence. Subjective time dilation was observed for the looming stimulus but not for the receding one, which was estimated to be of equal duration to the standards. The neural activation for targets (looming and receding) contrasted with the standards revealed an increased activation of the anterior insula and of the anterior cingulate cortex. Contrasting the looming with the receding targets (i.e., capturing the time dilation effect proper) revealed a specific activation of cortical midline structures. The implication of midline structures in the time dilation illusion is here interpreted in the context of self-referential processes

The proliferating cell nuclear antigen regulates retinoic acid receptor transcriptional activity through direct protein–protein interaction

Retinoic acid receptors (RARs) interact, in a ligand-dependent fashion, with many coregulators that participate in a wide spectrum of biological responses, ranging from embryonic development to cellular growth control. The transactivating function of these ligand-inducible transcription factors reside mainly, but not exclusively, in their ligand-binding domain (AF2), which recruits or dismiss coregulators in a ligand-dependent fashion. However, little is known about AF2-independent function(s) of RARs. We have isolated the proliferating cell nuclear antigen (PCNA) as a repressor of RAR transcriptional activity, able to interact with an AF2-crippled RAR. The N-terminus of PCNA interacts directly with the DNA-binding domain of RAR, and PCNA is recruited to a retinoid-regulated promoter in intact cells. This interaction affects the transcriptional response to retinoic acid in a promoter-specific manner, conferring an unanticipated role to PCNA in transcriptional regulation. Our findings also suggest a role for RAR as a factor coordinating DNA transcription and repair

Les processus inflammatoires chez les oiseaux : physiopathologie et implications cliniques en aviculture

Chez les oiseaux comme chez les mammifères, les processus inflammatoires font partie intégrante des mécanismes de défense de l’organisme. Ils se développent au cours de nombreuses maladies aviaires (tant virales, bactériennes que parasitaires), selon un schéma caractérisé par la mise en jeu d’évènements vasculaires et cellulaires. Les cellules de l’inflammation des oiseaux (les leucocytes et les thrombocytes) présentent des caractéristiques morphologiques et fonctionnelles les distinguant de celles des mammifères, et sont capables de libérer des médiateurs de l’inflammation intervenant dans le déclenchement et la régulation des processus inflammatoires. Les implications cliniques des processus inflammatoires sont multiples en aviculture. D’une part, leur intervention dans nombre de maladies aviaires justifie leur évaluation par le clinicien au cours de sa démarche diagnostique ; D’autre part, ils peuvent être associés à des baisses conséquentes des performances d’élevages, ce qui a motivé la recherche de solutions pour les contrôler, qu’il s’agisse de solutions thérapeutiques ou d’une modulation des capacités de défense via l’alimentation