Multiplex knockout of trichome-regulating MYBs in poplar affects light sensitivity and triterpene accumulation

ABSTRACTHair-like trichomes cover the aerial organs of many plant species and act as a barrier between a plant and its environment. They function in defense against biotic and abiotic stresses, while also serving as sites for synthesis and storage of secondary metabolites. Previously, the transcription factor PtaMYB186 was identified as a positive regulator of trichome initiation during early stages of leaf development in Populus tremula x P. alba (IRNA 717-1B4). However, trichome regulation in poplar remains largely unexplored, as does the functional redundancy of duplicated poplar genes. Here, we employed CRISPR/Cas9 to target a consensus region of PtaMYB186 and its close paralogs for knockout. Regeneration of glabrous mutants suggested their essential roles in poplar trichome development. No apparent differences in growth and leaf transpiration rates between the mutants and the controls were observed, but trichomeless poplars showed increased insect pest susceptibility. RNA-seq analysis revealed widespread down-regulation of circadian- and light-responsive genes in the mutants. When exposed to a high light regime, trichomeless mutants accumulated significantly higher levels of photoprotective anthocyanins. Cuticular wax and whole leaf analyses showed a complete absence of triterpenes in the mutants, suggesting biosynthesis and storage of triterpenes in poplar occurs in the non-glandular trichomes. This work also demonstrates that a single gRNA with SNP-aware design is sufficient for multiplex targeting of paralogous genes in outcrossing and/or hybrid species with unexpected copy number variations.ONE SENTENCE SUMMARYNon-glandular trichomes in poplar have roles both as a physical barrier and a chemical factory to mediate plant interactions with the environment.

Environmental effects on star formation main sequence in the COSMOS field

We investigate the relationship between environment and star formation main sequence (the relationship between stellar mass and star formation rate) to shed new light on the effects of the environments on star-forming galaxies. We use the large VLA-COSMOS 3 GHz catalogue that consist of star-forming galaxies (SFGs) and active galactic nuclei (AGN) in three different environments (field, filament, cluster) and for different galaxy types. We examine for the first time a comparative analysis for the distribution of SFGs with respect to the star formation main sequence (MS) consensus region from the literature, taking into account galaxy environment and using radio selected sample at 0.1 ≤ z ≤ 1.2 drawn from one of the deepest COSMOS radio surveys. We find that, as observed previously, SFRs increase with redshift independent on the environments. Furthermore, we observe that SFRs versus M* relation is flat in all cases, irrespective of the redshift and environments.

Static Kinks or Flexible Hinges: Conformational Distributions of Bent DNA Bound to Integration Host Factor Mapped by Fluorescence Lifetime Measurements

Gene regulation depends on proteins that bind to specific DNA sites. Such specific recognition often involves severe DNA deformations including sharp kinks. It has been unclear how rigid or flexible these protein-induced kinks are. Here, we investigated the dynamic nature of DNA in complex with integration host factor (IHF), a nucleoid-associated architectural protein known to bend one of its cognate sites (35 base pair H’) into a U-turn by kinking DNA at two sites. We utilized fluorescence lifetime based FRET spectroscopy to map the distribution of bent conformations in various IHF-DNA complexes. Our results reveal a surprisingly dynamic specific complex: while 80% of the IHF-H’ population exhibited FRET efficiency consistent with the crystal structure, 20% exhibited FRET efficiency indicative of unbent or partially bent DNA. This conformational flexibility is modulated by sequence variations in the cognate site. In another site (H1) that lacks an A-tract of H’ on one side of the binding site, the population in the fully U-bent conformation decreased to 36%, as did the extent of bending. A similar decrease in the U-bent population was observed with a single base mutation in H’ in a consensus region on the other side. Taken together, these results provide important insights into the finely tuned interactions between IHF and its cognate sites that keep the DNA bent (or not), and yield quantitative data on the dynamic equilibrium between different DNA conformations (kinked or not kinked) that depend sensitively on DNA sequence and deformability. Notably, the difference in dynamics between IHF-H’ and IHF-H1 reflects the different roles of these complexes in their natural context, in the phage lambda “intasome” (the complex that integrates phage lambda into theE. colichromosome).

Duplications at 19q13.33 in patients with neurodevelopmental disorders

ObjectiveAfter the recent publication of the first patients with disease-associated missense variants in the GRIN2D gene, we evaluate the effect of copy number variants (CNVs) overlapping this gene toward the presentation of neurodevelopmental disorders (NDDs).MethodsWe explored ClinVar (number of CNVs = 50,794) and DECIPHER (number of CNVs = 28,085) clinical databases of genomic variations for patients with copy number changes overlapping the GRIN2D gene at the 19q13.33 locus and evaluated their respective phenotype alongside their frequency, gene content, and expression, with publicly available reference databases.ResultsWe identified 11 patients with microduplications at the 19q13.33 locus. The majority of CNVs arose de novo, and comparable CNVs are not present in control databases. All patients were reported to have NDDs and dysmorphic features as the most common clinical phenotype (N = 8/11), followed by seizures (N = 6/11) and intellectual disability (N = 5/11). All duplications shared a consensus region of 405 kb overlapping 13 genes. After screening for duplication tolerance in control populations, positive gene brain expression, and gene dosage sensitivity analysis, we highlight 4 genes for future evaluation: CARD8, C19orf68, KDELR1, and GRIN2D, which are promising candidates for disease causality. Furthermore, investigation of the literature especially supports GRIN2D as the best candidate gene.ConclusionsOur study presents dup19q13.33 as a novel duplication syndrome locus associated with NDDs. CARD8, C19orf68, KDELR1, and GRIN2D are promising candidates for functional follow-up.

Duplications at 19q13.33 in patients with neurodevelopmental disorders

OBJECTIVEAfter recent publication of the first patients with disease associated missense variants in GRIN2D, we evaluate the effect of copy number variation (CNV) overlapping this gene towards the presentation of neurodevelopmental disorders.METHODSWe explored ClinVar (N°CNV = 41,398) and DECIPHER (N°CNV = 30,222) clinical databases of genomic variations for patients with copy number changes overlapping the GRIN2D gene at the 19q13.33 locus and evaluated their respective phenotype alongside their frequency, gene content and expression with publicly available reference databases.RESULTSWe identified 13 patients with microduplications at the 19q13.33 locus. The majority of CNVs arose de novo and comparable CNVs are not present in control databases. All patients were reported to have neurodevelopmental disorders and dysmorphic features as the most common clinical phenotype (N= 10/13), followed by seizures (N= 6/13) and intellectual disability (N= 5/13). All duplications shared a consensus region of 405 kb overlapping 13 genes. After screening for duplication tolerance in control populations, positive gene brain expression and gene dosage sensitivity analysis, we highlight four genes for future evaluation: CARD8, C19orf68, KDELR1 and GRIN2D, which are promising candidates for disease causality. Further, investigation of the literature especially supports GRIN2D as the best candidate gene.CONCLUSIONSOur study presents dup19q13.33 as novel duplication syndrome locus associated with neurodevelopmental disorders. CARD8, C19orf68, KDELR1 and GRIN2D are promising candidates for functional follow up.