Vincent Coustham

Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contribution of non-coding polymorphisms to gene expression regulation. Moreover, new studies are helping to unravel the role of expression polymorphisms and their orchestrated performance. Recent advances involving classical linkage analysis, GWAS and improved eQTL mapping strategies will provide a greater resolution to determine the genetic variants shaping the broad diversity in plant systems.

SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1

Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.

Effect of low incubation temperature and low ambient temperature until 21 days of age on performance and body temperature in fast-growing chickens

&NA; Thermal manipulation during embryogenesis was previously reported to decrease the occurrence of ascites and to potentially improve cold tolerance of broilers. The objective of our study was to explore the effects of the interaction of cold incubation temperatures and cool ambient temperatures until 21 d of age on performance and body temperature. Ross 308 eggs were incubated either under control conditions I0 (37.6°C) or with cyclic cold stimulations I1 (6 h/d at 36.6°C from d 10 to 18 of incubation) or with 2 cold stimulations I2 (30 min at 15°C) at d 18 and 19 of incubation. These treatments were followed by individual rearing and postnatal exposure to either standard rearing temperature T0 (from 33°C at hatching to 21°C at d 21) or continuously lower temperature T2 (from 28°C at hatching to 21°C at d 21) or exposure to cyclically lower temperature T1 (with circadian temperature oscillations). Treatments I1 and I2 did not significantly alter hatchability compared to control incubation (with 94.8, 95.1, and 92.3%, respectively), or hatching BW and overall chick quality. Hatching body temperature (Tb) was 0.5 and 0.3°C higher in I1 than in I0 and I2 groups, respectively (P = 0.007). A doubled occurrence of health problems was observed with T2 condition, regardless of incubation or sex. At d 3, BW was 2% lower with treatment I1 than with I0 and I2 and was 3% higher in T1 and T2 groups than in T0, but these effects disappeared with age. Group T2 presented a 5% higher feed intake than the control group T0 between 3 and 21 d of age (P = 0.025). Feed conversion ratio (FCR) was affected by experimental conditions (P < 0.001), with low FCR values obtained with I2 incubation in control or cyclically cold postnatal conditions. Maximal FCR values were observed in the continuously cold postnatal conditions, in males submitted to control incubation and in females submitted to I1 incubation, revealing sex‐dependent effects of the treatments on performance.

First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines

Setmar is a 3-exons gene coding a SET domain fused to a Hsmar1 transposase. Its different transcripts theoretically encode 8 isoforms with SET moieties differently spliced. In vitro, the largest isoform binds specifically to Hsmar1 DNA ends and with no specificity to DNA when it is associated with hPso4. In colon cell lines, we found they bind specifically to two chromosomal targets depending probably on the isoform, Hsmar1 ends and sites with no conserved motifs. We also discovered that the isoforms profile was different between cell lines and patient tissues, suggesting the isoforms encoded by this gene in healthy cells and their functions are currently not investigated.