Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals

Transcriptomics data of liver and adipose tissue highlight lncRNAs as candidates for the lipid metabolism regulation in broilers

Broilers’ body fat is not valued by food industry which must remove fat deposits on broilers’ carcass during slaughter stages. Adiposity variability has a multifactorial origin with a genetic part and genes which regulate lipid metabolism are not all known yet. The aim of this study is to contribute to a better knowledge of these regulatory genes in chicken, and particularly long noncoding (lncRNA) genes, which regulate genes expression implied in a lot of diseases and metabolic processes. Therefore, we used two broilers lines (lean/fat lines) divergently selected on abdominal fat weight and fed with two different diets (high/low fat/fibers). The genotype factor leads to a differential expression (DE) of genes involved in the cholesterol synthesis and the diet factor in the hepatic fatty acid synthesis and secretion. We used RNA‑seq data from two metabolic tissues: 16 livers and 16 adipose tissues and FEELnc has classified more than 6000 expressed lncRNAs. DE analyzes showed 160 (vs. 258) and 266 (vs. 396) lncRNA genes up- and down-regulated respectively between the lean and fat lines in liver (vs. adipose tissue). 30 (vs. 5) and 101 (vs. 1) lncRNA genes are DE between the low and the high fat diet. Amongst them, around 80 lncRNA genes are divergently localized with their nearest coding gene and potentially share a bidirectional promoter. We found some interesting examples concerning key enzymes in cholesterol and fatty acid synthesis for our both factors, genotype and diet which are good candidates for the lipid metabolism regulation in chicken

In the shadow of the wrinkle: experimental models.

International audienceResearch on aging has run for decades, and knowledge on the biologic process of skin chronological and photoaging is still increasing thanks to read across results generated between human, animal, and in vitro studies. However, wrinkles should not be considered to result only from the aging process. There are few reports on specific wrinkle histological features compared to the surrounding skin, and there is thus a need in really wrinkling skin animal and in vitro models. UV-irradiated Hr mouse is a good model because it develops wrinkles. Nevertheless, as mouse skin is somehow different from human skin, the innovative model of wrinkling human skin xenograft on SCID mice seems to be really promising. Concerning in vitro and ex vivo models, although there have been considerable advances in reconstructing realistic aged skins, there is still a lack of in vitro wrinkling skin model, and unfortunately, this gap will probably be difficult to fill

Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species

Background Lipids are important for the cell and organism life since they are major components of membranes, energy reserves and are also signal molecules. The main organs for the energy synthesis and storage are the liver and adipose tissue, both in humans and in more distant species such as chicken. Long noncoding RNAs (lncRNAs) are known to be involved in many biological processes including lipid metabolism. Results In this context, this paper provides the most exhaustive list of lncRNAs involved in lipid metabolism with 60 genes identified after an in-depth analysis of the bibliography, while all “review” type articles list a total of 27 genes. These 60 lncRNAs are mainly described in human or mice and only a few of them have a precise described mode-of-action. Because these genes are still named in a non-standard way making such a study tedious, we propose a standard name for this list according to the rules dictated by the HUGO consortium. Moreover, we identified about 10% of lncRNAs which are conserved between mammals and chicken and 2% between mammals and fishes. Finally, we demonstrated that two lncRNA were wrongly considered as lncRNAs in the literature since they are 3′ extensions of the closest coding gene. Conclusions Such a lncRNAs catalogue can participate to the understanding of the lipid metabolism regulators; it can be useful to better understand the genetic regulation of some human diseases (obesity, hepatic steatosis) or traits of economic interest in livestock species (meat quality, carcass composition). We have no doubt that this first set will be rapidly enriched in coming years

In the shadow of the wrinkle: theories.

International audienceAs time passes, wrinkles typically appear. These skin depressions that become deeper and deeper draw more and more coarser lines on almost all the visible parts of aging individual's skin. They are indeed the most obvious and maybe disliked signs of skin aging, and thus, preventing and treating them are a major topic for dermo-cosmetic laboratories. However, the cause and occurrence mechanism of these simplistic looking lines are not yet fully understood. Wrinkling is thought to be a complex biophysical process resulting from repeated strains on a progressively, structurally and biochemistry altered aging skin with impaired mechanical properties. Focus is made on the specific histological features of the wrinkle compared to the surrounding aging skin. The numerous age-related changes in human skin that are supposed to be involved in wrinkling are briefly reviewed, and the current theories on wrinkle formation linked to these changes are also discussed

Phenotype and multi-tissue transcriptome response to diet changes in laying hens

Adaptation to feed changes in laying hens is particularly important to promote innovation, in selection schemes and in dietary solutions, for the sustainability of the egg-production sector. In Europe and USA poultry feed is rich in cereals, while Asian countries privilege by-products to soybean meal, resulting in low energy diets.In this study, we investigated the effects of a sub-optimal low energy diet on different traits and multi-tissue transcriptomes of brown egg layers of 2 divergent lines selected for low (R-) and high (R+) residual feed intake. The 2 diets had a similar protein content, while the energy content was reduced by 15% as compared to the standard diet (2450 Kcal versus 2800 Kcal). The R+ and R- hens were fed ad libitum, with the standard diet until 17 wk of age; half of the birds were fed with the low energy feed until 33 wk of age when a subset of birds was slaughtered for tissue sampling (8 per line and diet). Food intake was increased in response to the suboptimal diet whereas egg number was unchanged showing that birds were able to adjust their energy intake by modifying feed intake. Nevertheless, hens fed the low energy diet had a higher feed efficiency (pval < 5%) and a higher residual feed intake (P-value <1%). No diet × line interaction was observed for these traits. PolyA+ RNA from different tissues were sequenced resulting in 90 M reads per sample. After bioinformatics treatment and differential analysis, we observed in liver and adipose tissue only few differentiallyexpressed genes (DEG) between diets (16 and 21 respectively). In contrast, we observed in blood 1179 DEG out of 17123 expressed genes with 463 and 716 over and under expressed in the suboptimal diet compared to the standard diet. No diet × line interaction was observed in the three tissues. GObp term enrichment revealed that under expressed DEG in blood were associated with glucose catabolism, cholesterol biosynthesis, mitotic cell cycle and protein catabolic process. Taken together, these results indicate an adaptation of birds to diet changes by increasing feed intake to maintain egg production, and a tissue-specific response with a limited role of metabolic tissues as liver and adipose tissue compared to the blood

An atlas of chicken long non-coding RNAs gathering multiple sources : gene models and expression across more than twenty tissues

Long non-coding RNAs (lncRNAs) appear as key regulators of gene expression through numerous mechanisms. Yet, particularly in domesticated species like chicken, their annotation is incomplete and their expression in different tissues poorly characterized. Here, we used data from 4 public databases (Ensembl, NONCODE, NCBI, ALDB), a recent lncRNA catalogue, and genes models from 364 RNA-seq samples from our lab to generate an extensive annotation of the chicken genome aggregating most of the currently known lncRNAs, plus robust models of newly discovered lncRNA from our dataset. Our extended lncRNAs annotation comprises 30084 lncRNA loci versus 4640 in the Ensembl reference. These lncRNAs follow the same trends as those in the reference for their genomic localization, structure and expression. To further characterize these lncRNAs, we studied their expression in over 20 chicken tissues with minimum 6 biological replicates. This allowed us to explore expression variability of both lncRNAs and protein-coding genes (mRNAs) across tissues, and across replicates in each tissue. Across these chicken tissues, we found interesting differences in the tissue-specificity patterns between lncRNAs and mRNAs. We characterized the expressions of both types of genes in relation with (i) their tissue-specificity and/or (ii) their genomic localization relative to each other (convergent, divergent, antisense, distant or proximal) in order to highlight some lncRNA–mRNA couples with a role in the functions or the maintenance of a given organ in chicken. Finally, we started a conservation study of interesting lncRNA–mRNA couples across species. Project funded by ANR-13-ADAP and H2020-Feed-a-Gene projects

Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species

Understanding genome-to-phenome relationships requires deep and cross-disciplinary genetic analyses among which functional annotation provides crucial insights. The development of High Throughput Sequencing and RNA-seq now help us to find a large number of heterogeneous and low-expressed transcripts known to be long non-coding RNAs (lncRNAs). One of the aims of the FAANG pilot project ‘FR-AgENCODE’ is to identify and characterise the long non-coding RNAs of multiple tissues and cell lines in 4 farm animals (chicken, bovine, pig and goat) of both sexes. Here, we focus our analysis on the liver tissue and two blood T-cell types (CD3+CD4+, CD3+CD8+) where samples were collected through 4 biological replicates (2 males and 2 females). It allows us to compare lncRNA repertoires between tissues, sex and species in relation with fundamental biological functions like energy storage and immunity. High depth strand-specific RNA-seq produced ~200M paired-end reads for each of the 16 RNA-seq datasets. After transcriptome reconstruction, we used the recently published FEELnc program (Wucher et al., 2017, Nucleic Acid Research) to identify lncRNAs longer than 200 bp and without protein-coding capabilities. FEELnc also classifies lncRNAs based on their genomic localizations with respect to the ENSEMBL protein-coding annotation: intergenic lncRNAs are categorized depending on the distance and orientation with respect to the closest mRNAs and the intragenic lncRNAs are extracted based on their overlap with mRNAs exons and introns. We will report these lncRNA repertoires in terms of intergenic/ intragenic lncRNA class, structure and expression and comparing these features between livestock species, tissues and sexes. By profiling the transcriptional landscape of lncRNAs in these 4 species, this data will further contribute to the global action for annotating functional elements of livestock genomes

Liver and whole blood transcriptome response to chronic heat exposure in laying hens

Adaptation to heat exposure is required to maintain animal welfare and productivity under high ambient temperature (AT) conditions. In this study we investigate the effects of chronic heat exposure (5 weeks at a constant temperature of 32°C) on the liver and whole blood transcriptome of brown egg layers from 2 divergent lines selected for low (R-) and high (R+) residual feed intake. The R+ and R- hens were equally distributed among 2 temperature-controlled chambers and reared under thermo-neutrality (22°C). At 28 wk of age the AT of one chamber was increased to 32°C until 33 wk of age, when 32 animals (8 per line and treatment) were slaughtered. Total RNA was obtained from the liver and blood and was sequenced using the Illumina HiSEqn 3000, yielding an average per sample of 90 million paired-end reads. The reads were mapped to the Gallus gallus-5 reference genome by STAR software and counted by RSEM software using the Ensembl V87 GTF annotation. Comparisons between the two AT groups were made using the edgeR-robust R/Bioconductor package. Patterns of AT-specific differential expression were largely shared by the two lines, and no evidence of temperature × line interactions were observed. In liver, a total of 229 differentially expressed genes (DEG) were identified (adjusted P-values < 0.05) with respectively 104 and 125 over and under expressed in the heat-exposed compared to the control group. In blood, 960 DEG were identified between the two AT groups with 479 and 481 over and under expressed. Most DEG were tissue specific, and only 18 genes were DE in both liver and blood. Ingenuity Pathway Analysis revealed that many of the DEG in liver were associated with amino acid and lipid metabolisms and energy production. Key genes involved in fatty acid β-oxidation, ketogenesis, cholesterol biosynthesis were under-expressed in the heat-exposed animals. In blood, many of the DEG were associated with cell related functions. Based on the DEG expression profile, down-regulation was observed for the PI3K/AKT, the VEGF and the PDGF signalling pathways involved in cell survival and growth, vasculogenesis and angiogenesis. Taken together, these results indicate a tissue-specific response to heat exposure