GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl &amp; Refseq genome annotations

Degalez, Fabien; Bardou, Philippe; Lagarrigue, Sandrine

doi:10.1101/2024.03.13.584813

2024

DOI: 10.1101/2024.03.13.584813

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GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Fabien Degalez,

Philippe Bardou,

Sandrine Lagarrigue

Abstract: GEGA is a user-friendly tool to navigate through different genomics and functional information related to an enriched gene atlas in chicken that unifies the gene catalogues from the two reference databases, NCBI-RefSeq & EMBL-Ensembl/GENCODE, and four other additional rich resources as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA offers a total of 78,323 genes, including 24,102 protein-coding genes (PCGs) and 44,428 long non-coding RNAs (lncRNAs), greatly enhancing the number of genes p… Show more

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Cited by 2 publications

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Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Karami,

Sabban,

Cerutti

et al. 2024

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Climate change, with its repercussions on agriculture, is one of the most important adaptation challenges for livestock production. Poultry production is a major source of proteins for human consumption all over the world. With a growing human population, improving poultry adaptation to environmental constraints becomes critical. Extensive evidence highlights the influence of environmental variations on epigenetic modifications. The aim of this paper is therefore to explore chickens molecular response to maternal heat stress. We employed Reduced Representation Bisulfite Sequencing (RRBS) to generate genome-wide single-base resolution DNA methylation profiling and RNA sequencing (RNA-seq) to profile the transcriptome of the brains of embryos hatched from dams reared under either heat stress (32 degrees Celsius) or thermoneutrality (22 degrees Celsius). We detected 289 significant differentially methylated CpG sites (DMCs) and one differentially methylated region (DMR) between heat stressed and control groups. These DMCs were associated with 357 genes involved in processes such as cellular response to stimulus, developmental processes and immune function. In addition, we identified 11 genes differentially expressed between the two groups of embryos, and identified ATP9A as a target gene of maternal heat stress on offspring. This study provides a body of fundamental knowledge on adaptive mechanisms concerning heat tolerance in chickens.

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Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Karami,

Sabban,

Cerutti

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

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Cross-species orthology detection of long non-coding RNAs (lncRNA) through 13 species using genomic and functional annotations

Degalez,

Allain,

Lagoutte

et al. 2024

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Long non-coding RNAs (lncRNAs), defined by a length of over 200 nucleotides and limited protein-coding potential, have emerged as key regulators of gene expression. However, their evolutionary conservation and functional roles remain largely unexplored. Comparative genomics, particularly through sequence conservation analysis, offers a promising approach to infer lncRNA functions. Traditional methods focusing on protein-coding genes (PCGs) fall short due to the rapid evolutionary divergence of lncRNA sequences. To address this, a workflow combining syntenic methods and motif analysis via the Mercator-Pecan genome alignment was developed and applied across 13 vertebrate species, from zebrafish to various amniotes and birds. Further analyses to infer functionality revealed co-expression patterns through 17 shared tissues between human and chicken but also functional short-motif enrichment across the 13 species using the LncLOOM tool, exemplified by the human OTX2-AS1 and its counterparts in other species. The study expanded the catalog of conserved lncRNAs, providing insights into their evolutionary conservation and information related to potential functions. The workflow presented serves as a robust tool for investigating lncRNA conservation across species, supporting future research in molecular biology to elucidate the roles of these enigmatic transcripts.

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GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Cited by 2 publications

References 33 publications

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Cross-species orthology detection of long non-coding RNAs (lncRNA) through 13 species using genomic and functional annotations

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