ArticleBMC biology2019
Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
Article in BMC biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
91 citing papers in PubMed, 190 citations in OpenAlex.
- Chromatin accessibility of the jejunum in two high-yielding laying hen strains under divergent mineral phosphorus supply during the transition to egg laying.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2026Article
- UnlockingNAR genomics and bioinformatics · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- Multi-omics characterization identifies conserved candidate gene and reveals breed-specific regulatory mechanisms underlying growth-related traits in pigs.BMC genomics · 2026Article
- Histone Modifications: Decoding the Epigenetic Basis of Economic Traits in Livestock and Poultry.Genes · 2026Review
- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics.Biology · 2026Review
- Tissue-specific epigenetic regulation of fat metabolism in pigs through integrated analysis of DNA methylation and gene expression networks.Journal of animal science and biotechnology · 2026Article
- Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world.Nucleic acids research · 2026Article
- Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Prediction of Enhancer RNAs in Chicken Genome.International journal of molecular sciences · 2025Article
- Tissue-Specific Chromatin Accessibility Regions and Transcription Factor Binding Sites in Pig Brain and Endocrine Tissues.Molecular neurobiology · 2025Article
- A dataset of single-cell transcriptomic atlas of Bama pig and potential marker genes across seven tissues.BMC genomic data · 2025Article
- Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.GigaScience · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Regulatory element map of sheep reproductive tissues: functional annotation of tissue-specific strong active enhancers.Frontiers in veterinary science · 2025Article
- Multi-tissue transcriptomic characterization of endogenous retrovirus-derived transcripts inFrontiers in genetics · 2025Article
- A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.Molecular biology and evolution · 2024Article
- The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases.The veterinary quarterly · 2024Article
- LncRNA NORFA promotes the synthesis of estradiol and inhibits the apoptosis of sow ovarian granulosa cells through SF-1/CYP11A1 axis.Biology direct · 2024Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
36 authors at 9 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).
resultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.
conclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.