Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development

Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

Rat is one of the most widely-used models in chemical safety evaluation and biomedical research. However, the knowledge about its microRNA (miRNA) expression patterns across multiple organs and various developmental stages is still limited. Here, we constructed a comprehensive rat miRNA expression BodyMap using a diverse collection of 320 RNA samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats with four biological replicates per group. Following the Illumina TruSeq Small RNA protocol, an average of 5.1 million 50 bp single-end reads was generated per sample, yielding a total of 1.6 billion reads. The quality of the resulting miRNA-seq data was deemed to be high from raw sequences, mapped sequences, and biological reproducibility. Importantly, aliquots of the same RNA samples have previously been used to construct the mRNA BodyMap. The currently presented miRNA-seq dataset along with the existing mRNA-seq dataset from the same RNA samples provides a unique resource for studying the expression characteristics of existing and novel miRNAs, and for integrative analysis of miRNA-mRNA interactions, thereby facilitating better utilization of rats for biomarker discovery.

Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

Background

Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control.

Results

We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens.

Conclusion

Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08388-w.

Landscape of circRNAs Across 11 Organs and 4 Ages in Fischer 344 Rats

Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs with a covalently closed loop. Aside from their recognized regulatory functions (e.g., sponging microRNAs to reduce their activity, and altering parental gene transcription by competing with the canonical splicing of pre-mRNA), expression of circRNAs is abundant, diverse, and conservative across species, rendering them as potential biomarker candidates. Consequently, the landscape of circRNAs has been studied for several species. Although the rat is one of the most important animal models for drug safety and toxicological research, few attempts have been made to understand the landscape of rat circRNAs. One noticeable challenge in analyzing circRNAs with next-generation sequencing (NGS) data is to find ways to use rapidly advancing bioinformatics approaches to improve accuracy while also reducing the number of resulting false positives that occur in circRNA identification with these new methods. Here, we applied two of the most advanced circRNA bioinformatics pipelines to provide a landscape of circRNAs in rats by analyzing an RNA-seq data set for 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testis or uterus) from Fischer 344 rats of both sexes in four age groups (juvenile, adolescence, adult, and aged). The circRNAs displayed organ-specific patterns and sex differences in most organs. Lowest numbers of circRNAs were seen in the liver and muscle, while highest numbers of circRNAs occurred in the brain, which correlated to gene expression patterns seen across those organs. Concordance of circRNAs between males and females was approximately 50% in nonsex organs, implying that some caution needs to be exercised when selecting specific circRNAs as biomarkers for both sexes. The number of common circRNAs between sexes increased with age for most organs except heart, spleen, and thymus. A dramatic drop in the number of circRNAs in kidney, thymus, and testis was observed in aged rats, suggesting that the regulatory function of circRNAs is age dependent. From the 1595 circRNAs identified with high confidence, only 6 appeared in all 9 of the nonsex organs in both sexes and four age groups. Forty-one and 48 circRNAs were identified in more than 5 nonsex organs in males and females, respectively, while close to 280 circRNAs were found in an organ for more than 2 age groups in both sexes. This study offers an overview of rat circRNAs, which contributes to the effort of identifying circRNAs as potential biomarkers for safety and risk assessment.

Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.