Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors

Abstract

The blue egg is both of biological interest and economic importance for consumers, egg retailers, and scientists. To date, the genetic mechanisms underlying pigment have mainly focused on protein-coding genes. However, the underpinning mechanism of non-coding RNAs on the pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was employed to profile the uterine gland transcriptome (lncRNA and mRNA) of 15 Changshun blue eggshell layers, to better understand the genetic mechanisms of deposition of blue eggshell color. Results showed that differentially expressed mRNAs, GO terms, and KEGG pathways among pink-eggshell and blue-eggshell chickens were mainly targeting immune- and transporter-related terms with the SLC family, IgJ, CD family, and MTMR genes. Furthermore, the progesterone-mediated oocyte maturation and cortisol synthesis and secretion pathway with targeted gene PGR and Pbx1 were significantly enriched between blue- and pink-eggshell chickens. Integrating analysis of lncRNA and mRNA profiles predicted 4 and 25 lncRNA–gene pairs by antisense and cis analysis. They were relative to immune, nerve, and lipids and amino acid metabolisms, porphyrin, and chlorophyll metabolism with targeted gene FECH and oxidative phosphorylation and cardiac muscle contraction pathways with targeted gene COX6A1. Within blue-eggshell chickens, the GO terms hindbrain tangential cell migration and phosphatidylinositol monophosphate phosphatase activity with targeted gene Plxna2 and MTRM1 were identified. Integrating analysis of lncRNA and mRNA profiles predicted 8 and 22 lncRNA–gene pairs. Most pathways were mainly enriched on lipid-related metabolisms as found in mRNA sequencing. The lncRNAs did exert similar functions in color formation by modulating pigment disposition and immune- and lipid-related metabolisms. Our results provide a catalog of chicken uterine lncRNAs and genes worthy of further studies to understand their roles in the selection for blue eggshell color layers.

Transcriptome Sequencing Reveals Pathways Related to Proliferation and Differentiation of Shitou Goose Myoblasts

“…The development of myogenesis is regulated by epigenetic factors, including DNA methylation, RNA methylation, histone modification, and noncoding RNA [ 35 , 36 , 37 ]. There have been many reports on the research of lncRNA in poultry [ 38 , 39 ]. In this study, we examined the differential expression analysis of lncRNA in the proliferation stage and differentiation stage of Shitou goose myoblasts.…”

Screening and Identification of Interacting Proteins of Mitfa in Red Tilapia

“…Meanwhile, we found that some interacting proteins are enriched abundantly in the cardiac muscle contraction and adrenergic signaling in cardiomyocyte pathways. Both cardiac muscle contraction and adrenergic signaling in cardiomyocyte pathways are involved in melanophore development, which consequently influences color pigmentation [30,38]. Thus, Mitfa and its interacting proteins might regulate melanogenesis.…”

Lnc-PKD2-2-3/miR-328/GPAM ceRNA Network Induces Cholangiocarcinoma Proliferation, Invasion and 5-FU Chemoresistance

“…Benefiting from the advancement of high-throughput sequencing and microarray technology, tens of thousands of lncRNAs have been discovered (20)(21)(22)(23). Most of their functions are obscure since they lack direct protein coding ability and have just been introduced for less than twenty years.…”