Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis

Abstract

Broodiness in laying hens results in atrophy of the ovary and consequently decreases productivity. However, the regulatory mechanisms that drive ovary development remain elusive. Thus, we collected atrophic ovaries (AO) from 380-day-old broody chickens (BC) and normal ovaries (NO) from even-aged egg-laying hens (EH) for RNA sequencing. We identified 3,480 protein-coding transcripts that were differentially expressed (DE), including 1,719 that were down-regulated and 1,761 that were up-regulated in AO. There were 959 lncRNA transcripts that were DE, including 56 that were down-regulated and 903 that were up-regulated. Among the116 miRNAs that were DE, 79 were down-regulated and 37 were up-regulated in AO. Numerous DE protein-coding transcripts and target genes for miRNAs/lncRNAs were significantly enriched in reproductive processes, cell proliferation, and apoptosis pathways. A miRNA-intersection gene-pathway network was constructed by considering target relationships and correlation of the expression levels between ovary development-related genes and miRNAs. We also constructed a competing endogenous RNA (ceRNA) network by integrating competing relationships between protein-coding genes and lncRNA transcripts, and identified several lncRNA transcripts predicted to regulate the CASP6, CYP1B1, GADD45, MMP2, and SMAS2 genes. In conclusion, we discovered protein-coding genes, miRNAs, and lncRNA transcripts that are candidate regulators of ovary development in broody chickens.

Epigenetic mediation of the onset of reproduction in a songbird

“…egg laying 36,37 . In chicken ovaries MYLK was up-regulated during egg laying 38 , again a pattern consistent with the decrease in DNA methylation we observed at LOC107215054 ( MYLK -like). Whether both genes function as myosin light chain kinases remains, however, to be established.…”

“…This indicated link is based on CpG sites that significantly vary in DNA methylation with the reproductive state and well-described functions for avian reproduction of the genes in which those CpG sites are located. Also, the methylation patterns found here are supported by multiple CpG sites within the regulatory region of genes and the methylation patterns match with expression patterns of the respective genes in chickens 35,38 . Nevertheless, future studies would be needed to experimentally establish a functional link between observed methylation patterns and the seasonal onset of reproduction.…”

Long noncoding RNAs regulate Wnt signaling during feather regeneration

“…Once considered the noise in transcription, lncRNAs have been shown to play important roles in a wide range of biological processes (reviewed in Batista and Chang, 2013;Fatica and Bozzoni, 2014). Although there has been tremendous effort to identify lncRNAs in chicken development and diseases (Liu et al, 2018(Liu et al, , 2017Li et al, , 2016Li et al, , 2012Ren et al, 2018;Wu et al, 2018;Wang et al, 2017b;Zhang et al, 2017;Lin et al, 2016), there are very few reports to functionally annotate them (Roeszler et al, 2012;Arriaga-Canon et al, 2014;Cai et al, 2017;Fan et al, 2017). The nomenclature of the chicken lncRNAs has not reached a consensus and the current databases are still under constant improvement.…”

“…In recent years, there has been tremendous effort to profile and characterize lncRNAs in the chicken genome in development and diseases (Liu et al, 2018(Liu et al, , 2017Li et al, , 2016Li et al, , 2012Ren et al, 2018;Wu et al, 2018;Wang et al, 2017b;Zhang et al, 2017;Lin et al, 2016). The NONCODE database (www.noncode.org) lists a total of 13,085 lncRNA transcripts, corresponding to 9688 lncRNA genes in the chicken genome (Xie et al, 2014;Zhao et al, 2016).…”

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

“…CeRNET plays a widely regulatory role in tissue and organ development (Xu et al, 2016;Li et al, 2017;Liu et al, 2018;Miao et al, 2018). To interpret the interplay among diverse RNAs (mRNA, miRNA, and lncRNA) during the antler development, ceRNET was constructed for the first time.…”