Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development

Abstract

The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.

Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens

“…LncRNAs are a new type of regulatory RNA that is longer than 200 bp and is transcribed by RNA polymerase II. They account for approximately 87 percent of all ncRNAs and play an important role in muscle development by regulating transcriptional and post-transcriptional [ 67 , 68 ]. LncRNAs are important members of the regulatory network of skeletal muscle development and have been demonstrated to affect skeletal muscle proliferation and differentiation via competing for endogenous RNAs (ceRNAs), such as binding to miRNA and inhibiting its functions.…”

“…Furthermore, they analyzed the LncRNA transcriptome of Shouguang chickens from embryonic stage (E12, E17) to post-hatching (D1, D14) and identified the following two profiles with opposite expression trends: profile 4 with a down-regulation pattern and profile 21 with an up-regulation pattern. According to functional analysis of the targets, profile 4 contributes to cell proliferation, while profile 21 is primarily involved in metabolism [ 67 ]. Li et al (2021) [ 82 ] established 12 RNA libraries in postnatal Gushi chicken pectoral muscle (6 w, 14 w, 22 w, and 30 w), and they found dynamic changes in LncRNA expression in pectoral muscle at various stages, suggesting that some LncRNAs that target MEF2C may be involved in muscle regulation via the MAPK signaling pathway.…”

Transcriptomic and epigenomic insights into pectoral muscle fiber formation at the late embryonic development in pure chicken lines

“…There are studies use RNA-seq to identify circRNAs affecting muscle development by comparing fast-growing and slow-growing chickens ( Wu et al, 2022 ). In addition to comparative transcriptomic studies of chickens with different growth rates, time-series transcriptomic analyses of muscles at various developmental stages have been conducted to identify important candidate genes regulating muscle development at key time points ( Yin et al, 2020 ; Liu et al, 2021 ). With the application of multi-omics approaches, identifying key genes based solely on gene expression levels at the transcriptional level is no longer reliable.…”