Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken

Ning, Chunyou; Ma, Tianyuan; Hu, Silu; Xu, Zhongxian; Zhang, Pu; Zhao, Xiaoling; Wang, Yan; Yin, Huadong; Hu, Yaodong; Fan, Xiaolan; Zeng, Bo; Yang, Mingyao; Yang, Dapeng; Ni, Qingyong; Li, Yan; Zhang, Mingwang; Xu, Huailiang; Yao, Yongfang; Zhu, Qing; Li, Diyan

doi:10.3389/fgene.2020.00574

Cited by 13 publications

(12 citation statements)

References 71 publications

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“…According to the present study, lncRNAs and mRNAs are expressed in a stage-dependent manner, consistent with previous studies [ 35 , 36 , 37 ]. The results of both hierarchical clustering and PCA showed that the GRI and MGI stages were more distinct than MGI and RSI stages at the mRNA or lncRNA level ( Figure 2 ), implying that a massive physiological change related to a shift in metabolism occurred during early muscle development.…”

Section: Discussionsupporting

confidence: 93%

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Tan

Gan

Shen

et al. 2021

IJMS

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Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.

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Section: Discussionsupporting

confidence: 93%

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Tan

Gan

Shen

et al. 2021

IJMS

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“…This complicated process of events requires a highly orchestrated program of gene expression and is regulated by various factors. According to the present study, lncRNAs and mRNAs tended to display a stage-dependent expression profile, consistent with other studies [ 36 , 37 , 38 ]. Hierarchical clustering and t-SNE analyses demonstrated that expression profiles between the ZT20 and ZT12 stages were markedly different from those of the ZT12 and ZT0 stages ( Figure 2 a,b), suggesting that the expression changes of lncRNAs and mRNAs were associated with serum LH level during the ovulatory cycle.…”

Section: Discussionsupporting

confidence: 93%

Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle

Liang

Deng

et al. 2021

Animals

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Long non-coding RNAs (lncRNAs) and mRNAs are temporally expressed during chicken follicle development. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone (LH) levels are rare. In this study, gene expression in Rohman layers was investigated at three distinct stages of the ovulatory cycle: zeitgeber time 0 (ZT0, 9:00 a.m.), zeitgeber time 12 (ZT12, 9:00 p.m.), and zeitgeber time 20 (ZT20, 5:00 a.m.) representing the early, middle, and LH surge stages, respectively, of the ovulatory cycle. Gene expression profiles were explored during follicle development at ZT0, ZT12, and ZT20 using Ribo-Zero RNA sequencing. The three stages were separated into two major stages, including the pre-LH surge and the LH surge stages. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages, and 4531, 523 differentially expressed genes (DEGs) and 2367, 211 differentially expressed lncRNAs (DELs) were identified in the ZT20 vs. ZT12, and ZT12 vs. ZT0, comparisons. Functional enrichment analysis revealed that genes involved in cell proliferation and metabolism processes (lipid-related) were mainly enriched in the ZT0 and ZT12 stages, respectively, and genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the ZT20 stage. These findings provide the basis for further investigation of the specific genetic and molecular functions of follicle development in chickens.

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“…According to the present study, lncRNAs and mRNAs are expressed in a stage-dependent manner, consistent with previous studies [34][35][36]. The results of both hierarchical clustering and PCA showed that the GRI and MGI stages were more distinct than MGI and RSI stages at the mRNA or lncRNA level (Fig.…”

Section: Discussionsupporting

confidence: 92%

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Tan¹,

Gan

Shen

et al. 2020

Preprint

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BackgroundGene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: of the inflection point with the maximum growth rate (MGI), inflection point of gradual increase stage to rapid increasing stage (GRI) and inflection point of rapid increasing stage to slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. ResultsQingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, RSI vs. MGI comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in energy and lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). ConclusionThese findings indicate lncRNAs and a certain lncRNA G1430 involved in the regulatory mechanism during pig muscle development. Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.

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Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken

Cited by 13 publications

References 71 publications

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle

Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

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