Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens

Jin, Wenjiao; Zhao, Yaping; Zhai, Bin; Li, Yuanfang; Fan, Shengxin; Yuan, Pengtao; Sun, Guirong; Jiang, Ruirui; Wang, Yanbin; Liu, Xiaojun; Tian, Yadong; Kang, Xiangtao; Li, Guoxi

doi:10.1371/journal.pone.0249288

Cited by 13 publications

(7 citation statements)

References 73 publications

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“…Therefore, this study predicted the miRNA binding sites on circRNA sequences and found that most of the identified circRNAs had multiple potential miRNA binding sites. These results are consistent with previous studies [ 8 , 16 , 32 ]. This suggests that circRNAs can play a regulatory role in skeletal muscle development by binding to miRNAs.…”

Section: Discussionsupporting

confidence: 94%

“…CircRNA is a newly developed non-coding RNA transcript, which has a unique closed ring structure, which makes circRNAs more stable than linear RNA [ 4 ]. In recent years, due to the rapid development of high-throughput sequencing, thousands of circRNAs have been discovered in various organisms [ 5 , 6 , 7 , 8 ]. CircRNAs are widespread in various tissues and cells of a variety of species [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

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CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Yuan

Zhao

et al. 2022

Genes

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Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1–9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.

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Section: Discussionsupporting

confidence: 94%

Section: Introductionmentioning

confidence: 99%

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Yuan

Zhao

et al. 2022

Genes

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“…As evident, the lncRNA and circRNA expression were tissue- and period-specific [ 31 , 32 ]. Even in the fat tissues, the numbers of lncRNAs and circRNAs identified varied among the different animals, such as 3716 lncRNAs [ 33 ] and 5141 circRNAs [ 34 ] identified in the subcutaneous fat of cattle, 9082 identified lncRNAs identified in the tail fat of sheep [ 35 ], and 1637 circRNAs identified in the chicken abdominal fat [ 36 ]. Coincidently, similar numbers of lncRNAs were identified in the broiler abdominal fat, but our study identified fewer numbers of circRNAs in the abdominal fat of 7 wks broilers than that in the other animals, possibly related to the various fat samples, species, and development stage.…”

Section: Discussionmentioning

confidence: 99%

The landscape of the long non-coding RNAs and circular RNAs of the abdominal fat tissues in the chicken lines divergently selected for fatness

et al. 2022

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Background Excessive deposition of abdominal fat poses serious problems in broilers owing to rapid growth. Recently, the evolution of the existing knowledge on long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have established their indispensable roles in multiple physiological metabolic processes, including adipogenesis and fat deposition. However, not much has been explored on their profiles in the abdominal fat tissues of broilers to date. In the study, we aimed to characterize the vital candidates of lncRNAs and circRNAs and their underlying regulations for abdominal fat deposition in broilers. Results The present study sequenced the lncRNAs and circRNAs expression profiles in the abdominal fat tissues isolated from 7-week-old broilers, who were divergently selected for their fatness. It identified a total of 3359 lncRNAs and 176 circRNAs, demonstrating differential expressed (DE) 30 lncRNAs and 17 circRNAs between the fat- and lean-line broilers (|log2FC| ≥ 1, P < 0.05). Subsequently, the 20 cis-targets and 48 trans-targets of the candidate DE lncRNAs were identified for depositing abdominal fat by adjacent gene analysis and co-expression analysis, respectively. In addition, the functional enrichment analysis showed the DE lncRNAs targets and DE circRNAs host genes to be mainly involved in the cellular processes, amino/fatty acid metabolism, and immune inflammation-related pathways and GO terms. Finally, the vital 16 DE lncRNAs located in cytoplasm and specifically expressed in fat/lean line and their targets were used to construct the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) regulatory network, comprising 7 DE lncRNAs, 28 miRNAs, 11 DE mRNAs. Notably, three lncRNAs including XR_001468036.2, XR_003077610.1 and XR_001466431.2 with the most connected degrees might play hub regulatory roles in abdominal fat deposition of broilers. Conclusions This study characterized the whole expression difference of lncRNAs and circRNAs between the two lines broilers with divergently ability of abdominal fat. The vital candidate DE lncRNAs/circRNAs and ceRNA regulations were identified related to the deposition of abdominal fat in chicken. These results might further improve our understanding of regulating the non-coding RNAs in obesity.

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“…proposed that the ciR-PTPN23-miR-15a-E2F3 axis is involved in the inhibition of H2S-induced cell proliferation and apoptosis in chickens ( Hu et al, 2021 ). CircRNAs regulated lipid metabolism and adipocyte proliferation and differentiation during chicken abdominal adipose tissue development through complex ceRNA networks ( Jin et al, 2021 ). circ-PLXNA1 played a role in duck adipocyte differentiation through circRNA expression profiling ( Wang et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Analysis of circRNA-miRNA-mRNA regulatory network of embryonic gonadal development in Mulard duck

Li,

Xin,

Zhang

et al. 2024

Poultry Science

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Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens

Cited by 13 publications

References 73 publications

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

The landscape of the long non-coding RNAs and circular RNAs of the abdominal fat tissues in the chicken lines divergently selected for fatness

Analysis of circRNA-miRNA-mRNA regulatory network of embryonic gonadal development in Mulard duck

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