Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light

Wang, Ying; Shi, Huanxian; Zhang, Genxi; Wu, Pengfei; Chen, Lan; Shen, Manman; Li, Tingting; Lv, Xiaoyang; Gu, Yunfei; Wang, Jinyu

doi:10.3389/fgene.2021.563623

Cited by 9 publications

(10 citation statements)

References 58 publications

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“…Moreover, RNA sequencing was used to analyze mRNAs and long noncoding RNAs (lncRNAs) from granulosa cells of SYFs from Jinghai Yellow chickens in exposure to red light and white light groups. One thousand one hundred eighty-two DEGs were identified and the integrated network analysis shown that several of them were involved in follicular development through steroid hormone synthesis, oocyte meiosis, and the PI3K-Akt signaling pathway [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

et al. 2021

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Background Ovarian follicle development plays an important role in determination of poultry egg production. The follicles at the various developmental stages possess their own distinct molecular genetic characteristics and have different biological roles in chicken ovary development and function. In the each stage, several genes of follicle-specific expression and biological pathways are involved in the vary-sized follicular development and physiological events. Identification of the pivotal genes and signaling pathways that control the follicular development is helpful for understanding their exact regulatory functions and molecular mechanisms underlying egg-laying traits of laying hens. Results The comparative mRNA transcriptomic analysis of ovarian follicles at three key developmental stages including slow growing white follicles (GWF), small yellow follicles (SYF) of recruitment into the hierarchy, and differentiated large yellow follicles (LYF), was accomplished in the layers with lower and higher egg production. Totally, 137, 447, and 229 of up-regulated differentially expressed genes (DEGs), and 99, 97, and 157 of down-regulated DEGs in the GWF, SYF and LYF follicles, including VIPR1, VIPR2, ADRB2, and HSD17B1 were identified, respectively. Moreover, NDUFAB1 and GABRA1 genes, two most promising candidates potentially associated with egg-laying performance were screened out from the 13 co-expressed DEGs in the GWF, SYF and LYF samples. We further investigated the biological effects of NDUFAB1 and GABRA1 on ovarian follicular development and found that NDUFAB1 promotes follicle development by stimulating granulosa cell (GC) proliferation and decreasing cell apoptosis, increases the expression of CCND1 and BCL-2 but attenuates the expression of caspase-3, and facilitates steroidogenesis by enhancing the expression of STAR and CYP11A1. In contrast, GABRA1 inhibits GC proliferation and stimulates cell apoptosis, decreases the expression of CCND1, BCL-2, STAR, and CYP11A1 but elevates the expression of caspase-3. Furthermore, the three crucial signaling pathways such as PPAR signaling pathway, cAMP signaling pathway and neuroactive ligand-receptor interaction were significantly enriched, which may play essential roles in ovarian follicle growth, differentiation, follicle selection, and maturation. Conclusions The current study provided new molecular data for insight into the regulatory mechanism underlying ovarian follicle development associated with egg production in chicken.

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Section: Introductionmentioning

confidence: 99%

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

et al. 2021

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“…Although numerous lncRNA studies have been performed in the chicken, − and adipogenesis-associated lncRNAs have been identified, ,− functional study on lncRNAs has been less explored. In the current study, we identified that a conserved lncPRDM16 in the abdominal adipose tissue in chickens could inhibit preadipocyte proliferation due to the functional importance of 250 nucleotides at 5′-end, which potentially regulate the transcriptional activity of both promoters of lncPRDM16 and PRDM16.…”

Section: Discussionmentioning

confidence: 99%

“…In the chicken, numerous lncRNA studies have been performed recently on its relationship with chicken growth and diseases. − lncRNAs associated with adipose tissue growth and development, or preadipocyte differentiation, were also identified. ,− Tissue-specific lncRNAs (liver and adipose tissues) were cataloged first and a large number of lncRNAs during abdominal and intramuscular preadipocyte differentiation were then enlisted. , Recently, a comprehensive transcriptome sequencing study on intramuscular and abdominal fat tissues identified an important lncRNA, lncAD, and another study found a novel lncRNA (IRLnc) related to intramuscular fat deposition . However, detailed functional investigation of the molecular function of these lncRNAs remains less explored.…”

Section: Introductionmentioning

confidence: 99%

Identification of a Long Noncoding RNA (lncPRDM16) Inhibiting Preadipocyte Proliferation in the Chicken

Chen

Zhao

Ding

et al. 2022

J. Agric. Food Chem.

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Long noncoding RNAs are vital to a variety of biological and physiological processes through multiple modes of functional interaction with DNA, RNA, and proteins. In chickens, numerous lncRNAs were discovered to be important to growth or disease progression. However, the detailed molecular function and role of lncRNAs remain less explored. Here, we performed lncRNA sequencing on abdominal adipose tissues from broiler lines divergently selected for abdominal fat content, and significantly differentially expressed lncRNAs were found, including lncPRDM16, a divergently transcribed and conserved lncRNA near PRDM16. Full lengths of two transcripts of lncPRDM16 were obtained, and their genomic structures were compared. Expression dynamics of lncPRDM16 in different tissues and during preadipocyte proliferation and differentiation were profiled. Moreover, a 250-nucleotide sequence at 5′-end was found to be inevitable to the function of lncPRDM16 in inhibiting preadipocyte proliferation and regulating the promoter activities of both lncPRDM16 and PRDM16. Taken together, we identified the 5′-end functional elements of lncPRDM16 and their potential importance in inhibiting preadipocyte proliferation. Our findings provide the foundation for further exploration of lncPRDM16 function and potential improvement of chicken muscle quality.

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“…In recent years, several studies have identi ed an important role for lncRNAs in the regulation of follicle development (19,20). Studies have identi ed differential expression of lncRNAs associated with reproductive function by using RNA-seq of OGCs obtained from humans (21), pigs (22), and chickens (23). Most of those studies have focused on PCOS (24,25), endometriosis (26, 27), and POF (28, 29).…”

Section: Discussionmentioning

confidence: 99%

Expression of Long Noncoding RNAs in the Ovarian Granulosa Cells of Women with Diminished Ovarian Reserve Using High-Throughput Sequencing

Dong

Xin

Chang

et al. 2022

Preprint

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Background: Infertility is a global reproductive-health problem, and diminished ovarian reserve (DOR) is one of the common causes of female infertility. Long noncoding RNAs (lncRNAs) are crucial regulators of numerous physiological and pathological processes in humans. However, whether lncRNAs are involved in the development of DOR remains to be elucidated. Methods: Ovarian granulosa cells (OGCs) extracted from infertile women with DOR and from women with normal ovarian reserve (NOR) were subjected to high-throughput sequencing. Comprehensive bioinformatics analysis was conducted to identify the differential expression of messenger RNAs (mRNAs) and lncRNAs. Sequencing results were validated by the selection of random lncRNAs using real-time reverse transcription-quantitative polymerase chain reaction.Results: Compared with the NOR group, a total of 244 lncRNAs were upregulated (53 known and 191 novel), and 222 lncRNAs were downregulated (36 known and 186 novel) in the DOR group. Similarly, 457 mRNAs had differential expression between the two groups. Of these, 169 were upregulated and 288 were downregulated. Bioinformatics analysis revealed that the differentially expressed genes of mRNA and lncRNAs were considerably enriched in “cell adhesion and apoptosis”, “steroid biosynthesis”, and “immune system”. A co-expression network comprising lncRNAs and their predicted target genes revealed the possible involvement of the “thyroid hormone signaling pathway” and “protein binding, digestion and absorption” in DOR pathogenesis. The expression of SLC16A10 was positively regulated by multiple lncRNAs. Seven differentially expressed lncRNAs (NEAT1, RAB5A, MEG3, GNG12, MST1L, GCN1, and ZEB2-AS1) were identified, among which the expression of NEAT1, GNG12 and ZEB2-AS1 was in accordance with RNA-sequencing. Conclusions: We presented the first data showing that the expression profiles of lncRNA and mRNA in OGCs between NOR and DOR patients using RNA sequencing. The lncRNAs that we identified may serve as novel diagnostic biomarkers or drug targets for patients with DOR.

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Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light

Cited by 9 publications

References 58 publications

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

Identification of a Long Noncoding RNA (lncPRDM16) Inhibiting Preadipocyte Proliferation in the Chicken

Expression of Long Noncoding RNAs in the Ovarian Granulosa Cells of Women with Diminished Ovarian Reserve Using High-Throughput Sequencing

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