Genome-wide differential expression of long noncoding RNAs and mRNAs in ovarian follicles of two different chicken breeds

Peng, Yanjie; Chang, Li; Wang, Yaqi; Wang, Ruining; Hu, Lulu; Zhao, Ziya; Geng, Lina; Liu, Zhengzhu; Gong, Yan; Li, Jingshi; Li, Xianglong; ChuanSheng, Zhang

doi:10.1016/j.ygeno.2018.09.012

Cited by 26 publications

(23 citation statements)

References 71 publications

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“…The results showed that differential circRNAs were related to oocyte development, cell proliferation, and apoptosis. These results were similar to the results of long noncoding RNA and microRNA enrichment analysis in previous studies (Kang, Cui, Zhang, Yang, & Jiang, 2013; Peng et al, 2018), suggesting that these circRNAs may compete with endogenous RNAs (ceRNAs) to regulate gene transcription. In summary, all the results suggest that the circRNAs detected in this paper mainly participate in follicle growth, reproduction, and other biological processes.…”

Section: Discussionsupporting

confidence: 90%

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

Xiao

et al. 2020

Journal Cellular Physiology

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Follicle development is a key factor that determines the reproductive performance of poultry. The existing evidence suggests that circular RNAs (circRNAs) play an important role in a variety of biological processes, especially in posttranscriptional regulation, but the regulatory mechanism of circRNAs in duck follicle development has rarely been reported. To better explore the molecular mechanism of follicle development in ducks, we sequenced and analyzed the follicular circRNAs; 4,204 circRNAs were predicted in the duck follicles. Fourteen circRNAs were differentially expressed between the white follicles and yellow follicles. The results of our studies showed that aplacirc_013267 promoted cell apoptosis in duck GCs. Moreover, a bioinformatics prediction analysis demonstrated that aplacirc_013267 was involved in a circRNA‐miRNA‐mRNA coexpression network and was observed to sponge two follicle‐related miRNAs by a luciferase activity assay. Furthermore, we found that overexpression of aplacirc_013267 significantly increased thrombospondin‐1 (THBS1) expression and downregulated granulosa cell apoptosis. The mechanistic study showed that aplacirc_013267 directly binds to and inhibits apla‐mir‐1‐13; then, aplacirc_013267 increases the expression of THBS1 and upregulates granulosa cell apoptosis. Taken together, our findings demonstrate that circRNAs have potential effects in duck ovarian follicles and that circRNAs may represent a new avenue to understand follicular development.

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Section: Discussionsupporting

confidence: 90%

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

Xiao

et al. 2020

Journal Cellular Physiology

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“…Although much efforts were made to unveil the mystery of lncRNAs in animals and humans in the last decades [58,59,65], the available data of lncRNAs in chicken tissues at physiological or disease conditions are limited. Using the RNA-seq technology, previous studies have identified 4404, 2481, 39,907, 8691, 1376, 6543, 2597 and 2056 lncRNAs in breast muscle, spleen, cerebrum, ovarian follicle, trachea, liver, testis and adipose of chickens, respectively [33,[92][93][94][95][96][97][98]. Moreover, Kern et al [99] found 9393 lncRNAs in eight tissue types (adipose, cerebellum, cortex, hypothalamus, liver, lung, skeletal muscle and spleen) of chickens and Hong et al [100] obtained 6900 lncRNAs genes in 20 different tissues (breast, gizzard, liver, pancreas, uterus, heart, bone marrow, kidney, cerebrum, cerebellum, eye, immature egg, mature egg, gall-bladder, comb, shank, skin, lung, spleen and fascia) of an individual Ogye, with c.75% of lncRNAs as tissue-specific.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

et al. 2020

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Background: Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear. Methods: The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique. Results: After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 senseoverlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection. Conclusions: To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.

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“…For instance, compared with the annual egg production of about 80 in Sichuan white geese (SWG), the annual egg production of Landes goose (LG) is 40~60 [2,3]. To our knowledge, most studies on poultry egg production performance have focused on the mechanisms underlying either inter-breed or intra-breed differences [4][5][6]. However, there lack studies that include comparisons not only between different breeds differing in egg numbers but also between different ages within the same breed to better reveal the mechanisms controlling egg production performance.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Ouyang

Wang

et al. 2020

Genes

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To date, research on poultry egg production performance has only been conducted within inter or intra-breed groups, while those combining both inter- and intra-breed groups are lacking. Egg production performance is known to differ markedly between Sichuan white goose (Anser cygnoides) and Landes goose (Anser anser). In order to understand the mechanism of egg production performance in geese, we undertook this study. Here, 18 ovarian stromal samples from both Sichuan white goose and Landes goose at the age of 145 days (3 individuals before egg production initiation for each breed) and 730 days (3 high- and low egg production individuals during non-laying periods for each breed) were collected to reveal the genome-wide expression profiles of ovarian mRNAs and lncRNAs between these two geese breeds at different physiological stages. Briefly, 58, 347, 797, 777, and 881 differentially expressed genes (DEGs) and 56, 24, 154, 105, and 224 differentially expressed long non-coding RNAs (DElncRNAs) were found in LLD vs. HLD (low egg production Landes goose vs. high egg production Landes goose), LSC vs. HSC (low egg production Sichuan White goose vs. high egg production Sichuan white goose), YLD vs. YSC (young Landes goose vs. young Sichuan white goose), HLD vs. HSC (high egg production Landes goose vs. high egg production Sichuan white goose), and LLD vs. LSC (low egg production Landes goose vs. low egg production Sichuan white goose) groups, respectively. Functional enrichment analysis of these DEGs and DElncRNAs suggest that the “neuroactive ligand–receptor interaction pathway” is crucial for egg production, and particularly, members of the 5-hydroxytryptamine receptor (HTR) family affect egg production by regulating ovarian metabolic function. Furthermore, the big differences in the secondary structures among HTR1F and HTR1B, HTR2B, and HTR7 may lead to their different expression patterns in goose ovaries of both inter- and intra-breed groups. These results provide novel insights into the mechanisms regulating poultry egg production performance.

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Genome-wide differential expression of long noncoding RNAs and mRNAs in ovarian follicles of two different chicken breeds

Cited by 26 publications

References 71 publications

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

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