Whole transcriptome sequencing reveals that non-coding RNAs are related to embryo morphogenesis and development in rabbits

Kuang, Liangde; Lei, Min; Li, Congyan; Guo, Zhiqiang; Ren, Yongjun; Zhang, Xiangyu; Zheng, Jie; Zhang, Cuixia; Mei, Xiuli; Tang, Li; Yang, Jicheng; Deng, Xingyi; Yang, Rui; Xie, Xiaohong

doi:10.1016/j.ygeno.2019.12.016

Cited by 16 publications

(14 citation statements)

References 39 publications

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“…Single‐cell sequencing technology has been used to analyze the diversity or heterogeneity of genomic transcripts, leading to the identification of various types of noncoding RNAs (IncRNAs, miRNAs, circRNAs, small nucleolar RNAs, and Piwi‐interacting RNAs) in pre‐implantation embryos (Fu et al, 2018). Using transcriptome sequencing, several circRNAs have been identified in many mammalian early embryos, such as mice (Fan et al, 2015), rabbits (Kuang et al, 2020), and human (Dang et al, 2016). Fan et al (2015) designed a single‐cell universal poly(A)‐independent RNA sequencing (SUPeR‐seq) method for identifying nonpolyadenylated RNAs.…”

Section: Circrnas In Embryogenesismentioning

confidence: 99%

“…In Gene Ontology (GO) analysis, 1316 host genes of the stage‐specific circRNAs were linked to chromosome organization, DNA damage stimulus and repair, cell cycle, and cell division. Moreover, 20,458 circRNAs were identified among which 744 circRNAs were differentially expressed between three stages of rabbit embryo development (Kuang et al, 2020). Among the differentially expressed circRNAs, the expression of circRNA_07129, circRNA_15209, and circRNA_12526 progressively increased.…”

Section: Circrnas In Embryogenesismentioning

confidence: 99%

“…The target genes of circRNAs in this network were associated with protein kinase activity, response to high‐density lipoprotein particle, insulin binding, Rap1, and PI3K‐Akt signaling pathways (Zhang, Ding, et al, 2019). Elsewhere, it was reported that some circRNAs were upregulated during rabbit embryo development and modulated embryo morphogenesis (Kuang et al, 2020).…”

Section: Circrnas In Embryogenesismentioning

confidence: 99%

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Circular RNAs: Novel potential regulators in embryogenesis, female infertility, and pregnancy‐related diseases

Gao

Wang

Pan

et al. 2021

Journal Cellular Physiology

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Circular RNAs (circRNAs) are endogenous noncoding RNAs with unique cyclic structures. Although they were previously considered as nonfunctional transcription byproducts, numerous studies have demonstrated that circRNAs regulate gene transcription and expression via different mechanisms. Reproductive health influences the quality of life and affects offspring propagation in women. CircRNAs have been found to modify pregnancy‐related diseases, gynecologic cancers, polycystic ovary syndrome, aging, gamete, and embryo development. It's promising for circRNAs to be the novel diagnostic and therapeutic targets for multiple reproductive diseases. With the widespread application of assisted reproduction technology (ART), it has been revealed that circRNA identification contributes to estimating the quality of gametes and embryos, reflecting the success rate of ART. CRISPR‐Cas9 gene editing technology has enabled the discovery of new roles of circRNAs. So far, the roles of circRNAs in the reproductive system remain poorly defined. In this review, we describe the classification and functions of circRNAs in embryogenesis and the female reproductive system diseases, revealing potential roles of circRNAs physiologically and pathologically. In so‐doing, we provide ideas for developing circRNA‐based therapeutic treatment and clinical application of various female reproductive system diseases.

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Section: Circrnas In Embryogenesismentioning

confidence: 99%

Section: Circrnas In Embryogenesismentioning

confidence: 99%

Section: Circrnas In Embryogenesismentioning

confidence: 99%

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Circular RNAs: Novel potential regulators in embryogenesis, female infertility, and pregnancy‐related diseases

Gao

Wang

Pan

et al. 2021

Journal Cellular Physiology

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“…Tens of thousands of lncRNAs have now been identified in humans, zebrafish, and mice (Zhao et al, 2016;Hu et al, 2018). LncRNAs can mediate the regulation of target genes by interacting with RNA, DNA, or proteins and are known to play a role in reproduction (Su et al, 2020), embryonic development (Kuang et al, 2020), sex differentiation (Cai et al, 2019), immunity (Liu et al, 2020), and metabolism (Li et al, 2020) at the transcriptional, posttranscriptional, and epigenetic levels. Other studies, involving fish, have shown that lncRNAs also play an important role in the network regulation of gene expression to cope with stress (Dettleff et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

Zhao

Liew

et al. 2021

Front. Physiol.

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Leuciscus waleckii is a freshwater fish that is known to inhabit the Dali Nor Lake, Inner Mongolia, China. The water in this lake has an HCO3–/CO32– concentration of 54 mM (pH 9.6) and a salinity of 0.6‰. The physiological mechanisms that allow this fish to tolerate these saline/alkaline conditions have yet to be elucidated. Transcriptional component analysis has shown that the expression levels of a large number of genes involved in the pathways responsible for osmo-ionoregulation and arachidonic acid metabolism pathway expression change significantly (p < 0.05) during the regulation of acid–base balance under high alkaline stress. In this study, we investigated the role of long non-coding RNAs (lncRNAs) during adaptation to high alkaline conditions. Fish were challenged to an NaHCO3-adjusted alkalinity of 0 mM, 30 mM (pH 9.44 ± 0.08), and 50 mM (pH 9.55 ± 0.06) for 20 days in the laboratory. Gill and kidney tissues were then collected for high-throughput sequencing assays. A total of 159 million clean reads were obtained by high-throughput sequencing, and 41,248 lncRNA transcripts were identified. Of these, the mean number of exons and the mean length of the lncRNA transcripts were 4.8 and 2,079 bp, respectively. Based on the analysis of differential lncRNA transcript expression, a total of 5,244 and 6,571 lncRNA transcripts were found to be differentially expressed in the gills and kidneys, respectively. Results derived from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the coding genes were correlated with the lncRNA expression profiles. GO analysis showed that many lncRNAs were enriched in the following processes: “transporter activity,” “response to stimulus,” and “binding.” KEGG analysis further revealed that metabolic pathways were significantly enriched. A random selection of 16 lncRNA transcripts was tested by RT-qPCR; these results were consistent with our sequencing results. We found that a large number of genes, with the same expression profiles as those with differentially expressed lncRNAs, were associated with the regulation of acid–base balance, ion transport, and the excretion of ammonia and nitrogen. Collectively, our data indicate that lncRNA-regulated gene expression plays an important role in the process of adaptation to high alkaline conditions in L. waleckii.

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“…LncRNAs have been reported that not expressed at each certain stages in development. Expression of a lncRNA in a speci c development stage indicate that it may have an important biological function at that time [23,24]. For example, Phillip Grote et al report that lncRNA locus Handsdown (Hdn) is active in early heart cells and essential for murine development [25].…”

Section: Introductionmentioning

confidence: 99%

Identification and characteristics of postnatal development-related long non-coding RNAs under microbiota dependent condition

Zheng¹,

Zhang²,

Zhang³

et al. 2020

Preprint

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BackgroundThe interplay of long-non coding RNAs (lncRNAs) and the intestinal microbiota may serve as an essential role in intestinal development and homeostasis. Microbiota could regulate a large numbers of lncRNAs expression in intestinal epithelial cells. However, the associations between lncRNAs and microbiota during early postnatal development stages are still need to understand. MethodsIn present study, the microbial effects on lncRNA of intestinal epithelial cells (IECs) during postnatal development stage were investigated. ResultsWe identified gut microbiota-specific lncRNAs in diverse postnatal development stages including week 1, week 4 and week 12/16 of mice. A large proportion of gut microbiota-specific lncRNAs only were differential expressed in a single postnatal development stage. Up- and down-regulated gut microbiota-specific lncRNAs both showed consistent expression pattern. We also constructed gut microbiota-specific lncRNAs and coding genes interacted co-expressed networks. Functional analysis indicated that gut microbiota-specific lncRNAs were associated with ABC transporters. ConclusionsIn summary, the present study characterizes the landscape of lncRNAs associated with gut microbiota in different postnatal development stages. It provide assistance for exploring the relationships among lncRNAs, gut microbiota and postnatal development stages.

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Whole transcriptome sequencing reveals that non-coding RNAs are related to embryo morphogenesis and development in rabbits

Cited by 16 publications

References 39 publications

Circular RNAs: Novel potential regulators in embryogenesis, female infertility, and pregnancy‐related diseases

Circular RNAs: Novel potential regulators in embryogenesis, female infertility, and pregnancy‐related diseases

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

Identification and characteristics of postnatal development-related long non-coding RNAs under microbiota dependent condition

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