Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

Jin, Long; Hu, Silu; Tu, Teng; Huang, Zhiqing; Tang, Qianzi; Ma, Jideng; Wang, Xun; Li, Xuewei; Zhou, Xuan; Shuai, Surong; Li, Mingzhou

doi:10.3390/genes9090443

Cited by 11 publications

(14 citation statements)

References 85 publications

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“…From the samples, 12,354 mRNA transcripts were expressed (FPKM >0.5 in at least one sample), and 5,946 lncRNA transcripts were substantially expressed (FPKM >0.1 in at least one sample). The lncRNAs shared similar features, such as relatively low exon numbers, low expression levels, short lengths, and low coding potentials, with previously reported vertebrate lncRNAs [14] (Supplementary Figure S2). Further analysis revealed that the number of expressed genes peaked at 180 days among the five time points.…”

Section: Messenger Rna and Lncrna Expression Profiles In Porcine Perisupporting

confidence: 78%

“…The transcripts that were annotated in the reference (marked by 'c' for partial matches and '=' for full matches) were removed using Coffcompare (part of Cufflinks, v.2.2.1). Next, transcripts longer than 200 nt were retained to predict coding potential using a previously described approach [14]. We considered a lncRNA transcript to be expressed if it had an expression value greater than 0.1 FPKM (FPKM >0.1) in at least one sample.…”

Section: Lncrna Identification and Expression Analysismentioning

confidence: 99%

“…Several functions were commonly enriched for both universally expressed mRNAs and lncRNAs in all five time points, such as protein folding, nucleus, cytoplasm, ATP binding, poly(A) RNA binding and endocytosis. This suggested that maintaining of basic bood functions required coregulation of mRNAs and lncRNAs, and lncRNAs may regulate mRNAs with similar biological functions [14].…”

Section: Messenger Rna and Lncrna Expression Profiles In Porcine Perimentioning

confidence: 99%

“…Among them, the expression levels of 300 adjacently located mRNAs (100 kb up-and downstream) were highly correlated with 95 DE lncRNAs (|r|>0.95 and p<0.05). (Supplementary Table S4) We considered that these mRNAs may have similar structures or functions to the corresponding lncRNAs [14]. Notably, among these lncRNA-mRNA pairs, lncRNA TCONS-00086451 was a sense-overlapping lncRNA of NFATC2 ( Supplementary Table S5).…”

Section: Functional Enrichment Analysis Of Differentially Expressed Mmentioning

confidence: 99%

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Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development

Zhou

Jin

et al. 2020

Asian-Australas J Anim Sci

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Objective: We investigated the temporal expression profiles of long noncoding RNA (lncRNA) and mRNA in the peripheral blood of pigs during development and identified the lncRNAs that are related to the blood-based immune system.Methods: Peripheral blood samples were obtained from the pigs at 0, 7, 28, and 180 days and 2 years of age. RNA sequencing was performed to survey the lncRNA and mRNA transcriptomes in the samples. Short time-series expression miner (STEM) was used to show temporal expression patterns in the mRNAs and lncRNAs. Gene ontology and Kyoto encyclopedia of genes and genomes analyses were performed to assess the genes’ biological relevance. To predict the functions of the identified lncRNAs, we extracted mRNAs that were nearby loci and highly correlated with the lncRNAs.Results: In total of 5,946 lncRNA and 12,354 mRNA transcripts were identified among the samples. STEM showed that most lncRNAs and mRNAs had similar temporal expression patterns during development, indicating the expressional correlation and functional relatedness between them. The five stages were divided into two classes: the suckling period and the late developmental stage. Most genes were expressed at low level during the suckling period, but at higher level during the late stages. Expression of several T-cell-related genes increased continuously during the suckling period, indicating that these genes are crucial for establishing the adaptive immune system in piglets at this stage. Notably, lncRNA TCONS-00086451may promote blood-based immune system development by upregulating nuclear factor of activated T-cells cytoplasmic 2 expression.Conclusion: This study provides a catalog of porcine peripheral blood-related lncRNAs and mRNAs and reveals the characteristics and temporal expression profiles of these lncRNAs and mRNAs during peripheral blood development from the newborn to adult stages in pigs.

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Section: Messenger Rna and Lncrna Expression Profiles In Porcine Perisupporting

confidence: 78%

Section: Lncrna Identification and Expression Analysismentioning

confidence: 99%

Section: Messenger Rna and Lncrna Expression Profiles In Porcine Perimentioning

confidence: 99%

Section: Functional Enrichment Analysis Of Differentially Expressed Mmentioning

confidence: 99%

See 2 more Smart Citations

Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development

Zhou

Jin

et al. 2020

Asian-Australas J Anim Sci

Self Cite

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show abstract

“…With the development of genetic array and high throughput sequencing technology, more and more lncRNAs have been discovered in human, rat and mouse (Zhao et al 2016). Recently, lncRNAs have also been identified in pig (Yang et al 2017;Jin et al 2018;Kern et al 2018), chicken (Muret et al 2017;Kern et al 2018;Li et al 2019), sheep (Ren et al 2016;Ling et al 2017;Bush et al 2018;Sulayman et al 2019) and cattle (Billerey et al 2014;Koufariotis et al 2015;Tong et al 2017;Bush et al 2018;Kern et al 2018;Weikard et al 2018;Yang et al 2018;Choi et al 2019;Wang et al 2019;Yue et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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Long non-coding RNAs (lncRNAs) have been essentially involved in all kinds of important biological processes, such as cell differentiation and development. In this study, we comprehensively profiled genome-wide lncRNAs of bovine skeletal muscle in two Chinese cattle breeds using RNAseq approach. The longissimus dorsi samples were collected from three Charolais (CH) and three Tongjiang (TJ) adult cattle, respectively. Approximately 80 million reads were obtained per library, and by which we assembled 31,009 unique transcripts. We successfully identified a total of 4155 different lncRNAs in six muscle samples, consisting of 3204 intronic lncRNAs, 737 intergenic lncRNAs, 113 sense lncRNAs and 101 antisense lncRNAs. Among them, 32 lncRNAs were differentially expressed (Fold Change >1.0, FDR < 0.05) between CH and TJ. Among these lncRNAs, 1744 identified bovine lncRNAs were located adjacent to 1146 protein-coding genes (<100 kb upstream and downstream) and functionally enriched in organ development, gene regulation and signal transduction. Our results provide a catalogue of bovine skeletal muscle-related lncRNAs, which will complement the list of bovine lncRNAs and contribute to understanding of the molecular mechanism of underpinning muscle development in cattle. HIGHLIGHTS The first study to compare specialised beef cattle breed with Chinese local beef cattle breed on long non-coding RNA (lncRNA). The 4155 different lncRNAs in beef cattle genome were identified to complement the list of bovine lncRNAs. The 1146 protein-coding genes were found maybe in cis-regulatory relationships with lncRNAs to understand the molecular mechanism underpinning muscle development in cattle.

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Review: Long non-coding RNA in livestock

Kosińska-Selbi

Mielczarek

Szyda

2020

Animal

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Less than 2% of mammalian genomes code for proteins, but ‘the majority of its bases can be found in primary transcripts’ – a phenomenon termed the pervasive transcription, which was first reported in 2007. Even though most of the transcripts do not code for proteins, they play a variety of biological functions, with regulation of gene expression appearing as the most common one. Those transcripts are divided into two groups based on their length: small non-coding RNAs, which are maximally 200 bp long, and long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides. The advances in next-generation sequencing methods provided a new possibility of investigating the full set of RNA molecules in the cell. In this review, we summarized the current state of knowledge on lncRNAs in three major livestock species – Sus scrofa, Bos taurus and Gallus gallus, based on the literature and the content of biological databases. In the NONCODE database, the largest number of identified lncRNA transcripts is available for pigs, but cattle have the largest number of lncRNA genes. Poultry is represented by less than a half of records. Genomic annotation of lncRNAs showed that the majority of them are assigned to introns (pig, poultry) or intergenic (cattle). The comparison with well-annotated human and mouse genomes indicates that such annotation is a result of lack of proper lncRNA annotation data. Since lncRNAs play an important role in genomic studies, their characterization in farm animals’ genomes is critical in bridging the gap between genotype and phenotype.

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Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

Cited by 11 publications

References 85 publications

Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development

Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Review: Long non-coding RNA in livestock

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