Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection

Ma, Qiman; Li, Liangyuan; Tang, Yan; Fu, Qiang; Liu, Sheng; Hu, Shengwei; Qiao, Jun; Chen, Chuangfu; Ni, Wei

doi:10.1016/j.rvsc.2017.09.020

Cited by 26 publications

(24 citation statements)

References 59 publications

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“…HIV, porcine circovirus 2, HSV-1, rabies virus, avian leukosis virus J, bovine viral diarrhea virus) and parasites (e.g. Echinococcus granulosus, Cryptosporidium parvum, Cryptosporidium baileyi) in animals and humans [28,33,[66][67][68][69][70][71][72][73]. The expression profiles of host circRNAs were also elucidated after infections of avian leukosis virus J [74], bovine viral diarrhea virus [75], human cytomegalovirus [76], Orf virus [30], porcine endemic diarrhea virus [29], HIV [77], transmissible gastroenteritis virus [78], Mycobacterium tuberculosis [79], Clostridium perfringens [80] and C. baileyi [33].…”

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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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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“…Long noncoding RNAs are a class of mRNA-like transcripts that have been operationally defined as mostly 5′-capped, polyadenylated and spliced, exhibiting lengths greater than 200 nt (nucleotide), and lacking ORFs (open reading frames) [1]. According to genomic localization of these RNAs with respect to nearby mRNAs, lncRNAs are divided into five loose categories: (1) sense lncRNAs, overlapped with one or more exons from another transcript on the same strand; (2) antisense lncRNAs, overlapped with one or more exons from another transcript on the other strand; (3) bidirectional lncRNAs, which initiate a similar expression pattern to its nearing mRNA counterpart on the other strand; (4) intronic lncRNAs, overlapped with one or more introns in another transcript; (5) and intergenic lncRNAs (lincRNAs), located in the interval between two protein coding genes on the same strand [2,3]. Nevertheless, recent functional studies in mammals have found that lncRNAs serve as critical regulators in various biological processes by regulating gene expression at the epigenetic, transcription, and postttranscription levels.…”

Section: Introductionmentioning

confidence: 99%

“…Nevertheless, recent functional studies in mammals have found that lncRNAs serve as critical regulators in various biological processes by regulating gene expression at the epigenetic, transcription, and postttranscription levels. LncRNAs are widely involved in various important physiological and pathological processes, such as, cell differentiation, morphogenesis, gown, development and death, immunity responses, oncogenesis and cancer [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

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“…In addition, > 3000 differentially expressed genes (DEG) were associated with lncRNAs during infectious salmon anaemia (ISA) virus infection and most were regulated in response to infection [14]. A total of 1236 lncRNA transcripts were differentially regulated at different stages of bovine viral diarrhea virus infected Madin Darby bovine kidney (MDBK) cells [15].…”

Section: Introductionmentioning

confidence: 99%

Analysis of long non-coding RNAs in neonatal piglets at different stages of porcine deltacoronavirus infection

Tang

Lan

et al. 2019

BMC Vet Res

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Background PDCoV (Porcine Deltacoronavirus) is a novel porcine coronavirus that causes intestinal necrosis of piglets, thinning of the intestinal wall and severe villus atrophy in the small intestine. PDCoV is a highly contagious infectious disease characterized by diarrhea, dehydration and vomiting. It has been reported that lncRNA has a significant effect on viral replication and increased or decreased virulence. At present, there is almost no research on lncRNA related to PDCoV infection. With the development of the research, a large number of lncRNAs related to PDCoV infection have been discovered. Identifying the role of these lncRNAs in the infection process facilitates the screening of diagnostically significant biomarkers. Results Using high throughput sequencing to screen differentially expressed long non-coding RNA (lncRNA) during PDCoV infection, we identified 99, 41 and 33 differentially expressed lncRNAs in the early, middle and late stages of infection, respectively. These lncRNAs were involved in glycolysis / gluconeogenesis, histidine metabolism and pentose and Chloroalkane and chloroalkene degradation pathway. We obtained expression data of miRNAs, lncRNAs and mRNAs during PDCoV infection and constructed and investigated an interaction network. The qRT-PCR validation results of 6 differentially expressed lncRNAs were consistent with RNA-Seq results. Conclusions This study is the first to examine differentially expressed lncRNAs after PDCoV infection of piglets. These results can provide new insights into PDCoV infection and antiviral strategies. Electronic supplementary material The online version of this article (10.1186/s12917-019-1862-4) contains supplementary material, which is available to authorized users.

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Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection

Cited by 26 publications

References 59 publications

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

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

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Analysis of long non-coding RNAs in neonatal piglets at different stages of porcine deltacoronavirus infection

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