Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics

Li, Diangeng; Bao, Pengtao; Yin, Zhiwei; Sun, Lei; Jin, Feng; He, Zheng; Jin, Meiling; Liu, Changting

doi:10.7717/peerj.5721

Cited by 12 publications

(12 citation statements)

References 24 publications

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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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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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“…Based on the sequencing results described previously [ 9 , 12 ], we selected certain microRNAs for further analysis. The target genes of the differently expressed miRNAs were identified using the miRanda, PITA, and RNAhybrid databases [ 13 – 15 ]. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of target genes were performed through The Database for Annotation, Visualization, and Integrated Discovery (DAVID), and statistical significance was set at P < 0.05 [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

Overexpression of miR-150-5p Alleviates Apoptosis in Sepsis-Induced Myocardial Depression

Zhu

Zhang

Wen

et al. 2020

BioMed Research International

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Sepsis-induced myocardial depression has high mortality and is very common in intensive care units. Previous studies have found that microRNAs play an important role in regulating sepsis-induced myocardial depression. miR-150-5p is involved in many biological processes; however, the mechanism underlying its role in sepsis-induced myocardial depression is still unclear. In this study, we generated rat models of septic shock induced by lipopolysaccharide. Whole genomic RNA sequencing was performed on 12 left ventricles collected after LPS treatment to identify miRNAs. Most of the target genes of the differently expressed microRNAs were involved in apoptosis, according to Gene Ontology. We also observed apoptosis in the heart tissue and in H9C2 cardiomyocytes stimulated with lipopolysaccharide, indicating that cell apoptosis may be an important mechanism in sepsis-induced myocardial depression. Furthermore, the expression of miR-150-5p was reduced, and overexpression of miR-150-5p with mimics resulted in a decrease in apoptosis, decreased expression of cleaved caspase3 and Bax, and increased expression of Bcl-2. Additionally, after H9C2 cells were transfected with miR-150-5p mimics or an inhibitor, the expression of Akt2 decreased or increased, respectively. These findings suggest that miR-150-5p can alleviate apoptosis and may be a novel therapeutic target for sepsis-induced myocardial depression.

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“…LncRNA NEAT1 is crucial for the nucleocytoplasmic transport of mRNA in response to stimuli [35]. Recent studies have also shown that virus lncRNA, or lncRNA produced during the viral life cycle, can regulate the host's antiviral immune response, thus playing an important role in promoting the replication and proliferation of the virus and packaging of the genome into the virions [36,37]. Cellular lncRNA and virus-encoded lncRNA can form chimeric lncRNA, which impacts virus infection [38,39].…”

Section: Discussionmentioning

confidence: 99%

Long Non-coding RNA NONSUST006715.1 Suppresses Japanese Encephalitis Virus Proliferation in PK-15 Cells

Zhou¹,

Yuan²,

Zhang³

et al. 2020

Preprint

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Background: Japanese encephalitis virus is a mosquito-borne neurotropic flavivirus that causes acute viral encephalitis in humans. Pigs are crucial amplifier host of JEV. Recently, long non-coding RNAs have received increasing attention for their antiviral function. Methods: LncRNA-NONSUST006715.1 was overexpression or knockdown using western blotting and reverse-transcription polymerase chain reaction (RT-PCR) to detect the effect of lncRNA on JEV proliferation. CCR1 was found to regulate the expression of lncRNA-NONSUST006715.1 by inhibitors screen. Transcription factor SP1 was overexpression or knockdown using RT-PCR to detect the influence of SP1 on the expression of lncRNA. In addition, the enrichments of transcription factor SP1 on the promoter of lncRNA-NONSUST006715.1 were analyzed by Chromatin immunoprecipitation.Results: In this study, we demonstrated a new function of lncRNA-NONSUST006715.1, the inhibition of JEV proliferation in PK-15 cells. We found that C-C chemokine receptor type 1 inhibited the expression of lncRNA-NONSUST006715.1 via the transcription factor SP1. Knockdown of CCR1 could upregulated the expression of SP1 and lncRNA-NONSUST006715.1, resulting in resistance to JEV proliferation. Conclusions: These findings illustrate the importance of lncRNAs in virus proliferation, and reveal how this virus regulates lncRNAs in host cells to promote its proliferation.

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Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics

Cited by 12 publications

References 24 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

Overexpression of miR-150-5p Alleviates Apoptosis in Sepsis-Induced Myocardial Depression

Long Non-coding RNA NONSUST006715.1 Suppresses Japanese Encephalitis Virus Proliferation in PK-15 Cells

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Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics

Cited by 12 publications

References 24 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

Overexpression of miR-150-5p Alleviates Apoptosis in Sepsis-Induced Myocardial Depression

Long Non-coding RNA NONSUST006715.1&nbsp;Suppresses Japanese Encephalitis Virus Proliferation in PK-15 Cells

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Long Non-coding RNA NONSUST006715.1 Suppresses Japanese Encephalitis Virus Proliferation in PK-15 Cells