Effect of Focal Ischemia on Long Noncoding RNAs

Dharap, Ashutosh; Nakka, Venkata Prasuja; Vemuganti, Raghu

doi:10.1161/strokeaha.112.669465

Cited by 166 publications

(134 citation statements)

References 13 publications

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“…They were significantly correlated with non-coding RNAs [18]. Moreover, in the rat cerebral cortex, the promoters of stroke-responsive long non-coding genes and their homologous protein-coding genes showed highly overlapping transcription factor binding sites [36]. These two researches supported the possible sharing of common transcription factors between proteincoding and non-coding genes.…”

Section: Lncrnas May Share Common Transcription Factors With Protein mentioning

confidence: 68%

Regulation of lncRNA expression

Liu

et al. 2014

Cellular and Molecular Biology Letters

178

122

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Long non-coding RNAs (lncRNAs) are series of transcripts with important biological functions. Various diseases have been associated with aberrant expression of lncRNAs and the related dysregulation of mRNAs. In this review, we highlight the mechanisms of dynamic lncRNA expression. The chromatin state contributes to the low and specific expression of lncRNAs. The transcription of non-coding RNA genes is regulated by many core transcription factors applied to protein-coding genes. However, specific DNA sequences may allow their unsynchronized transcription with their location-associated mRNAs. Additionally, there are multiple mechanisms involved in the post-transcriptional regulation of lncRNAs. Among these, microRNAs might have indispensible regulatory effects on lncRNAs, based on recent discoveries.

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Section: Lncrnas May Share Common Transcription Factors With Protein mentioning

confidence: 68%

Regulation of lncRNA expression

Liu

et al. 2014

Cellular and Molecular Biology Letters

178

122

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“…LncRNA profiles have been identified through microarray and high-throughput sequencing analyses to determine the regulatory function of lncRNAs in diseases. Dharap performed microarray analysis of rat cerebral cortex and revealed that lncRNA expression profiles are significantly altered after stroke [7]. Wu [8] and Dharap [9] performed microarray analysis of rat brain tissues to identify and explore the potential function of lncRNA-N1LR.…”

Section: Introductionmentioning

confidence: 99%

Identification of Novel LncRNA Biomarkers and Construction of LncRNA-Related Networks in Han Chinese Patients with Ischemic Stroke

Guo

Yang

Liang

et al. 2018

Cell Physiol Biochem

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Background/Aims: Long non-coding RNAs (lncRNAs) are potential biomarkers of tumors, cardiac disease, and cerebral disease because of their interaction with coding RNAs. This work focused on ischemic stroke (IS) and aimed to identify novel lncRNA biomarkers and construct lncRNA-related networks in IS. Methods: Differentially expressed lncRNAs were identified using Arraystar Human LncRNA Microarray v4.0, and validated with qRT-PCR. A lncRNA–mRNA co-expression network and a lncRNA–miRNA–mRNA regulatory network were constructed. Functional and pathway analyses were then performed. Results: In total, 560 up-regulated and 690 down-regulated differentially expressed lncRNAs were found (P < 0.05, false discovery rate < 0.05, absolute fold change ≥ 2). qRT-PCR results confirmed that lncRNA-ENST00000568297, lncRNA-ENST00000568243, and lncRNA-NR_046084 exhibited significant differential expression between IS and controls (all P < 0.05). Areas under the curves (AUCs) for these lncRNAs were 0.733, 0.743, and 0.690, respectively, and the combined AUC was 0.843. A coding–noncoding co-expression (CNC) network was constructed based on Pearson’s correlation coefficient. A specific lncRNA–miRNA–mRNA regulatory network of ENST00000568297, ENST00000568243, and NR_046084 was also constructed. Functional annotation of the up- and down-regulated mRNAs was performed. Pathway analysis enriched IS-related pathways with mRNAs in the lncRNA–miRNA–mRNA regulatory network. Conclusion: LncRNA and mRNA expression profiles in human peripheral blood were altered after IS. ENST00000568297, ENST00000568243, and NR_046084 were identified as novel potential diagnostic biomarkers of IS. Analysis of the CNC network and lncRNA–miRNA–mRNA regulatory network suggested that lncRNAs may participate in IS pathophysiology by regulating pivotal miRNAs, mRNAs, or IS-related pathways.

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“…Another study showed that the overexpression of the RERT lncRNA upregulated EGLN2 (34). Dharap et al found 62 stroke-responsive lncRNAs showing 90% sequence homology with exons of protein-coding genes in their study on lncRNA expression profiles in focal ischemia (35). Similarly, Ziats et al reported that most differentially expressed lncRNAs in autism spectrum disorders (ASD) were from intergenic regions (~60%), from antisense to proteincoding loci (~15%), or within introns of protein-coding genes (~10%), with the others representing overlapping transcripts from exons or introns in both sense and antisense directions (36).…”

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confidence: 99%

Differential expression of long non-coding RNAs in bleomycin-induced lung fibrosis

Cao

Zhang

Wang

et al. 2013

International Journal of Molecular Medicine

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Abstract. Recent studies suggest that long non-coding RNAs (lncRNAs) are more involved in human diseases than previously realized. A growing body of evidence links lncRNA mutation and dysregulation to diverse human diseases. However, the association of lncRNAs with the pathogenesis of lung fibrosis remains poorly understood. In this study, we detected changes in hydroxyproline and collagen levels, as well as the ultrastructure of lung tissue to develop a rat model of lung fibrosis. The differentially expressed lncRNAs and mRNA profiles between fibrotic lung and normal lung tissue were analyzed using microarrays. Gene Ontology analysis and pathway analysis were performed for further research. Two differentially expressed lncRNAs, namely, AJ005396 and S69206, were detected by in situ hybridization to validate the microarray data. The results revealed that the number of collagen fibers in the interstitial lung tissue significantly increased in the model group compared with the normal group. In total, 210 and 358 lncRNAs were upregulated and downregulated, respectively, along with 415 upregulated and 530 downregulated mRNAs in the rats with lung fibrosis. AJ005396 and S69206 were upregulated in the fibrotic lung tissue, consistent with the microarray data, and were located in the cytoplasm of the interstitial lung cells. In conclusion, the expression profile of the lncRNAs was significantly altered in the fibrotic lung tissue and these transcripts are potential molecular targets for inhibiting the development of lung fibrosis. IntroductionIdiopathic pulmonary fibrosis (IPF) is a common, chronic, progressive and usually lethal fibrotic lung disease with poor prognosis (1). This disease is characterized by focal areas of alveolar epithelial cell injury and the excessive proliferation of mesenchymal cells in the interstitium, which results in the excessive deposition of extracellular matrix (ECM) and distorted architecture leading to impaired gas exchange (2,3). Although many pathobiological concepts are emerging, including the role of aging and cellular senescence, oxidative stress, endoplasmic reticulum stress, cellular plasticity, microRNA (miRNA) and mechanotransduction, the molecular mechanisms behind IPF are not yet completely understood (4).The Encyclopedia of DNA Elements (ENCODE) project, which aimed to comprehensively characterize the human genome, has shown that >90% of the genome has been transcribed; however, only 1-2% of that is composed of genes (5). The majority of these transcripts are not translated into proteins and are, therefore, termed non-coding RNAs (ncRNAs).Long non-coding RNAs (lncRNAs), a type of ncRNA, vary in size from 200 bp to >100 kb, and are transcribed by RNA polymerase II (6). They play an important role in imprinting (7), enhancing various biological functions (8), X chromosome inactivation (9), chromatin structure (10) and genomic rearrangement during the generation of antibody diversity (11). Thus, lncRNAs are critical for normal development and, in many cases, are deregulated in d...

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Effect of Focal Ischemia on Long Noncoding RNAs

Cited by 166 publications

References 13 publications

Regulation of lncRNA expression

Regulation of lncRNA expression

Identification of Novel LncRNA Biomarkers and Construction of LncRNA-Related Networks in Han Chinese Patients with Ischemic Stroke

Differential expression of long non-coding RNAs in bleomycin-induced lung fibrosis

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