scholarly journals Human Long Noncoding RNAs Are Substantially Less Folded than Messenger RNAs

2015 ◽  
Vol 32 (4) ◽  
pp. 970-977 ◽  
Author(s):  
Jian-Rong Yang ◽  
Jianzhi Zhang
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas

Crosstalk between prognostic long noncoding RNAs and messenger RNAs as transcriptional hallmarks in gastric cancer

Epigenomics ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 433-443 ◽  
Author(s):  
Jian Zhang ◽  
Yujie Yuan ◽  
Zhewei Wei ◽  
Jianwei Ren ◽  
Xun Hou ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas

A preliminary study on the differential expression of long noncoding RNAs and messenger RNAs in obese and control mice

2019 ◽  
Vol 121 (2) ◽  
pp. 1126-1143 ◽  
Author(s):  
Ping Li ◽  
Xiaoyu Chen ◽  
Xuelian Chang ◽  
Tiantian Tang ◽  
Kemin Qi
Keyword(s):  
Differential Expression ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas ◽  
Preliminary Study ◽  
And Control

scholarly journals Long Noncoding RNAs and Messenger RNAs Expression Profiles Potentially Regulated by ZBTB7A in Nasopharyngeal Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-16
Author(s):  
Fei Liu ◽  
Jiazhang Wei ◽  
Yanrong Hao ◽  
Fengzhu Tang ◽  
Wei Jiao ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Regulatory Pathways ◽  
Different Levels

Our previous studies showed that ZBTB7A played an important role in promoting nasopharyngeal carcinoma (NPC) progression. However, molecular mechanisms of different levels of ZBTB7A are still unclear. It is necessary to search molecular markers which are closely connected with ZBTB7A. We selected NPC sublines CNE2 with stably transfecting empty plasmid (negative control, NC) and short hair RNA (shRNA) plasmid targeting ZBTB7A as research objectives. Microarray was used to screen differentially expressed long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) via shRNA-CNE2 versus NC-CNE2. Quantitative PCR (qPCR) was used to validate lncRNAs and mRNAs from the sublines, chronic rhinitis, and NPC tissues. Bioinformatics was used to analyze regulatory pathways which were connected with ZBTB7A. The 1501 lncRNAs (long noncoding RNAs) and 1275 differentially expressed mRNAs were upregulated or downregulated over 2-fold. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the upregulated or downregulated carbohydrate and lipid metabolisms probably involved in carcinogenicity of shRNA-CNE2 (P-value cut-off was 0.05). In order to find the molecular mechanisms of ZBTB7A, we validated 12 differentially expressed lncRNAs and their nearby mRNAs by qPCR. Most of the differentially expressed mRNAs are closely connected with carbohydrate and lipid metabolisms in multiply cancers. Furthermore, part of them were validated in NPC and rhinitis tissues by qPCR. As a result, NR_047538, ENST00000442852, and fatty acid synthase (FASN) were closely associated with NPC. ZBTB7A had a positive association with NR_047538 and negative associations with ENST00000442852 and FASN. The results probably provide novel candidate biomarkers for NPC progression with different levels of ZBTB7A.

Signatures of altered long noncoding RNAs and messenger RNAs expression in the early acute phase of spinal cord injury

2018 ◽  
Vol 234 (6) ◽  
pp. 8918-8927 ◽  
Author(s):  
Zhongju Shi ◽  
Guangzhi Ning ◽  
Bin Zhang ◽  
Shiyang Yuan ◽  
Hengxing Zhou ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Acute Phase ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas ◽  
Cord Injury

scholarly journals Expression profiles of long noncoding RNAs and messenger RNAs in the border zone of myocardial infarction in rats

2019 ◽  
Vol 24 (1) ◽  
Author(s):  
Qingkun Meng ◽  
Zhijun Sun ◽  
Hui Gu ◽  
Jiaying Luo ◽  
Jingjing Wang ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Cytokine Receptor ◽  
Border Zone ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Chromosomal Distribution

Abstract Background The participation of long noncoding RNAs (lncRNAs) in myocardial infarction has recently been noted. However, their underlying roles in the border zone of myocardial infarction remain unclear. This study uses microarrays to determine the profiles of lncRNAs and mRNAs in the border zone. Methods Bioinformatics methods were employed to uncover their underlying roles. Highly dysregulated lncRNAs was further validated via PCR. Results Four hundred seven lncRNAs and 752 mRNAs were upregulated, while 132 lncRNAs and 547 mRNAs were downregulated in the border zone of myocardial infarction. A circos graph was constructed to visualize the chromosomal distribution and classification of the dysregulated lncRNAs and mRNAs. The upregulated mRNAs in the border zone were most highly enriched in cytokine activity, binding, cytokine receptor binding and related processes, as ascertained through Go analysis. Pathway analysis of the upregulated mRNAs showed the most significant changes were in the TNF signaling pathway, cytokine–cytokine receptor interaction and chemokine signaling pathway and similar pathways and interactions. An lncRNA–mRNA co-expression network was established to probe into the underlying functions of the 10 most highly dysregulated lncRNAs based on their co-expressed mRNAs. In the co-expression network, we found 16 genes directly involved in myocardial infarction, including Alox5ap, Itgb2 and B4galt1. The lncRNAs AY212271, EF424788 and MRAK088538, among others, might be associated with myocardial infarction. BC166504 is probably a key lncRNA in the border zone of myocardial infarction. Conclusions The results may have revealed some aberrantly expressed lncRNAs and mRNAs that contribute to the underlying pathophysiological mechanisms of myocardial infarction.

scholarly journals Dysregulated long noncoding RNAs in the brainstem of the DBA/1 mouse model of SUDEP

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Deng Chen ◽  
Lina Zhu ◽  
Xin Lin ◽  
Dong Zhou ◽  
Ling Liu
Keyword(s):  
Neurological Diseases ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas ◽  
Unexpected Death ◽  
Priming Process ◽  
Antisense Lncrnas ◽  
Dependent Protein ◽  
Normal Controls

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in many neurological diseases. This study aimed to investigate differentially expressed lncRNAs and messenger RNAs (mRNAs) in the susceptibility gaining process of primed DBA/1 mice, a sudden unexpected death in epilepsy (SUDEP) model, to illustrate the potential role of lncRNAs in SUDEP. Methods The Arraystar mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD) was applied to identify the aberrantly expressed lncRNAs and mRNAs between primed DBA/1 mice and normal controls. The differences were verified by qRT-PCR. We conducted gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and coexpression analyses to explore the possible function of the dysregulated RNAs. Results A total of 502 lncRNAs (126 upregulated and 376 downregulated lncRNAs) and 263 mRNAs (141 upregulated and 122 downregulated mRNAs) were dysregulated with P < 0.05 and a fold change over 1.5, among which Adora3 and Gstt4 were possibly related to SUDEP. GO analysis revealed that chaperone cofactor-dependent protein refolding and misfolded protein binding were among the top ten downregulated terms, which pointed to Hspa1a, Hspa2a and their related lncRNAs. KEGG analysis identified 28 upregulated and 10 downregulated pathways. Coexpression analysis showed fifteen dysregulated long intergenic noncoding RNAs (lincRNAs) and three aberrantly expressed antisense lncRNAs, of which AK012034 and NR_040757 are potentially related to SUDEP by regulating LMNB2 and ITPR1, respectively. Conclusions LncRNAs and their coexpression mRNAs are dysregulated in the priming process of DBA/1 in the brainstem. Some of these mRNAs and lncRNAs may be related to SUDEP, including Adora3, Lmnb2, Hspa1a, Hspa1b, Itrp1, Gstt4 and their related lncRNAs. Further study on the mechanism of lncRNAs in SUDEP is needed.

Comprehensive analysis of long noncoding RNAs and mRNAs expression profiles and functional networks during chondrogenic differentiation of murine ATDC5 cells

2019 ◽  
Vol 51 (8) ◽  
pp. 778-790
Author(s):  
Wei Wang ◽  
Yu Ding ◽  
Yanhua Xu ◽  
Hefeng Yang ◽  
Wenjing Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pathway Analysis ◽  
Chondrogenic Differentiation ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Receptor Interaction ◽  
Messenger Rnas ◽  
Kegg Pathway Analysis

AbstractChondrogenic differentiation is a coordinated biological process orchestrated by various cell signaling pathways, involving complex pathways regulated at both transcriptional and post-transcriptional levels. Long noncoding RNAs (lncRNAs) are emerging as important regulators in the modulation of multiple cell processes. However, the potential roles of lncRNAs and their regulatory mechanisms in chondrogenic differentiation remain largely unclear. In this study, microarray was performed to detect the expression profiles of lncRNAs and messenger RNAs (mRNAs) during chondrogenic differentiation of murine chondrogenic cell line ATDC5. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore their functions. Coding-noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) networks were also constructed with bioinformatics methods. The results revealed that 1009 lncRNAs and 1206 mRNAs were differentially regulated during chondrogenic differentiation. GO and KEGG pathway analysis indicated that the principal functions of the transcripts were associated with system development and extracellular matrix-receptor interaction, TGF-β signaling, and PI3K-Akt signaling pathways. The CNC network showed that lncRNA AK136902 was positively correlated with prostaglandin F receptor (FP). The ceRNA network covered 3 lncRNAs, 121 miRNAs and 241 edges. The upregulated lncRNA AK136902, AK016344, and ENSMUST00000180767 might promote chondrogenic differentiation by acting as ceRNAs. Knockdown of lncRNA AK136902 could inhibit the mRNA expression of FP and other chondrogenic related genes, including Aggrecan and Col2a1 during chondrogenic differentiation. Our results provide a new perspective on the modulation of lncRNAs during chondrogenic differentiation.

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