Reference-Based Identification of Long Noncoding RNAs in Plants with Strand-Specific RNA-Sequencing Data

2019 ◽  
pp. 245-255
Author(s):  
Xiao Lin ◽  
Meng Ni ◽  
Zhixia Xiao ◽  
Ting-Fung Chan ◽  
Hon-Ming Lam
Keyword(s):  
Rna Sequencing ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Sequencing Data

RNA sequencing identifies two novel liver-specific long noncoding RNAs with potential diagnostic value in hepatocellular carcinoma

2021 ◽  
Author(s):  
Chao Tan ◽  
Xi Zeng ◽  
Meile Mo ◽  
Xiaoyun Ma ◽  
Qiuli Liang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Rna Sequencing ◽  
Reverse Transcription ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Area Under The Curve ◽  
Long Noncoding Rnas ◽  
Normal Tissues ◽  
Quantitative Reverse Transcription Pcr ◽  
Reverse Transcription Pcr

Aim: To explore the expression profiles of long noncoding RNAs (lncRNAs) and identify novel lncRNAs as biomarkers for early diagnosis and therapy of hepatocellular carcinoma (HCC). Materials & methods: Expression profiles of lncRNAs and mRNAs in five paired HCC and adjacent normal tissues were obtained by RNA sequencing. Eight lncRNAs, including two novel liver-specific lncRNAs (NONHSAT059247.2 and NONHSAT013897.2), were validated in another 74 pairs of HCC and adjacent normal tissues by quantitative reverse transcription PCR. Results: The results of quantitative reverse transcription PCR showed that NONHSAT252133.1, NONHSAT112116.2 and NONHSAT242657.1 were significantly upregulated in HCC tissues, whereas NONHSAT169790.1, NONHSAT059247.2 and NONHSAT013897.2 were significantly downregulated. Two liver-specific lncRNAs demonstrated excellent diagnostic performance: NONHSAT059247.2 (area under the curve = 0.941, 95% CI: 0.902–0.979, p < 0.0001), NONHSAT013897.2 (area under the curve = 0.944, 95% CI: 0.906–0.983, p < 0.0001). Conclusion: The liver-specific lncRNAs NONHSAT059247.2 and NONHSAT013897.2, may provide new biomarkers for the future study on diagnosis, therapy, and mechanisms of HCC.

scholarly journals Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing

2016 ◽  
Vol 5 ◽  
pp. e343 ◽  
Author(s):  
Shuai Zhang ◽  
Chunxia Qin ◽  
Guoqiong Cao ◽  
Wenfeng Xin ◽  
Chengqiang Feng ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Systematic Analysis ◽  
Senescence Accelerated Mouse

scholarly journals Novel and Annotated Long Noncoding RNAs Associated with Ischemia in the Human Heart

2021 ◽  
Vol 22 (21) ◽  
pp. 11324
Author(s):  
Zoe Ward ◽  
Sebastian Schmeier ◽  
Louis Saddic ◽  
Martin I. Sigurdsson ◽  
Vicky A. Cameron ◽  
...  
Keyword(s):  
Correlation Coefficient ◽  
Myocardial Dysfunction ◽  
Pearson Correlation ◽  
Noncoding Rnas ◽  
Subcellular Location ◽  
Early Response ◽  
Long Noncoding Rnas ◽  
Pearson Correlation Coefficient ◽  
Sequencing Data ◽  
Before And After

Background: Long noncoding RNAs (lncRNAs) have been implicated in the pathogenesis of cardiovascular diseases. We aimed to identify novel lncRNAs associated with the early response to ischemia in the heart. Methods and Results: RNA sequencing data gathered from 81 paired left ventricle samples from patients undergoing cardiopulmonary bypass was collected before and after a period of ischemia. Novel lncRNAs were validated with Oxford Nanopore Technologies long-read sequencing. Gene modules associated with an early ischemic response were identified and the subcellular location of selected lncRNAs was determined with RNAscope. A total of 2446 mRNAs, 270 annotated lncRNAs and one novel lncRNA differed in response to ischemia (adjusted p < 0.001, absolute fold change >1.2). The novel lncRNA belonged to a gene module of highly correlated genes that also included 39 annotated lncRNAs. This module associated with ischemia (Pearson correlation coefficient = −0.69, p = 1 × 10−23) and activation of cell death pathways (p < 6 × 10−9). A further nine novel cardiac lncRNAs were identified, of which, one overlapped five cis-eQTL eSNPs for the gene RWD Domain-Containing Sumoylation Enhancer (RWDD3) and was itself correlated with RWDD3 expression (Pearson correlation coefficient −0.2, p = 0.002). Conclusion: We have identified 10 novel lncRNAs, one of which was associated with myocardial ischemia and may have potential as a novel therapeutic target or early marker for myocardial dysfunction.

scholarly journals Identification of Long Noncoding RNAs in Distinct Subtypes of Mouse Retinal Ganglion Cells 

2021 ◽  
Author(s):  
Ana Ayupe ◽  
Felipe Beckedorff ◽  
Konstantin Levay ◽  
Ramin Shiekhattar ◽  
Kevin Park
Keyword(s):  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Axonal Injury ◽  
Noncoding Rnas ◽  
Small Population ◽  
Long Noncoding Rnas ◽  
Biological Processes ◽  
Retinal Ganglion ◽  
Sequencing Data ◽  
Specific Expression

Abstract Background: Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including central nervous system injury. Retinal ganglion cells (RGCs), whose axons form the optic nerve, are a heterogeneous population of neurons with more than 20 molecularly distinct subtypes. While most RGCs, including the ON-OFF direction-selective RGCs (ooDSGCs), are vulnerable to axonal injury, a small population of RGCs, including the intrinsically photosensitive RGCs (ipRGCs), are more resilient. Results: By performing systematic analyses on RNA-sequencing data, here we identify lncRNAs that are expressed in ooDSGCs and ipRGCs with and without axonal injury. Our results reveal a repertoire of different classes of lncRNAs, including long intergenic noncoding RNAs and antisense ncRNAs that are differentially expressed between these RGC types. Strikingly, we also found dozens of lncRNAs whose expressions are altered markedly in response to axonal injury, some of which are expressed exclusively in either one of the subtypes. Moreover, analyses into these lncRNAs unraveled their neighboring coding genes, many of which encode transcription factors and signaling molecules, suggesting that these lncRNAs may act in cis to regulate important biological processes in these neurons. Lastly, guilt-by-association analysis showed that lncRNAs are correlated with apoptosis associated genes, suggesting potential roles for these lncRNAs in RGC survival.Conclusions: Overall, the results of this study reveal RGC type-specific expression of lncRNAs and provide a foundation for future investigation of the function of lncRNAs in regulating neuronal type specification and survival.

scholarly journals Identification of long noncoding RNAs in injury-resilient and injury-susceptible mouse retinal ganglion cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ana C. Ayupe ◽  
Felipe Beckedorff ◽  
Konstantin Levay ◽  
Benito Yon ◽  
Yadira Salgueiro ◽  
...  
Keyword(s):  
Retinal Ganglion Cells ◽  
Ganglion Cells ◽  
Axonal Injury ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Biological Processes ◽  
Retinal Ganglion ◽  
Sequencing Data ◽  
Susceptible Mouse ◽  
Specific Expression

Abstract Background Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including central nervous system injury. Retinal ganglion cells (RGCs), whose axons form the optic nerve, are a heterogeneous population of neurons with more than 40 molecularly distinct subtypes in mouse. While most RGCs, including the ON-OFF direction-selective RGCs (ooDSGCs), are vulnerable to axonal injury, a small population of RGCs, including the intrinsically photosensitive RGCs (ipRGCs), are more resilient. Results By performing systematic analyses on RNA-sequencing data, here we identify lncRNAs that are expressed in ooDSGCs and ipRGCs with and without axonal injury. Our results reveal a repertoire of different classes of lncRNAs, including long intergenic noncoding RNAs and antisense ncRNAs that are differentially expressed between these RGC types. Strikingly, we also found dozens of lncRNAs whose expressions are altered markedly in response to axonal injury, some of which are expressed exclusively in either one of the types. Moreover, analyses into these lncRNAs unraveled their neighboring coding genes, many of which encode transcription factors and signaling molecules, suggesting that these lncRNAs may act in cis to regulate important biological processes in these neurons. Lastly, guilt-by-association analysis showed that lncRNAs are correlated with apoptosis associated genes, suggesting potential roles for these lncRNAs in RGC survival. Conclusions Overall, the results of this study reveal RGC type-specific expression of lncRNAs and provide a foundation for future investigation of the function of lncRNAs in regulating neuronal type specification and survival.

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