scholarly journals Genome-Wide Expression Screening Discloses Long Noncoding RNAs Involved in Thyroid Carcinogenesis

2016 ◽  
Vol 101 (11) ◽  
pp. 4005-4013 ◽  
Author(s):  
Sandya Liyanarachchi ◽  
Wei Li ◽  
Pearlly Yan ◽  
Ralf Bundschuh ◽  
Pamela Brock ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Expression Screening ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

scholarly journals Deep learning identifies genome-wide DNA binding sites of long noncoding RNAs

RNA Biology ◽  
2018 ◽  
Vol 15 (12) ◽  
pp. 1468-1476 ◽  
Author(s):  
Fan Wang ◽  
Pranik Chainani ◽  
Tommy White ◽  
Jin Yang ◽  
Yu Liu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Dna Binding ◽  
Binding Sites ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Dna Binding Sites ◽  
Genome Wide

scholarly journals Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients

2018 ◽  
Vol 78 (15) ◽  
pp. 4411-4423 ◽  
Author(s):  
Lei Wang ◽  
Sara J. Felts ◽  
Virginia P. Van Keulen ◽  
Adam D. Scheid ◽  
Matthew S. Block ◽  
...  
Keyword(s):  
Immune Cell ◽  
Noncoding Rnas ◽  
Cell Types ◽  
Long Noncoding Rnas ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Melanoma Patients

Genome-wide identification and functional analysis of long noncoding RNAs involved in the response to graphene oxide

Biomaterials ◽  
2016 ◽  
Vol 102 ◽  
pp. 277-291 ◽  
Author(s):  
Qiuli Wu ◽  
Xuefeng Zhou ◽  
Xiaoxiao Han ◽  
Yizhou Zhuo ◽  
Siting Zhu ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Graphene Oxide ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide

scholarly journals Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

2020 ◽  
Author(s):  
PENG MA ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.

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