Genome-wide analysis of differentially expressed lncRNAs and mRNAs in primary gonadotrophin adenomas by RNA-seq

Li, Jiye; Li, Chuzhong; Wang, Jianpeng; Song, Guidong; Zhao, Zheng; Wang, Haoyuan; Wang, Wen; Li, Hailong; Li, Zhenye; Miao, Yun‐gen; Li, Guilin; Zhang, Yazhou

doi:10.18632/oncotarget.13948

Cited by 19 publications

(29 citation statements)

References 49 publications

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“…Until now, the functions of most wheat lncRNAs have not been annotated. The functional prediction of lncRNAs is based on the annotations of co-expressed mRNAs (Li et al, 2017 ). Therefore, we calculated and constructed an lncRNA-mRNA co-expressed correlation based on their expression enrichment (FPKM); this result is presented in Table S5 .…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker

Shi

et al. 2018

Front. Plant Sci.

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It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker

Shi

et al. 2018

Front. Plant Sci.

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“…The literature is sparse in this manner and to date two studies analyzed these tumors with some limitations. The first study presented differentially expressed long non-coding RNAs (lncRNA) and mRNAs in GAs vs normal pituitary tissues (28). In addition to the concern regarding the comparison of a tumor containing mainly of one cellular subtype (i.e.…”

Section: Discussionmentioning

confidence: 99%

Gene expression profiling of fast- and slow-growing non-functioning gonadotroph pituitary adenomas

Falch

Sundaram

Øystese

et al. 2018

European Journal of Endocrinology

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“…Genome-wide analysis of lncRNAs identified 839 differentially-expressed lncRNAs in GT-PTs compared to normal pituitary ( 282 ). Similar analysis in NFPTs identified 113 lncRNAs ( 283 ).…”

Section: Epigenetic Mechanisms Of Tumorigenesismentioning

confidence: 99%

Novel Insights into Pituitary Tumorigenesis: Genetic and Epigenetic Mechanisms

Nadhamuni

Korbonits

2020

Endocrine Reviews

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Substantial advances have been made recently in the pathobiology of pituitary tumors. Similar to many other endocrine tumors, over the last few years we have recognized the role of germline and somatic mutations in a number of syndromic or non-syndromic conditions with pituitary tumor predisposition. These include the identification of novel germline variants in patients with familial or simplex pituitary tumors and establishment of novel somatic variants identified through next generation sequencing. Advanced techniques have allowed the exploration of epigenetic mechanisms mediated through DNA methylation, histone modifications and non-coding RNAs, such as microRNA, long noncoding RNAs and circular RNAs. These mechanisms can influence tumor formation, growth and invasion. While genetic and epigenetic mechanisms often disrupt similar pathways, such as cell cycle regulation, in pituitary tumors there is little overlap between genes altered by germline, somatic and epigenetic mechanisms. The interplay between these complex mechanisms driving tumorigenesis are best studied in the emerging multi-omics studies. Here, we summarize insights from the recent developments in the regulation of pituitary tumorigenesis.

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Genome-wide analysis of differentially expressed lncRNAs and mRNAs in primary gonadotrophin adenomas by RNA-seq

Cited by 19 publications

References 49 publications

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker

Gene expression profiling of fast- and slow-growing non-functioning gonadotroph pituitary adenomas

Novel Insights into Pituitary Tumorigenesis: Genetic and Epigenetic Mechanisms

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