Breast cancer associated germline structural variants harboring small noncoding RNAs impact post-transcriptional gene regulation

Introduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles of small noncoding RNAs in human breast cancer cells.Methods. We separated breast cancer cell nuclei from cytoplasm, and identified small RNA sequences using a high-throughput sequencing platform. To determine the relationship between miRNA sub-cellular distribution and cancer progression, we used microarray analysis to examine the miRNA expression levels in nucleus and cytoplasm of three human cell lines, one normal breast cell line and two breast cancer cell lines. Logistic regression and SVM were used for further analysis.Results. The sub-cellular distribution of small noncoding RNAs shows that numerous miRNAs and their isoforms (isomiR) not only locate to the cytoplasm but also appeare in the nucleus. Subsequent microarray analyses indicated that the miRNA nuclear-cytoplasmic-ratio is a significant characteristic of different cancer cell lines.Conclusions. Our results indicate that the sub-cellular distribution is important for miRNA function, and that the characterization of the small RNAs sub-cellular localizome may contribute to cancer research and diagnosis.

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Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽

10.12688/f1000research.18142.2 ◽

2019 ◽

Vol 8 ◽

pp. 232 ◽

Cited By ~ 1

Author(s):

Lorena Pantano ◽

Francisco Pantano ◽

Eulalia Marti ◽

Shannan Ho Sui

Keyword(s):

Gene Regulation ◽

Small Rna ◽

Small Rnas ◽

Noncoding Rnas ◽

Model Organisms ◽

Visualization Tool ◽

Rna Seq ◽

Small Noncoding Rnas ◽

Different Types ◽

Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease.

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Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽

10.12688/f1000research.18142.1 ◽

2019 ◽

Vol 8 ◽

pp. 232

Author(s):

Lorena Pantano ◽

Francisco Pantano ◽

Eulalia Marti ◽

Shannan Ho Sui

Keyword(s):

Gene Regulation ◽

Small Rna ◽

Small Rnas ◽

Noncoding Rnas ◽

Model Organisms ◽

Visualization Tool ◽

Rna Seq ◽

Small Noncoding Rnas ◽

Different Types ◽

Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

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Abstract 3499: Differentially expressed small noncoding RNAs in triple-negative breast cancer

10.1158/1538-7445.am2017-3499 ◽

2017 ◽

Author(s):

Srinivas V. Koduru ◽

Amit K. Tiwari ◽

Ashley Leberfinger ◽

Sprague W. Hazard ◽

Yuka Imamura Kawasawa ◽

...

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Noncoding Rnas ◽

Differentially Expressed ◽

Small Noncoding Rnas

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Bistability and Oscillations in Gene Regulation Mediated by Small Noncoding RNAs

PLoS ONE ◽

10.1371/journal.pone.0017029 ◽

2011 ◽

Vol 6 (3) ◽

pp. e17029 ◽

Cited By ~ 28

Author(s):

Dengyu Liu ◽

Xiao Chang ◽

Zengrong Liu ◽

Luonan Chen ◽

Ruiqi Wang

Keyword(s):

Gene Regulation ◽

Noncoding Rnas ◽

Small Noncoding Rnas

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Faculty Opinions recommendation of The Ess1 prolyl isomerase is required for transcription termination of small noncoding RNAs via the Nrd1 pathway.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1362960.834058 ◽

2009 ◽

Author(s):

Daniel Reines ◽

Kevin Van Bortle

Keyword(s):

Transcription Termination ◽

Noncoding Rnas ◽

Prolyl Isomerase ◽

Small Noncoding Rnas

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The Prognostic and Predictive Value of microRNAs in Patients with H. pylori-positive Gastric Cancer

Current Pharmaceutical Design ◽

10.2174/1381612825666190110144254 ◽

2019 ◽

Vol 24 (39) ◽

pp. 4639-4645 ◽

Cited By ~ 4

Author(s):

Seyed Mostafa Parizadeh ◽

Reza Jafarzadeh-Esfehani ◽

Amir Avan ◽

Maryam Ghandehari ◽

Fatemeh Goldani ◽

...

Keyword(s):

Gastric Cancer ◽

Tumor Suppressors ◽

Ectopic Expression ◽

Noncoding Rnas ◽

World Population ◽

Normal Flora ◽

Small Noncoding Rnas ◽

Control Gene Expression ◽

The World ◽

H Pylori

Gastric cancer (GC) has a high mortality rate with a poor 5-year survival. Helicobacter pylori (H. pylori) is present as part of the normal flora of stomach. It is found in the gastric mucosa of more than half of the world population. This bacterium is involved in developing H. pylori-induced GC due to the regulation of different micro ribonucleic acid (miRNA or miR). miRNAs are small noncoding RNAs and are recognized as prognostic biomarkers for GC that may control gene expression. miRNAs may function as tumor suppressors, or oncogenes. In this review, we evaluated studies that investigated the ectopic expression of miRNAs in the prognosis of H. pylori positive and negative GC.

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MicroRNAs and gene regulation in breast cancer

Journal of Biochemical and Molecular Toxicology ◽

10.1002/jbt.22567 ◽

2020 ◽

Vol 34 (11) ◽

Author(s):

Fatma Abdalla ◽

Bhupendra Singh ◽

Hari K. Bhat

Keyword(s):

Breast Cancer ◽

Gene Regulation

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The Role of lncRNA in the Development of Tumors, Including Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22168427 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8427

Author(s):

Beata Smolarz ◽

Anna Zadrożna-Nowak ◽

Hanna Romanowicz

Keyword(s):

Breast Cancer ◽

Breast Carcinoma ◽

Present Article ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Regulation Of Transcription ◽

Ribonucleic Acids ◽

Detailed Review ◽

Cellular Processes

Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great importance for the proper functioning of the organism. Studies have shown a relationship between disturbed lncRNA expression and the pathogenesis of many diseases, including cancer. The present article presents a detailed review of the latest reports and data regarding the importance of lncRNA in the development of cancers, including breast carcinoma.

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