Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer
Autor: | Joëlle Collignon, Corinne Fasquelle, Latifa Karim, Meriem Boukerroucha, Vincent Bours, Jean-Hubert Caberg, Claire Josse, Benoit Hennuy, Veronique Jossa, Fabrice Olivier, Hélène Schroeder, Warda Bezzaou, Guy Jerusalem, Sonia ElGuendi, Benoit Charloteaux, Pierre Frères, Stephane Wenric |
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Jazyk: | angličtina |
Rok vydání: | 2017 |
Předmět: |
Adult
0301 basic medicine RNA Untranslated Receptor ErbB-2 lcsh:Medicine Breast Neoplasms RNA-Seq Biology Article Transcriptome 03 medical and health sciences Gene expression Biomarkers Tumor medicine Humans RNA Antisense lcsh:Science Gene Aged Retrospective Studies Aged 80 and over Genetics Multidisciplinary Sequence Analysis RNA Gene Expression Profiling lcsh:R Cancer RNA Middle Aged medicine.disease Non-coding RNA Survival Analysis Long non-coding RNA 030104 developmental biology Receptors Estrogen Female lcsh:Q |
Zdroj: | Scientific Reports, Vol 7, Iss 1, Pp 1-12 (2017) Scientific Reports |
ISSN: | 2045-2322 |
DOI: | 10.1038/s41598-017-17811-2 |
Popis: | Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that are complementary and overlapping to those of either protein-coding (PCT) or non-coding transcripts. Several ncNATs were described as regulating protein coding gene expression on the same loci, and they are expected to act more frequently in cis compared to other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired adjacent non-malignant tissues were analyzed by strand-specific RNA sequencing. To highlight ncNATs potentially playing a role in protein coding gene regulations that occur in breast cancer, three different data analysis methods were used: differential expression analysis of ncNATs between tumor and non-malignant tissues, differential correlation analysis of paired ncNAT/PCT between tumor and non-malignant tissues, and ncNAT/PCT read count ratio variation between tumor and non-malignant tissues. Each of these methods yielded lists of ncNAT/PCT pairs that were enriched in survival-associated genes. This work highlights ncNAT lists that display potential to affect the expression of protein-coding genes involved in breast cancer pathology. |
Databáze: | OpenAIRE |
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