Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing
CircRNAs have become a novel scientific research hotspot, and an increasing number of studies have shed light on their involvement in malignant progression. Prompted by the apparent scientific gap in circRNAs from apoptosis-related genes, such as <i>BOK</i>, we focused on the identificat...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-09-01
|
| Series: | Non-Coding RNA |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-553X/9/5/57 |
| _version_ | 1797572699312095232 |
|---|---|
| author | Christos K. Kontos Despina Hadjichambi Maria Papatsirou Paraskevi Karousi Spyridon Christodoulou Diamantis C. Sideris Andreas Scorilas |
| author_facet | Christos K. Kontos Despina Hadjichambi Maria Papatsirou Paraskevi Karousi Spyridon Christodoulou Diamantis C. Sideris Andreas Scorilas |
| author_sort | Christos K. Kontos |
| collection | DOAJ |
| description | CircRNAs have become a novel scientific research hotspot, and an increasing number of studies have shed light on their involvement in malignant progression. Prompted by the apparent scientific gap in circRNAs from apoptosis-related genes, such as <i>BOK</i>, we focused on the identification of novel <i>BOK</i> circRNAs in human ovarian and prostate cancer cells. Total RNA was extracted from ovarian and prostate cancer cell lines and reversely transcribed using random hexamer primers. A series of PCR assays utilizing gene-specific divergent primers were carried out. Next, third-generation sequencing based on nanopore technology followed by extensive bioinformatics analysis led to the discovery of 23 novel circRNAs. These novel circRNAs consist of both exonic and intronic regions of the <i>BOK</i> gene. Interestingly, the exons that form the back-splice junction were truncated in most circRNAs, and multiple back-splice sites were found for each <i>BOK</i> exon. Moreover, several <i>BOK</i> circRNAs are predicted to sponge microRNAs with a key role in reproductive cancers, while the presence of putative open reading frames indicates their translational potential. Overall, this study suggests that distinct alternative splicing events lead to the production of novel <i>BOK</i> circRNAs, which could come into play in the molecular landscape and clinical investigation of ovarian and prostate cancer. |
| first_indexed | 2024-03-10T20:59:19Z |
| format | Article |
| id | doaj.art-185f4874f6524e2f9c0269ff445009d5 |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T20:59:19Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-185f4874f6524e2f9c0269ff445009d52023-11-19T17:36:45ZengMDPI AGNon-Coding RNA2311-553X2023-09-01955710.3390/ncrna9050057Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore SequencingChristos K. Kontos0Despina Hadjichambi1Maria Papatsirou2Paraskevi Karousi3Spyridon Christodoulou4Diamantis C. Sideris5Andreas Scorilas6Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceFourth Department of Surgery, University General Hospital “Attikon”, National and Kapodistrian University of Athens, 12462 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, GreeceCircRNAs have become a novel scientific research hotspot, and an increasing number of studies have shed light on their involvement in malignant progression. Prompted by the apparent scientific gap in circRNAs from apoptosis-related genes, such as <i>BOK</i>, we focused on the identification of novel <i>BOK</i> circRNAs in human ovarian and prostate cancer cells. Total RNA was extracted from ovarian and prostate cancer cell lines and reversely transcribed using random hexamer primers. A series of PCR assays utilizing gene-specific divergent primers were carried out. Next, third-generation sequencing based on nanopore technology followed by extensive bioinformatics analysis led to the discovery of 23 novel circRNAs. These novel circRNAs consist of both exonic and intronic regions of the <i>BOK</i> gene. Interestingly, the exons that form the back-splice junction were truncated in most circRNAs, and multiple back-splice sites were found for each <i>BOK</i> exon. Moreover, several <i>BOK</i> circRNAs are predicted to sponge microRNAs with a key role in reproductive cancers, while the presence of putative open reading frames indicates their translational potential. Overall, this study suggests that distinct alternative splicing events lead to the production of novel <i>BOK</i> circRNAs, which could come into play in the molecular landscape and clinical investigation of ovarian and prostate cancer.https://www.mdpi.com/2311-553X/9/5/57circRNAsalternative splicingtranscriptomicsthird-generation sequencingmiRNAsreproductive cancers |
| spellingShingle | Christos K. Kontos Despina Hadjichambi Maria Papatsirou Paraskevi Karousi Spyridon Christodoulou Diamantis C. Sideris Andreas Scorilas Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing Non-Coding RNA circRNAs alternative splicing transcriptomics third-generation sequencing miRNAs reproductive cancers |
| title | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing |
| title_full | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing |
| title_fullStr | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing |
| title_full_unstemmed | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing |
| title_short | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related <i>BOK</i> Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing |
| title_sort | discovery and comprehensive characterization of novel circular rnas of the apoptosis related i bok i gene in human ovarian and prostate cancer cells using nanopore sequencing |
| topic | circRNAs alternative splicing transcriptomics third-generation sequencing miRNAs reproductive cancers |
| url | https://www.mdpi.com/2311-553X/9/5/57 |
| work_keys_str_mv | AT christoskkontos discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT despinahadjichambi discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT mariapapatsirou discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT paraskevikarousi discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT spyridonchristodoulou discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT diamantiscsideris discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing AT andreasscorilas discoveryandcomprehensivecharacterizationofnovelcircularrnasoftheapoptosisrelatedibokigeneinhumanovarianandprostatecancercellsusingnanoporesequencing |