Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches
<p>Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular proce...
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2022
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| _version_ | 1864513536181403648 |
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| author | Hibah Shaath (5599658) |
| author2 | Radhakrishnan Vishnubalaji (3563306) Ramesh Elango (7542068) Ahmed Kardousha (17562654) Zeyaul Islam (5867387) Rizwan Qureshi (15279193) Tanvir Alam (638619) Prasanna R. Kolatkar (124118) Nehad M. Alajez (7397276) |
| author2_role | author author author author author author author author |
| author_facet | Hibah Shaath (5599658) Radhakrishnan Vishnubalaji (3563306) Ramesh Elango (7542068) Ahmed Kardousha (17562654) Zeyaul Islam (5867387) Rizwan Qureshi (15279193) Tanvir Alam (638619) Prasanna R. Kolatkar (124118) Nehad M. Alajez (7397276) |
| author_role | author |
| dc.creator.none.fl_str_mv | Hibah Shaath (5599658) Radhakrishnan Vishnubalaji (3563306) Ramesh Elango (7542068) Ahmed Kardousha (17562654) Zeyaul Islam (5867387) Rizwan Qureshi (15279193) Tanvir Alam (638619) Prasanna R. Kolatkar (124118) Nehad M. Alajez (7397276) |
| dc.date.none.fl_str_mv | 2022-11-01T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1016/j.semcancer.2022.05.013 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Long_non-coding_RNA_and_RNA-binding_protein_interactions_in_cancer_Experimental_and_machine_learning_approaches/24745122 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Information and computing sciences Machine learning Long non-coding RNA LncRNA, RNA-binding protein RBP, lncRNA-protein interaction (LPI) Cancer Mechanisms of action Structural and functional domains Machine learning Deep learning |
| dc.title.none.fl_str_mv | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p>Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.</p><h2>Other Information</h2> <p> Published in: Seminars in Cancer Biology<br> License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.semcancer.2022.05.013" target="_blank">https://dx.doi.org/10.1016/j.semcancer.2022.05.013</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_c46661757e9eed20a4851be1592d35df |
| identifier_str_mv | 10.1016/j.semcancer.2022.05.013 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/24745122 |
| publishDate | 2022 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approachesHibah Shaath (5599658)Radhakrishnan Vishnubalaji (3563306)Ramesh Elango (7542068)Ahmed Kardousha (17562654)Zeyaul Islam (5867387)Rizwan Qureshi (15279193)Tanvir Alam (638619)Prasanna R. Kolatkar (124118)Nehad M. Alajez (7397276)Biological sciencesBiochemistry and cell biologyBioinformatics and computational biologyBiomedical and clinical sciencesOncology and carcinogenesisInformation and computing sciencesMachine learningLong non-coding RNALncRNA, RNA-binding proteinRBP, lncRNA-protein interaction (LPI)CancerMechanisms of actionStructural and functional domainsMachine learningDeep learning<p>Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.</p><h2>Other Information</h2> <p> Published in: Seminars in Cancer Biology<br> License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.semcancer.2022.05.013" target="_blank">https://dx.doi.org/10.1016/j.semcancer.2022.05.013</a></p>2022-11-01T00:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1016/j.semcancer.2022.05.013https://figshare.com/articles/journal_contribution/Long_non-coding_RNA_and_RNA-binding_protein_interactions_in_cancer_Experimental_and_machine_learning_approaches/24745122CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/247451222022-11-01T00:00:00Z |
| spellingShingle | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches Hibah Shaath (5599658) Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Information and computing sciences Machine learning Long non-coding RNA LncRNA, RNA-binding protein RBP, lncRNA-protein interaction (LPI) Cancer Mechanisms of action Structural and functional domains Machine learning Deep learning |
| status_str | publishedVersion |
| title | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| title_full | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| title_fullStr | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| title_full_unstemmed | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| title_short | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| title_sort | Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches |
| topic | Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Information and computing sciences Machine learning Long non-coding RNA LncRNA, RNA-binding protein RBP, lncRNA-protein interaction (LPI) Cancer Mechanisms of action Structural and functional domains Machine learning Deep learning |