MicroRNA Assisted Gene Regulation in Colorectal Cancer
Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulatio...
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| Veröffentlicht in: | International journal of molecular sciences 2019-10, Vol.20 (19), p.4899 |
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| description | Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC. |
| doi_str_mv | 10.3390/ijms20194899 |
| format | Article |
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Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms20194899</identifier><identifier>PMID: 31623294</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Cancer ; Cell Line, Tumor ; Chemical bonds ; Colorectal cancer ; Colorectal carcinoma ; Colorectal Neoplasms - genetics ; Computational Biology - methods ; Disease ; Gene expression ; Gene Expression Regulation, Neoplastic ; Gene regulation ; Gene Regulatory Networks ; Gene Silencing ; Humans ; Hydrogen Bonding ; Ligands ; MicroRNAs ; MicroRNAs - chemistry ; MicroRNAs - genetics ; miRNA ; Models, Molecular ; Molecular docking ; Molecular Sequence Annotation ; mRNA ; Non-coding RNA ; Nucleic Acid Conformation ; Protein Binding ; Proteins ; Public health ; RNA Interference ; RNA, Messenger - chemistry ; RNA, Messenger - genetics ; RNA-Binding Proteins - metabolism ; RNA-mediated interference ; Target recognition</subject><ispartof>International journal of molecular sciences, 2019-10, Vol.20 (19), p.4899</ispartof><rights>2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). 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Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. 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Pretorius, Ashley ; Klein, Ashwil</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-fafca6a32dbd76f67336a4220b2bb995df0e03e295960fecf731e1055002bbf83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Cancer</topic><topic>Cell Line, Tumor</topic><topic>Chemical bonds</topic><topic>Colorectal cancer</topic><topic>Colorectal carcinoma</topic><topic>Colorectal Neoplasms - genetics</topic><topic>Computational Biology - methods</topic><topic>Disease</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Gene regulation</topic><topic>Gene Regulatory Networks</topic><topic>Gene Silencing</topic><topic>Humans</topic><topic>Hydrogen Bonding</topic><topic>Ligands</topic><topic>MicroRNAs</topic><topic>MicroRNAs - chemistry</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Models, Molecular</topic><topic>Molecular docking</topic><topic>Molecular Sequence Annotation</topic><topic>mRNA</topic><topic>Non-coding RNA</topic><topic>Nucleic Acid Conformation</topic><topic>Protein Binding</topic><topic>Proteins</topic><topic>Public health</topic><topic>RNA Interference</topic><topic>RNA, Messenger - chemistry</topic><topic>RNA, Messenger - genetics</topic><topic>RNA-Binding Proteins - metabolism</topic><topic>RNA-mediated interference</topic><topic>Target recognition</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fadaka, Adewale O</creatorcontrib><creatorcontrib>Pretorius, Ashley</creatorcontrib><creatorcontrib>Klein, Ashwil</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection (Proquest)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>ProQuest research library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fadaka, Adewale O</au><au>Pretorius, Ashley</au><au>Klein, Ashwil</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MicroRNA Assisted Gene Regulation in Colorectal Cancer</atitle><jtitle>International journal of molecular sciences</jtitle><addtitle>Int J Mol Sci</addtitle><date>2019-10-03</date><risdate>2019</risdate><volume>20</volume><issue>19</issue><spage>4899</spage><pages>4899-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>31623294</pmid><doi>10.3390/ijms20194899</doi><orcidid>https://orcid.org/0000-0002-3952-2098</orcidid><orcidid>https://orcid.org/0000-0002-5606-886X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Cancer Cell Line, Tumor Chemical bonds Colorectal cancer Colorectal carcinoma Colorectal Neoplasms - genetics Computational Biology - methods Disease Gene expression Gene Expression Regulation, Neoplastic Gene regulation Gene Regulatory Networks Gene Silencing Humans Hydrogen Bonding Ligands MicroRNAs MicroRNAs - chemistry MicroRNAs - genetics miRNA Models, Molecular Molecular docking Molecular Sequence Annotation mRNA Non-coding RNA Nucleic Acid Conformation Protein Binding Proteins Public health RNA Interference RNA, Messenger - chemistry RNA, Messenger - genetics RNA-Binding Proteins - metabolism RNA-mediated interference Target recognition |
| title | MicroRNA Assisted Gene Regulation in Colorectal Cancer |
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