Small molecule quercetin binds MALAT1 triplex and modulates its cellular function
The triple-helix structure at the 3′ end of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, has been considered to be a target for modulating the oncogenic functions of MALAT1. This study examines the binding of quercetin—a known triplex binding molecule—to th...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Molecular Therapy: Nucleic Acids |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253122002591 |
| _version_ | 1798021823006244864 |
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| author | Isha Rakheja Asgar Hussain Ansari Arjun Ray Dheeraj Chandra Joshi Souvik Maiti |
| author_facet | Isha Rakheja Asgar Hussain Ansari Arjun Ray Dheeraj Chandra Joshi Souvik Maiti |
| author_sort | Isha Rakheja |
| collection | DOAJ |
| description | The triple-helix structure at the 3′ end of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, has been considered to be a target for modulating the oncogenic functions of MALAT1. This study examines the binding of quercetin—a known triplex binding molecule—to the MALAT1 triplex. By employing UV-visible spectroscopy, circular dichroism spectroscopy, and isothermal titration calorimetry, we observed that quercetin binds to the MALAT1 triplex with a stoichiometry of 1:1 and Kd of 495 ± 61 nM, along with a negative change in free energy, indicating a spontaneous interaction. Employing real-time PCR measurements, we observed around 50% downregulation of MALAT1 transcript levels in MCF7 cells, and fluorescence in situ hybridization (FISH) experiments showed concomitantly reduced levels of MALAT1 in nuclear speckles. This interaction is likely a result of a direct interaction between the molecule and the RNA, as indicated by a transcription-stop experiment. Further, transcriptome-wide analysis of alternative splicing changes induced by quercetin revealed modulation of MALAT1 downstream genes. Collectively, our study shows that quercetin strongly binds to the MALAT1 triplex and modulates its functions. It can thus be used as a scaffold for further development of therapeutics or as a chemical tool to understand MALAT1 functions. |
| first_indexed | 2024-04-11T17:19:44Z |
| format | Article |
| id | doaj.art-fe1f09b2321645b9af2489e0533c2795 |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-04-11T17:19:44Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-fe1f09b2321645b9af2489e0533c27952022-12-22T04:12:31ZengElsevierMolecular Therapy: Nucleic Acids2162-25312022-12-0130241256Small molecule quercetin binds MALAT1 triplex and modulates its cellular functionIsha Rakheja0Asgar Hussain Ansari1Arjun Ray2Dheeraj Chandra Joshi3Souvik Maiti4Chemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, IndiaChemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, IndiaDepartment of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Industrial Estate, Phase III, New Delhi 110020, IndiaChemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, IndiaChemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India; Institute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research-NCL, Pune 411008, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India; Corresponding author Souvik Maiti, Chemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India.The triple-helix structure at the 3′ end of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, has been considered to be a target for modulating the oncogenic functions of MALAT1. This study examines the binding of quercetin—a known triplex binding molecule—to the MALAT1 triplex. By employing UV-visible spectroscopy, circular dichroism spectroscopy, and isothermal titration calorimetry, we observed that quercetin binds to the MALAT1 triplex with a stoichiometry of 1:1 and Kd of 495 ± 61 nM, along with a negative change in free energy, indicating a spontaneous interaction. Employing real-time PCR measurements, we observed around 50% downregulation of MALAT1 transcript levels in MCF7 cells, and fluorescence in situ hybridization (FISH) experiments showed concomitantly reduced levels of MALAT1 in nuclear speckles. This interaction is likely a result of a direct interaction between the molecule and the RNA, as indicated by a transcription-stop experiment. Further, transcriptome-wide analysis of alternative splicing changes induced by quercetin revealed modulation of MALAT1 downstream genes. Collectively, our study shows that quercetin strongly binds to the MALAT1 triplex and modulates its functions. It can thus be used as a scaffold for further development of therapeutics or as a chemical tool to understand MALAT1 functions.http://www.sciencedirect.com/science/article/pii/S2162253122002591MT: Oligonucleotides: Therapies and ApplicationsMALAT1triple helixquercetinsmall-molecule bindingisothermal titration calorimetry |
| spellingShingle | Isha Rakheja Asgar Hussain Ansari Arjun Ray Dheeraj Chandra Joshi Souvik Maiti Small molecule quercetin binds MALAT1 triplex and modulates its cellular function Molecular Therapy: Nucleic Acids MT: Oligonucleotides: Therapies and Applications MALAT1 triple helix quercetin small-molecule binding isothermal titration calorimetry |
| title | Small molecule quercetin binds MALAT1 triplex and modulates its cellular function |
| title_full | Small molecule quercetin binds MALAT1 triplex and modulates its cellular function |
| title_fullStr | Small molecule quercetin binds MALAT1 triplex and modulates its cellular function |
| title_full_unstemmed | Small molecule quercetin binds MALAT1 triplex and modulates its cellular function |
| title_short | Small molecule quercetin binds MALAT1 triplex and modulates its cellular function |
| title_sort | small molecule quercetin binds malat1 triplex and modulates its cellular function |
| topic | MT: Oligonucleotides: Therapies and Applications MALAT1 triple helix quercetin small-molecule binding isothermal titration calorimetry |
| url | http://www.sciencedirect.com/science/article/pii/S2162253122002591 |
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