Small molecule quercetin binds MALAT1 triplex and modulates its cellular function

Isha Rakheja; Asgar Hussain Ansari; Arjun Ray; Dheeraj Chandra Joshi; Souvik Maiti

doi:10.1016/j.omtn.2022.09.016

Small molecule quercetin binds MALAT1 triplex and modulates its cellular function

Mol Ther Nucleic Acids. 2022 Sep 23:30:241-256. doi: 10.1016/j.omtn.2022.09.016. eCollection 2022 Dec 13.

Authors

Isha Rakheja^{1

2}, Asgar Hussain Ansari^{1

2}, Arjun Ray³, Dheeraj Chandra Joshi^{1

2}, Souvik Maiti^{1

4

2}

Affiliations

¹ Chemical and Systems Biology Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India.
² Academy of Scientific & Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India.
³ Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Industrial Estate, Phase III, New Delhi 110020, India.
⁴ Institute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research-NCL, Pune 411008, India.

Abstract

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 K _d 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.

Keywords: MALAT1; MT: Oligonucleotides: Therapies and Applications; RNA FISH; in silico docking; isothermal titration calorimetry; quercetin; small-molecule binding; triple helix.