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van Emmerik CL, Lobbia V, Neefjes J, Nelissen FHT, van Ingen H. Monitoring Anthracycline Cancer Drug-Nucleosome Interaction by NMR Using a Specific Isotope Labeling Approach for Nucleosomal DNA. Chembiochem 2024; 25:e202400111. [PMID: 38476018 DOI: 10.1002/cbic.202400111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/03/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Chromatinized DNA is targeted by proteins and small molecules to regulate chromatin function. For example, anthracycline cancer drugs evict nucleosomes in a mechanism that is still poorly understood. We here developed a flexible method for specific isotope labeling of nucleosomal DNA enabling NMR studies of such nucleosome interactions. We describe the synthesis of segmental one-strand 13C-thymidine labeled 601-DNA, the assignment of the methyl signals, and demonstrate its use to observe site-specific binding to the nucleosome by aclarubicin, an anthracycline cancer drug that intercalates into the DNA minor grooves. Our results highlight intrinsic conformational heterogeneity in the 601 DNA sequence and show that aclarubicin binds an exposed AT-rich region near the DNA end. Overall, our data point to a model where the drug invades the nucleosome from the terminal ends inward, eventually resulting in histone eviction and nucleosome disruption.
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Affiliation(s)
- Clara L van Emmerik
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vincenzo Lobbia
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jacques Neefjes
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC, Leiden, The Netherlands
| | - Frank H T Nelissen
- Biophysical Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Ma S, Howden SA, Keane SC. Use of steric blocking antisense oligonucleotides for the targeted inhibition of junction containing precursor microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588531. [PMID: 38645194 PMCID: PMC11030329 DOI: 10.1101/2024.04.08.588531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antisense oligonucleotides (ASOs) are widely used as therapeutics for neurodegenerative diseases, cancers, and virus infections. One class of ASOs functions to enhance protein expression by sequestering the mature microRNA (miRNA) in a double-stranded structure within the RNA-induced silencing complex (RISC). An alternative approach for the targeted control of gene expression is to use ASOs that bind to the pre-elements of miRNAs (pre-miRNAs) and modulate their enzymatic processing. Here, we demonstrate that ASOs can be used to disrupt a specific structural feature, "junction," within pre-miR-31 that is important in directing efficient processing by the Dicer/TRBP complex. Furthermore, we extend and validate this strategy to pre-miR-144, which has a similar junction-dependent structure-function relationship. We found that a significant number of human pre-miRNAs are predicted to contain junctions, and validated our ASO approach on several members of this group. Importantly, we also verified the application of junction-targeting ASOs for the specific inhibition of pre-miRNA processing in cell . Our study reemphasizes the important roles of RNA structure in regulating Dicer/TRBP processing of pre-miRNAs and provides the framework to develop structure-informed ASOs that serve to inhibit miRNA production.
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Dadhwal G, Samy H, Bouvette J, El-Azzouzi F, Dagenais P, Legault P. Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications. Cell Mol Life Sci 2024; 81:53. [PMID: 38261114 PMCID: PMC10806991 DOI: 10.1007/s00018-023-05090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'-mono-uridylation, and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rates. Thus, this study extends current knowledge regarding the broad substrate specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.
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Affiliation(s)
- Gunjan Dadhwal
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Hebatallah Samy
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Jonathan Bouvette
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Molecular Biology Department, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Fatima El-Azzouzi
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Biochemistry Department, Wake Forest Biotech Place, 575 Patterson Avenue, Winston-Salem, NC, 27101, USA
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada.
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