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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
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The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the
Luca Ducoli1,2, Saumya Agrawal3,4, Chung-Chau Hon3,4
1Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
BMC Genomic Data
|September 15, 2021
Summary
Investigating long noncoding RNAs (lncRNAs) in vascular biology requires careful selection of negative control antisense oligonucleotides (ASOs). Proper controls are crucial for accurate analysis of lncRNA knockdown effects on cell transcriptomes.
Area of Science:
- Vascular Biology
- Molecular Biology
- Genomics
Background:
- The lymphatic and blood vascular systems share developmental origins but have distinct adult functions regulated by lineage-specific programs.
- Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators of cell-type-specific gene expression.
Purpose of the Study:
- To investigate the role of lncRNAs in vascular endothelial cells (LECs and BECs).
- To establish quality control measures for antisense oligonucleotide (ASO) knockdown experiments in vascular biology.
Main Methods:
- Antisense oligonucleotide (ASO) knockdowns of candidate lncRNAs in human lymphatic endothelial cells (LECs) and blood vascular endothelial cells (BECs).
- Cap Analysis of Gene Expression (CAGE-Seq) to analyze transcriptomes after knockdown.
- Detailed quality control of the analysis pipeline, focusing on negative control ASO selection.
Main Results:
- The choice of negative control ASOs significantly impacts the interpretation of knockdown effects on LEC and BEC transcriptomes.
- Quality control steps are essential before assessing lncRNA knockdown effects.
Conclusions:
- Selecting appropriate, cell-type-specific negative control ASOs is critical for reliable lncRNA research in vascular biology.
- This study emphasizes the need for a robust control strategy in ASO-based gene regulation studies.
