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09:36
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
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Functional annotation of human long noncoding RNAs via molecular phenotyping.
Jordan A Ramilowski1,2, Chi Wai Yip1,2, Saumya Agrawal1,2
1RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Genome Research
|July 29, 2020
Summary
This study systematically knocked down long noncoding RNAs (lncRNAs) in human cells, revealing their functions and creating a large dataset for future research on gene expression and cellular phenotypes.
Area of Science:
- Genomics
- Molecular Biology
- Cell Biology
Background:
- Long noncoding RNAs (lncRNAs) are abundant transcripts in mammalian genomes, but their functions are largely uncharacterized.
- Understanding lncRNA function is crucial for deciphering complex biological processes.
Purpose of the Study:
- To systematically investigate the functional roles of 285 lncRNAs in human dermal fibroblasts.
- To generate a comprehensive dataset of lncRNA knockdown effects on cellular phenotypes and transcriptomic responses.
Main Methods:
- Systematic knockdown of 285 lncRNAs using antisense oligonucleotides in human dermal fibroblasts.
- Quantification of cellular growth and morphology.
- Transcriptomic profiling using Capped Analysis of Gene Expression (CAGE).
Main Results:
- lncRNA knockdown led to observable changes in cellular growth and morphology.
- CAGE-based molecular phenotyping correlated with cellular phenotypes and identified affected genes and pathways.
- A large dataset of over 1000 CAGE libraries from lncRNA knockdown experiments was generated.
- Functional roles for specific lncRNAs, ZNF213-AS1 and lnc-KHDC3L-2, were highlighted.
Conclusions:
- This study provides the largest dataset to date for lncRNA knockdown and molecular phenotyping.
- The findings offer insights into the functional significance of lncRNAs in cellular processes.
- The generated data serves as a valuable resource for future research in lncRNA biology.
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