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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

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Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.

Martine Boccara¹, Alexis Sarazin², Bernard Billoud³

¹PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France. martine.boccara@upmc.fr.

Methods in Molecular Biology (Clifton, N.J.)

|October 23, 2016

Summary

This summary is machine-generated.

This study introduces a DNA tiling array method to analyze small noncoding RNA (sRNA) expression in plants. The technique effectively detects significant changes in sRNA populations following stress, offering a new tool for plant epigenetics research.

Keywords:

Cy-dye indirect labeling DNA tiling array Harpin protein Hypersensitive response Microarray Small RNA cDNA libraries

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RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

Area of Science:

Plant molecular biology
Epigenetics
Genomics

Background:

Plant stress responses involve epigenetic modifications, including changes in DNA methylation, histone modifications, and small noncoding RNA (sRNA) expression.
Understanding sRNA dynamics is crucial for deciphering plant adaptation mechanisms.

Purpose of the Study:

To present and validate a novel method for analyzing differential expression of sRNA populations using DNA tiling arrays.
To assess the utility of DNA tiling arrays in detecting stress-induced changes in sRNA abundance in Arabidopsis thaliana.

Main Methods:

Extraction of sRNA from Arabidopsis thaliana plants subjected to pathogen elicitor treatment or control conditions.
Reverse transcription of sRNA into cDNA, followed by labeling and hybridization to a custom DNA tiling array covering Arabidopsis chromosome 4.
Validation of hybridization signals using control cDNA clones and comparison with existing massive parallel sequence signature (MPSS) data.

Main Results:

The DNA tiling array method demonstrated robust and specific hybridization signals.
Hybridization signals generally agreed with previously determined sRNA abundance in untreated plants.
Substantial differences in hybridization signals were observed after stress treatment, indicating major changes in sRNA abundance.

Conclusions:

Hybridization to DNA tiling arrays is a viable and effective method for analyzing differential expression of sRNA populations.
This technique can detect significant alterations in sRNA abundance in response to environmental stress in plants.
The method provides a valuable tool for studying plant epigenetic responses to stress.