Botany JoVE (Open Access) Citable · DOI

In Situ Hybridization for the Precise Localization of Transcripts in Plants

Name: In Situ Hybridization for the Precise Localization of Transcripts in Plants
Uploaded: 2026-07-13
Duration: 12 min 15 s
Description: With the advances in genomics research of the past decade, plant biology has seen numerous studies presenting large-scale quantitative analyses of gene ...

DOI: 10.3791/3328-v

What you'll learn

✓ Prepare paraffin-embedded plant tissue sections for in situ hybridization
✓ Perform in situ hybridization to localize mRNA and small RNA transcripts
✓ Apply post-hybridization treatments and interpret fluorescent/chromogenic results
✓ Adapt protocol across diverse plant species and tissue types

Protocol

Biopharma Insights The in situ hybridization protocol described here allows a direct localization of mRNA and small RNA expression at the cellular level with high sensitivity and specificity. The procedure is optimized for paraffin-embedded plant tissue sections, is applicable to a wide range of plants and tissues, and can be completed within ten days.

Difficulty

intermediate

Total time

~10 days (including embedding and sectioning steps)

Steps

Embed plant tissue in paraffin blocks

Prepare and embed plant tissue samples in paraffin wax to create blocks suitable for sectioning. This foundational step preserves tissue architecture for downstream hybridization.

▶ 01:42

Section embedded tissue blocks

Cut serial sections from paraffin-embedded plant tissue blocks using a microtome and mount sections on glass slides for in situ hybridization.

▶ 02:36

Perform in situ hybridization with probes

Apply labeled RNA or DNA probes to tissue sections to hybridize with target mRNA or small RNA transcripts at the cellular level.

▶ 04:14

Treat slides post-hybridization

Perform washing and post-hybridization treatments to remove non-specifically bound probes and enhance signal-to-background ratio before visualization.

▶ 06:30

Visualize and document hybridization results

Examine slides under fluorescence or brightfield microscopy to locate transcripts and capture representative images showing spatial expression patterns at cellular resolution.

▶ 08:27

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