Northern blotting of endogenous full-length human-specific LINE-1 RNA

TL;DR

This paper introduces a method to detect active LINE-1 RNA in humans using northern blotting with RNA probes.

Contribution

The novel contribution is an optimized method for detecting endogenous full-length LINE-1 RNA using RNA probes.

Findings

A classical long RNA probe can detect active LINE-1 RNA effectively.

Multiple short RNA probes offer an alternative detection method.

Optimized conditions make LINE-1 RNA detection practical.

Abstract

LINE-1 belongs to a family of DNA elements that move to new locations in the genome in a process called “retrotransposition.” This is achieved by a copy-and-paste mechanism with the aid of an RNA intermediate. The full-length LINE-1 is responsible for most retrotransposition activity in the human genome. Detecting the active LINE-1 RNA at the endogenous level is challenging due to its small percentage among inactive copies and its different forms of transcripts. Here, we describe a method of designing RNA probes to detect active LINE-1 by northern blotting and use optimized conditions and tools to make the detection practical. This method uses a classical long RNA probe and provides an alternative way to detect LINE-1 RNA using multiple short RNA probes.

Graphical Abstract

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