Why Does Insect RNA Look Degraded?

Abstract

The integrity of extracted ribonucleic acid (RNA) is commonly assessed by gel electrophoresis and subsequent analysis of the ribosomal RNA (rRNA) bands. Using the honey bee, Apis mellifera (Hymenoptera: Apidae), as an example, the electrophoretic rRNA profile of insects is explained. This profile differs significantly from the standard benchmark since the 28S rRNA of most insects contains an endogenous “hidden break.” Upon denaturation, the masking hydrogen bonds are disrupted, releasing two similar sized fragments that both migrate closely with 18S rRNA. The resulting rRNA profile thus reflects the endogenous composition of insect rRNA and should not be misinterpreted as degradation.

High-quality RNA extraction from copepods for Next Generation Sequencing: A comparative study

“…2). A similar lack of a 28S rRNA peak was recently reported in the insect Apis mellifera (Winnebeck et al, 2010), the crustacean Artemia parthenogenetica and the planarian Dugesia japonica (Sun et al, 2012), and was related to the 'hidden break' present in protostome 28S rRNA (Ishikawa, 1977). Upon heat-denaturation, the two fragments of 28S rRNA separate and migrate with the 18S rRNA (Winnebeck et al, 2010).…”

Validation of reference genes in leaf-cutting ant Atta sexdens rubropilosa in different developmental stages and tissues

“…1). As previously described for insects [34], only one intense RNA band can be seen in the denaturing gel, which corresponds to the two fragments of the 28S rRNA that co-migrate with 18S rRNA. The RNA extracted from worker and from gaster using the Trizol method was degraded.…”

Virus Status, Varroa Levels, and Survival of 20 Managed Honey Bee Colonies Monitored in Luxembourg Between the Summer of 2011 and the Spring of 2013

“…Two aliquots of RNA were quantified using a Nanodrop ND1000 spectrophotometer (Thermo Scientific), measuring the absorbance at 230 nm, 260 nm and 280 nm. Quality was assessed using the RNA Nano 6000 assay on the Bioanalyzer 2100 (Agilent Technologies) RNA chip comparing profiles to previously defined standards (Winnebeck et al, 2010). RNA was then stored at -80°C until use in rt-PCR.…”