Insights into how environment shapes post-mortem RNA transcription in mouse brain

Abstract

Most biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

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“…This bias has been reported previously for poly(A)+ enrichment methods and is most likely caused by partially degraded transcripts particularly in samples with highly degraded RNA ( 14 ). RNA quality and integrity play a major role in sequencing experiments and are directly connected to sampling conditions, transportation, and storage ( 15 – 17 ). While we used qualified and robust methods for RNA extraction and preservation ( 18 ), the RNA preparations used for comparison of the different methods originated from brain tissues of two wild-trapped rodents that were sampled under suboptimal conditions.…”

An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model

“…Similar deficiencies can also persist during the large-scale amplification of extracts with low RNA quantities. Previous studies have also evinced organismal death and the post-mortem interval (PMI) as external factors that mediate alterations to tissue transcriptomes [43][44][45] . Conversely, previous research has challenged the alterations to RNA integrity following prolonged ischemia finding no correlation between RNA quality and the PMI in human skeletal muscle and colonic epithelial tissue 13,46 .…”

An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model

“…Similar deficiencies can also persist during the large-scale amplification of extracts with low RNA quantities. Previous studies have also evinced organismal death and the post-mortem interval (PMI) as external factors that mediate alterations to tissue transcriptomes 36–38 . Conversely, previous research has challenged the alterations to RNA integrity following prolonged ischemia finding no correlation between RNA quality and the PMI in human skeletal muscle 11 and colonic epithelial tissue 39 .…”

“…Similar deficiencies can also persist during the large-scale amplification of extracts with low RNA quantities. Previous studies have also evinced organismal death and the post-mortem interval (PMI) as external factors that mediate alterations to tissue transcriptomes [36][37][38] .…”