Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle

Ruslan Deviatiiarov,Genshiro A Sunagawa,Masayo Takahashi,Guzel Gazizova,Oleg Gusev,Takaya Abe,Hiroshi Kiyonari,Kiyomi Ishikawa

doi:10.1038/s42003-021-02819-2

Abstract

Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. During torpor, the oxygen consumption rate in some animals drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the gene expression landscape on the level of the RNA transcription start sites in mouse skeletal muscles under various metabolic states to identify torpor-specific transcribed regulatory patterns. We analyzed the soleus muscles from 38 mice in torpid and non-torpid conditions and identified 287 torpor-specific promoters out of 12,862 detected promoters. Furthermore, we found that the transcription factor ATF3 is highly expressed during torpor deprivation and its binding motif is enriched in torpor-specific promoters. Atf3 was also highly expressed in the heart and brown adipose tissue during torpor and systemically knocking out Atf3 affected the torpor phenotype. Our results demonstrate that mouse torpor combined with powerful genetic tools is useful for studying active hypometabolism.

Highlights

Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature
Based on the transcription start sites (TSS) distribution, we identified 12,862 total peak clusters, reflecting genome-wide expression profile on promoters’ level with single-nucleotide precision
We found that transcription factor ATF3, one of the torporspecific genes at the soleus muscle, is highly expressed during torpor deprivation

Summary

Introduction

Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. Sunagawa proposed four conditions to be required in mammalian active hypometabolism:4 1) tolerance to low body temperature, 2) tolerance to low oxygen consumption, 3) suppression of body temperature homeostasis, and 4) heat production ability under a low metabolic rate Of these conditions, 1) and 2) were found to be cell/tissue-specific or local functions, which prompted researchers to analyze genome-wide molecular changes in various tissues of hibernators, including the brain, liver, heart, skeletal muscles, and adipose tissues. One group identified neurons regulating the induction of FIT22, and our group identified genetically labeled neurons that can induce a hibernationlike state in mice[23] Such recent discoveries make the mouse a suitable and convenient animal model for studying active hypometabolism. We present evidence that the torpor-specific promoters are related to the torpor phenotype by deleting the gene

Objectives

Methods

Results

Conclusion