Identification and Differential Abundance of Mitochondrial Genome Encoding Small RNAs (mitosRNA) in Breast Muscles of Modern Broilers and Unselected Chicken Breed

Abstract

Background: Although small non-coding RNAs are mostly encoded by the nuclear genome, thousands of small non-coding RNAs encoded by the mitochondrial genome, termed as mitosRNAs were recently reported in human, mouse and trout. In this study, we first identified chicken mitosRNAs in breast muscle using small RNA sequencing method and the differential abundance was analyzed between modern pedigree male (PeM) broilers (characterized by rapid growth and large muscle mass) and the foundational Barred Plymouth Rock (BPR) chickens (characterized by slow growth and small muscle mass).Methods: Small RNA sequencing was performed with total RNAs extracted from breast muscles of PeM and BPR (n = 6 per group) using the 1 × 50 bp single end read method of Illumina sequencing. Raw reads were processed by quality assessment, adapter trimming, and alignment to the chicken mitochondrial genome (GenBank Accession: X52392.1) using the NGen program. Further statistical analyses were performed using the JMP Genomics 8. Differentially expressed (DE) mitosRNAs between PeM and BPR were confirmed by quantitative PCR.Results: Totals of 183,416 unique small RNA sequences were identified as potential chicken mitosRNAs. After stringent filtering processes, 117 mitosRNAs showing >100 raw read counts were abundantly produced from all 37 mitochondrial genes (except D-loop region) and the length of mitosRNAs ranged from 22 to 46 nucleotides. Of those, abundance of 44 mitosRNAs were significantly altered in breast muscles of PeM compared to those of BPR: all mitosRNAs were higher in PeM breast except those produced from 16S-rRNA gene. Possibly, the higher mitosRNAs abundance in PeM breast may be due to a higher mitochondrial content compared to BPR. Our data demonstrate that in addition to 37 known mitochondrial genes, the mitochondrial genome also encodes abundant mitosRNAs, that may play an important regulatory role in muscle growth via mitochondrial gene expression control.

BOARD INVITED REVIEW: Oxidative stress and efficiency: the tightrope act of mitochondria in health and disease1,2

“…Global gene and protein expression analyses were conducted in muscle from high and low FE PedM broiler phenotypes to gain greater understanding of how the proteogenomic landscape might differ between the phenotypes: inherent differences or differences that resulted from ROS-mediated signal transduction (Kong et al, 2011(Kong et al, , 2016Bottje et al, 2017a). Additional FE-mitochondrial relationships were observed with the elevation of the mitoproteome in the high FE phenotype (Kong et al, 2016;Bottje et al, 2017a) that provided further evidence of a link between mitochondria and FE in this PedM broiler model.…”

“…Global gene and protein expression analyses were conducted in muscle from high and low FE PedM broiler phenotypes to gain greater understanding of how the proteogenomic landscape might differ between the phenotypes: inherent differences or differences that resulted from ROS-mediated signal transduction (Kong et al, 2011(Kong et al, , 2016Bottje et al, 2017a). Additional FE-mitochondrial relationships were observed with the elevation of the mitoproteome in the high FE phenotype (Kong et al, 2016;Bottje et al, 2017a) that provided further evidence of a link between mitochondria and FE in this PedM broiler model. The proteogenomic investigations also revealed evidence of enhanced expression of proteins requisite for ADP: ATP and creatine shuttles in the high FE mitochondria (Bottje et al, 2017b; see Figure 1), enrichment of ribosome assembly and protein translation components (Bottje et al, 2017c; see Figure 2), and enrichment of the autophagy and proteosomal pathways (Piekarski-Welsher et al, 2018; see Figures 3 and 4) in breast muscle of the high FE PedM broiler phenotype.…”

“…In a pedigree male (PedM) broiler model of feed efficiency (FE), an inextricable link between mitochondria and FE has been reported that includes lower electron transport chain (ETC) coupling with higher mitochondrial ROS production and protein oxidation in tissues obtained from animals exhibiting a low FE phenotype (Bottje et al, 2002;Iqbal et al, 2004Iqbal et al, , 2005Ojano-Dirain et al, 2004, 2005Bottje and Carsons 2009). The finding of higher ROS production in low FE spurred examination of the proteogenomic landscape of muscle associated with the phenotypic expression of FE in PedM broilers (e.g., Kong et al, 2011Kong et al, , 2016Bottje and Kong, 2013;Bottje et al, 2017a). Enrichment of autophagy and proteosome expression in the high FE phenotype muscle suggests that repair processes are enhanced in high FE (Piekarski-Welsher et al, 2018, see below).…”

The Living Dead: Mitochondria and Metabolic Arrest

“…For example, freeze‐responsive elevation of miR‐21 in wood frog liver and skeletal muscle suggests that its inhibition of the translation of caspase‐3, APAF1, and programmed cell death protein‐4 facilitates antiapoptotic protection during freezing . The term “mitomiR” describes a unique signature of miRNAs that localize to and are enriched in mitochondria of diverse species . Whether they are transcribed from mitochondrial genomes or simply imported/processed in mitochondria has yet to be elucidated.…”

MitosRNAs and extreme anoxia tolerance in embryos of the annual killifish Austrofundulus limnaeus

“…Post-ovulatory aging of the eggs resulted in decreased expression of the mitosRNAs. MitosRNAs are also present in chicken breast muscle, and results suggest they may play a role in muscle growth 15 . While these studies indicate that differential expression of mitosRNAs may play a role in growth and development, the study on anoxia tolerant annual killifish was the first to document mitosRNAs, many of which were derived from tRNAs, changing in abundance in response to stress 7 .…”