Annotation of novel transcripts putatively relevant for bovine fat metabolism

Abstract

Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal muscle containing different amount of intramuscular fat in a pilot screening experiment. However, for both loci any role in the regulation of energy or fat metabolism is not yet described. In this study, we validated and refined gene structure, screened for mRNA splice variants and analyzed the tissue-specific gene expression patterns of both loci as a prerequisite to elucidate their potential physiological function. Based on comparative sequence analysis, a new full-length gene model for the bovine IRAK1 gene was developed and confirmed experimentally. Expression of IRAK1 mRNA was found in a variety of tissues, and a splice variant was identified in skeletal muscle caused by an in-frame deleted segment of 210 bp affecting regions of intrinsic disorder in the respective protein. For the locus LOC618944, our data contributed to a revised gene model and its assignment to BTA23 (bovine chromosome 23) on the current bovine genome assembly supported by comparative similarity analysis between the bovine and human genomes and experimental data. Furthermore, we identified several splice variants in mammary gland, fat and skeletal muscle tissue and detected a highly similar processed pseudogene on BTA26. All transcript variants of LOC618944 detected in the analyzed tissues represent noncoding RNAs. For both loci, our results suggest yet undetected physiological functions in tissues relevant for fat or energy metabolism in cattle.

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip

“…We found IRAK3 to be one identified candidate gene in a QTL locus associated with intramuscular fat levels. In cattle, the interleukin-1 receptor-associated kinase 1 ( IRAK1 ) gene has been found to be differentially expressed in skeletal muscle samples containing different amounts of intramuscular fat, but the underlying mechanistic link remains uncertain [86]. The IRAK3 gene, which shares substantial homology with IRAK1 , may therefore also participate in yak intramuscular fat deposition, making it a viable candidate gene for future studies aimed at improving meat quality.…”

Genomic structure of nucleotide diversity among Lyon rat models of metabolic syndrome

“…The bovine ortholog of RGD1562963 falls within bovine QTL223, involving in beef marbling, i.e. the deposition of fat in bovine muscles [38, 39]. This gene contains three non-synonymous SNPs in LH, albeit the prediction software categorized as the variants as being “benign.” Amphiphysin ( Amph) is a gene in haplotype block 7 with a nonsynonymous mutation causing a R632L amino acid change that is categorized as “benign” by PolyPhen2 in the LH rat .…”

Gene expression phenotypes for lipid metabolism and intramuscular fat in skeletal muscle of cattle1

“…The expression of many genes or their products in muscle has been reported to be positively correlated with IMF% or marbling in cattle: ADIPOQ, SCD, and THRSP (Wang et al, 2009b), G6PD and leptin (LEP; Graugnard et al, 2009), FABP4 (Lee et al, 2008;Pickworth et al, 2011), ADAM metallopeptidase with thrombospondin type 1 motif, 4 (ADAMTS4), and transforming growth factor, β 1 (TGFB1; Lee et al, 2010), coiled-coil domain containing 3 (CCDC3; Eberlein et al, 2010), IL-1 receptor-associated kinase 1 (IRAK1; Eberlein et al, 2011), CEBPA and PPARG (Kim et al, 2011;, delta-like 1 homolog (DLK1; Pickworth et al, 2011), runt-related transcription factor 1; translocated to 1 (cyclin D-related; RUNX1T1; Lim et al, 2011), GPAM, ACACA, FASN, LPL, CD36 molecule (thrombospondin receptor), solute carrier family 27 (fatty acid transporter) member 1 [SLC27A1, also known as (aka) FATP1], 1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, α; AGPAT1), diacylglycerol O-acyltransferase 1 (DGAT1), and DGAT2 (Jeong et al, 2012). An additional set of genes has been shown to be negatively correlated with IMF% or marbling, including titin (TTN), nebulin (NEB; Lee et al, 2008), calcium/calmodulin-dependent protein kinase II α (CAMK2A; Lee et al, 2008;Lim et al, 2011), retinoid X receptor α (RXRA; Lim et al, 2011), heat shock 27 kDa protein 1 (HSPB1), TNF receptor superfamily member 6 (FAS), angiotensinogen [serpin peptidase inhibitor clade A member 8 (AGT); Kim et al, 2011], patatin-like phospholipase domain containing 2 (PNPLA2, aka ATGL), monoglyceride lipase (MGLL, aka MGL), acyl-CoA dehydrogenase very long chain (ACADVL, aka VLCAD), and acyl-CoA dehydrogenase C-4 to C-12 straight chain (ACADM, aka MCAD; Jeong et al, 2012).…”