A Genome-Wide Investigation of Expression Characteristics of Natural Antisense Transcripts in Liver and Muscle Samples of Pigs
نویسندگان
چکیده
Natural antisense transcripts are endogenous transcripts that are complementary to the sense-strand of DNA. These transcripts have been identified in various eukaryotic species and are involved in a broad range of regulatory events and biological processes. However, their general biological functions, expression characteristics and regulatory mechanisms are still unclear. In this study, 497 liver and 586 muscle samples were harvested from a White Duroc×Erhualian F(2) resource population. The expression profiles of sense and antisense transcripts were determined by tag-based RNA sequencing. We identified 33.7% and 20.4% of transcripts having both sense and antisense expression, and 12.5% and 6.1% of transcripts only expressing antisense transcripts in liver and muscle, respectively. More than 32.2% of imprinting or predicted imprinting genes in the geneimprint database were detected with both sense and antisense expression. The correlations between sense and antisense expression in sense-antisense pairs were diverse in both liver and muscle, showing positive, negative or absent correlation. Antisense expression increases gene expression variability. More interestingly, compared to eQTL mapping of sense transcripts in which more than one eQTL was mapped for a transcript, only one eQTL was identified for each antisense transcript, and the percentage of cis-eQTL in antisense eQTL was higher than that in sense eQTL. This suggests that the expressions of antisense transcripts tend to be cis-regulated by a single genomic locus. To our knowledge, this study is the first systematical investigation of antisense transcription in pigs. The findings improve our understanding of the complexity of porcine transcriptome.
منابع مشابه
Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Feed efficiency (FE) is essential for pig production. In this study, 300 significantly differentially expressed (DE) transcripts, including 232 annotated genes, 28 cis- natural antisense transcripts (cis-NATs), and 40 lncRNAs, were identified between the liver of Yorkshire pigs with extremely high and low FE. Among these transcripts, 25 DE lncRNAs were significantly correlated with 125 DE annot...
متن کاملWRAP53 Polymorphism, rs2287498: A Case Study in Northwest of Iran?
Background: Non-coding RNAs apply regulations on expression or function of a gene. A class of non-coding RNAs, natural antisense transcripts, might overlap with their flanking genes and emerge a new complexity upon regulation. WRAP53, is a natural antisense transcript overlapped in a head-to-head manner on the opposite strand of TP53. It has 3 transcripts of which WRAP53β produ...
متن کاملC-Kit expression in the gallbladder of guinea pig with chronic calculous cholecystitis and the effect of Artemisia capillaris Thunb on interstitial cells of Cajal
Objective(s): To study the c-Kit expression in the gallbladder of cholesterol lithogenic guinea pig model and the effect of Artemisia capillaris Thunb on interstitial cells of Cajal (ICCs). Materials and Methods:A total of 45 guinea pigs were randomly assigned into three groups: the control group (guinea pigs fed a standard diet, normal group); the model group (guinea pigs fed a cholesterol gal...
متن کاملI-10: Transcriptomics in Oocyte Mediated Cellular Reprogramming
a:4:{s:10:"Background";s:1707:"Early embryonic development in mammals begins in transcriptional silence with an oocyte-mediated transcriptional reprogramming of parental gametes occurs during a so called across-the-board process of “erase-and-rebuild”. In this process, the parental transcription programs are erased long before (maternal) or soon thereafter (paternal) fertilization to generate a...
متن کاملCis-Natural Antisense Transcripts Are Mainly Co-expressed with Their Sense Transcripts and Primarily Related to Energy Metabolic Pathways during Muscle Development
Cis-natural antisense transcripts (cis-NATs) are a new class of RNAs identified in various species. However, the biological functions of cis-NATs are largely unknown. In this study, we investigated the transcriptional characteristics and functions of cis-NATs in the muscle tissue of lean Landrace and indigenous fatty Lantang pigs. In total, 3,306 cis-NATs of 2,469 annotated genes were identifie...
متن کامل