Deep sequencing of small non-coding RNA highlights brain-specific expression patterns and RNA cleavage

Abstract

With the advance of high-throughput sequencing technology numerous new regulatory small RNAs have been identified, that broaden the variety of processing mechanisms and functions of non-coding RNA. Here we explore small non-coding RNA (sncRNA) expression in central parts of the physiological stress and anxiety response system. Therefore, we characterize the sncRNA profile of tissue samples from Amygdala, Hippocampus, Hypothalamus and Adrenal Gland, obtained from 20 pigs. Our analysis reveals that all tissues but Amygdala and Hippocampus possess distinct, tissue-specific expression pattern of miRNA that are associated with Hypoxia, stress responses as well as memory and fear conditioning. In particular, we observe marked differences in the expression profile of limbic tissues compared to those associated to the HPA/stress axis, with a surprisingly high aggregation of 3´-tRNA halves in Amygdala and Hippocampus. Since regulation of sncRNA and RNA cleavage plays a pivotal role in the central nervous system, our work provides seminal insights in the role/involvement of sncRNA in the transcriptional and post-transcriptional regulation of negative emotion, stress and coping behaviour in pigs, and mammals in general.

Expression of microRNAs in the hypothalamus of pregnant and non-pregnant goats

“…In the rat hypothalamus, let-7 family, miR-136, miR-125a, miR-138, miR-124a, miR-338, let-7c, miR-7a/b, and miR-212 expression levels were high (Amar et al 2012). Moreover, miR-16, miR-21, and miR-148a were the most abundant in the porcine hypothalamus (Haack et al 2019). Our data are consistent with the results on the enrichment of the miR-7 and let-7 families in mice and rats, both families were expressed in excess of 10 000 and were upregulated during pregnancy.…”

Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System

“…Tissue samples of porcine adrenal gland, amygdala, hippocampus and hypothalamus using microarray-based mRNA expression profiling as well as sncRNA deep sequencing from our previous studies were used for downstream analyses ( Gley et al, 2019a , b ; Haack et al, 2019 ). Discovered sncRNA structures mainly consisted of miRNA, Rrna, and tRNA, with additional low abundance RNA species including yRNA, piRNA as well as snoRNA.…”

“…In our previous study ( Haack et al, 2019 ), raw sncRNA deep sequencing datasets were converted to FASTQ format and submitted to ArrayExpress. It can be accessed at http://www.ebi.ac.uk/arrayexpress (accession number: E-MTAB-7499 ).…”

“…The produced reads are referred to as clean reads. The number of reads (in millions) and mapping statistics from all samples have been reported previously ( Haack et al, 2019 ). Briefly, in amygdala, hippocampus, hypothalamus, and adrenal gland, there are 101, 99, 139, and 59 M unique reads, respectively, with an average of 95% mapped reads in the porcine genome (Ssc11.1).…”

“…In our previous studies, we analyzed differential mRNA expression between two haplotypes in a coping behavior associated QTL region in the four tissue types adrenal gland, hypothalamus, amygdala and hippocampus ( Gley et al, 2019a , b ). In a further study, we used a deep sequencing approach to explore small non-coding RNA (sncRNA) expression in central parts of the physiological stress and anxiety response system in the same animals ( Haack et al, 2019 ). The non-coding fraction of the transcriptome consists of several types of RNA molecules which share the characteristic that they are not translated into a protein.…”