MicroRNA profiling of ileum of Japanese quails differing in their Phosphorus utilization
ABSTRACT: MicroRNAs, a class of small non-coding RNAs, play an important role as gene regulators in an array of biological pathways and physiological functions across animal species including Japanese quails. In this study, we profiled and cataloged microRNAs derived from ileum mucosa of Japanese quails with different Phosphorus (P) utility. The aims of this study were to identify differentially expressed miRNAs between high- and low-P utilization groups and to determine candidate microRNAs, target genes and pathways related to P utility in Quail.
Project description:Phosphorus (P) is essential for metabolism and homeostasis of living organisms. However, a major source of P in animal feed comes in a form of inositol phosphate (InsPx) which is inefficiently used by monogastrics animals due to an intrinsic minimal activity of endogenous phytase. This study aims to understand molecular mechanisms of P utilization in quails using an mRNA-Seq analysis of high- and low-P utilization quails selected from discordant sib pairs from different families. The results of differentially expressed genes and pathways related to P utility should serve as an important knowledge for field applications aiming to improve P utility in animal production and to reduce source of P pollution into environment.
Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder. Small RNAs were sequenced from metamorphosis stages of Japanese flounder
Project description:MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are not known to function in other posttranscriptional regulatory pathways or to affect smRNA levels. Here, we show that the P-body/decapping protein DCP5 is required for miRNA-mediated translational repression but not cleavage, and to regulate the transcription of specific miRNAs. We find that this protein also affects the abundance of tRNA-derived smRNAs. Significantly, DCP5 is required for the transcriptional silencing and DNA methylation of numerous transposable/repetitive elements and imprinted genes, indicating that it is a novel component of the RNA-directed DNA methylation pathway. Our results demonstrate that DCP5 and likely the P-body itself are required for multiple smRNA-mediated silencing pathways and provide the first evidence for the spatial separation of translational inhibition and cleavage by miRNAs. small RNA (smRNA) expression comparison between wildtype (Col-0) and dcp5 mutant plants in Arabidopsis
Project description:24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to produce primary transcripts that serve as precursors to siRNAs. Yet, no such transcripts have ever been reported. Here, through RNA sequencing and double-stranded RNA sequencing in genotypes that compromise the dicing of siRNA precursors, we were able to identify Pol IV-dependent transcripts from tens of thousands of loci. We show that Pol IV-dependent transcripts correspond to both DNA strands, while the Pol II-dependent transcripts produced upon de-repression of the loci are derived from primarily one strand. We show that Pol IV-dependent transcripts have a 5’ monophosphate, lack a polyA tail at the 3’ end, and contain no introns; these features distinguish them from Pol II-dependent transcripts. Moreover, RDR2 is shown to play similar roles with Pol IV in both the abundance of siRNA precursors and siRNAs as well as the CHH DNA methylation. The decreased CHH methylation at dcl234 can inhibit the transcription of Pol IV at DRM2-target sites. Finally, the regulations of siRNA biogenesis were explored. To detect siRNA precursors transcribed by RNA polymerase IV, the genome wide profiling of RNA were carried out at dcl234 and dcl234 nrpd1. Different types of RNA (including Total RNA, polyA+ RNA, polyA- RNA, double stranded RNA) libraries were built to detect different transcripts. RDR2 is a RNA-dependent RNA polymerase in Pol IV complex, so the RNA-seq libraries with the mutation of RDR2 were also built. In addition, smRNA libraries with mutations blocking siRNA biogenesis were also built
Project description:We examine the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. We profiled two technically replicated FFPE specimens on both DASL and RNA-seq. This submission represents the RNA-seq component of study. The DASL samples used in the study are GSM876557, GSM876558, GSM876564, and GSM876565.
Project description:Skeletal muscle degenerates progressively, loses mass (sarcopenia) along in years, and leads to reduced physical ability, often causing secondary diseases such as diabetes and obesity. It is known that regulation of gene expression by microRNAs is a key event in muscle development and disease. To understand genome-wide changes in microRNAs and mRNAs during muscle aging, we sequenced microRNAs as well as mRNAs from mouse gastrocnemius muscles at two different ages (6 versus 24-month-old). Thirty-four microRNAs (15 up-regulated and 19 down-regulated) were differentially expressed with age among which were microRNAs such as miR-206 or -434 which were differentially expressed in aged muscle in previous studies. Interestingly, seven microRNAs in a microRNA cluster at imprinted Dlk1-Dio3 locus on chromosome 12 were coordinately down-regulated. In addition, sixteen novel microRNAs were identified. Integrative analysis of microRNA and mRNA expression revealed that microRNAs contribute to muscle aging possibly through the positive regulation of transcription, metabolic process, and kinase activity. Many of the age-related microRNAs were implicated in human muscular diseases. We suggest that genome-wide microRNA profiling helps to expand our knowledge of microRNA function in the muscle aging process. miRNA profiles of gastrocnemius muscle tissues (n=10) were generated by deep sequencing using Illumina Hiseq-2000
Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes. Eighteen mRNA-seq samples, five smRNA-seq samples, five bisulfite-seq samples, twenty ChIP-seq samples. Bisulfite-seq data for cmt2-7 single mutants, cmt3 single mutants, drm1/2 double mutants, drm1/2 cmt3 triple mutants are deposited in GSE39901. Processed wiggle format files for all datasets can be downloaded at http://genomes.mcdb.ucla.edu/AthBSseq/
Project description:C/EBPalpha is an important myeloid transcription factor that is inactivated in approximately 50% of acute myeloid leukemia cases. We were interested in microRNAs that are regulated by C/EBPalpha during myeloid differentiation. We induced K562-C/EBPalpha-ER cells for 6 hours with 5µM ß-estradiol or ethanol as control. NGS was performed out of 3 independent experiments.
Project description:We used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation, Three sterile female japanese flounders were control samples and three fertile ones were references samples
Project description:We undertook an integrative technological approach to compare miRNA detection capability of three high-throughput commercial platforms. We artificially introduced human precursor, 2’-O-methyl modified and mature spiked-in miRNAs in a controlled fashion into native human placenta total RNA.