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Toxicogenomics
Published in Frank A. Barile, Barile’s Clinical Toxicology, 2019
Anirudh J. Chintalapati, Zacharoula Konsoula, Barile Frank A.
Genome-wide analysis in eukaryotes reveals a very small amount, 1 to 2%, of the transcribed genome to be functionally active, encoding proteins essential for regulating biological processes; the transcribed, non-protein-coding segment of DNA is referred to as junk DNA, and its nontranslatable product is labeled noncoding RNA. microRNAs (miRNAs), small nucleolar RNAs (snoRNAs), transcribed ultraconserved regions (T-UCRs), PIWI-interacting RNAs (piRNAs), and a diverse group of long noncoding RNAs (lncRNAs) have been discovered, which differentially target and modulate genomic transcription and translation. miRNAs specifically target and bind to functional mRNA, which leads to posttranscriptional gene silencing and suppression of translation. lncRNAs are postulated to recruit chromatin remodeling complexes to specific gene loci, resulting in progressive transcriptional manipulation.
Introduction to Molecular Biology
Published in Martin G. Pomper, Juri G. Gelovani, Benjamin Tsui, Kathleen Gabrielson, Richard Wahl, S. Sam Gambhir, Jeff Bulte, Raymond Gibson, William C. Eckelman, Molecular Imaging in Oncology, 2008
Small nucleolar RNAs (snoRNA) are a large group of snRNAs located in the nucleus and the cajal bodies of eukaryotic cells. These are small RNA molecules that play an essential role in RNA biogenesis, particularly in ribosome formation by splicing the 45S rRNA precursor into 28S, 18S, and 5S molecules. snoRNAs also guide chemical modifications of nucleotides in rRNAs and other RNA genes.
Introduction to Genomics
Published in Altuna Akalin, Computational Genomics with R, 2020
Recent years have witnessed an explosion in non-coding RNA (ncRNA)-related research. Many publications implicated ncRNAs as important regulatory elements. Plants and animals produce many different types of ncRNAs such as long non-coding RNAs (lncRNAs), small interferring RNAs (siRNAs), microRNAs (miRNAs), promoter-associated RNAs (PARs) and small nucleolar RNAs (snoRNAs) (Morris and Mattick, 2014). lncRNAs are typically ¿ 200-bp long, they are involved in epigenetic regulation by interacting with chromatin remodeling factors and they function in gene regulation. siRNAs are short double-stranded RNAs which are involved in gene regulation and transposon control; they silence their target genes by cooperating with Argonaute proteins. miRNAs are short single-stranded RNA molecules that interact with their target genes by using their complementary sequence and mark them for quicker degradation. PARs may regulate gene expression as well: they are approximately 18-to -200-bp-long ncRNAs originating from promoters of coding genes (Morris and Mattick, 2014). snoRNAs are also shown to play roles in gene regulation, although they are mostly believed to guide ribosomal RNA modifications (Morris and Mattick, 2014).
Comparison of proteomic profiles from the testicular tissue of males with impaired and normal spermatogenesis
Published in Systems Biology in Reproductive Medicine, 2021
Jiaying Liang, Yichun Zheng, Weihong Zeng, Liuqing Chen, Shaofen Yang, Peng Du, Yujiang Wang, Xingsu Yu, Xiqian Zhang
FBL is a 2′-O-RNA methyltransferase located in the dense fibrillar component of the nucleolus. It is homologous to yeast NOP1, a protein essential for ribosome synthesis. And it associates with U3 snoRNA which is involved in regulating pre-RNA splicing (Tollervey et al. 1993). Some of the mechanisms of action of ribosome and spliceosome are similar (Francisco-Velilla et al. 2016). The interaction of ribosome and spliceosome pathway-associated proteins has been suggested to exert gene regulatory functions and to regulate spermatogenesis (Francisco-Velilla et al. 2016; Mageeney and Ware 2019). Ribosome-related pathways include ribosomal components as well as non-ribosomal proteins, ribosomal proteins, and small nucleolar RNA (snoRNA). The abnormal expression of ribosome pathway-related proteins in patients with spermatogenesis impairment supports the involvement of the ribosome pathway in the regulation of spermatogenesis. We specifically verified the downregulation of FBL expression in the testes of men with impaired spermatogenesis. Hassouni believed that targeting key protein rRNA methyltransferase FBL revealed great potential, because of its pivotal role in ribosome biogenesis (Hassouni et al. 2019). Also, Gentric found that FBL17 is a regulator of DNA-damage response (Gentric et al. 2020). WB and IHC expressed the downregulation of FBL in patients with impaired spermatogenesis in our study, implying that abnormal RNA splicing of key proteins may be involved in sperm differentiation and maturation in the testes of these patients.
MiR-483-3p regulates oxaliplatin resistance by targeting FAM171B in human colorectal cancer cells
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2019
Hui Liang, Yisong Xu, Qiang Zhang, Yu Yang, Yueyang Mou, Yingchun Gao, Rui Chen, Chao Chen, Penggao Dai
Three replicate samples of HCT-116 and HCT-116/L were used for small RNA sequencing. A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEB NextUltraTM small RNA Sample Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations. The library preparations were sequenced on an Illumina Hiseq 2500 platform. The clean reads were performed sequence alignment with Silva database, GtRNAdb database, Rfam database and Repbase database, respectively. The ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats were filtered out. The remaining reads were used to detect known miRNAs and novel miRNAs predicted by comparing with known miRNAs from miRBase. The expression levels of miRNAs in each sample were statistically analyzed and normalized using the TPM algorithm [22]. Differential expression analysis of two groups was performed using the DESeq R package (1.10.1) [23]. The resulting p values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). In the process of differentially expressed miRNAs detection, |log2 FC|≥1 and FDR ≤ 0.05 were used as screening standard. The Fold Change (FC) indicated the ratio of the expression levels between the two groups. Target genes of miRNAs were predicted using miRanda [24] and RNAhybrid [25] based on known miRNAs and novel miRNAs and gene sequence information of corresponding species.
Functional role of miR-148a in oropharyngeal cancer: influence on pregnane X receptor and P-glycoprotein expression
Published in Journal of Receptors and Signal Transduction, 2019
Tasmin Reuter, Christel Herold-Mende, Gerhard Dyckhoff, Juan Pablo Rigalli, Johanna Weiss
miR-148a and mRNA of PXR were quantified in untransfected and transfected cells. Total RNA was isolated using the miRNeasy Kit according to the manufacturer’s protocol. After isolation, miRNA was reverse transcribed with the miScript II RT Kit using the High Spec buffer. Subsequently, cDNA was diluted 1:100 and quantified via RT-qPCR using the QuantiTect SYBR Green PCR Kit using a specific primer for miR-148a (sequence: 5-TCAGTGCACTACAGAACTTTGT-3) and the poly-T-primer provided with the kit. Small Nucleolar RNA, C/D Boxes (SNORD61 and SNORD68) were used as reference genes using the respective Hs_SNORD miScript primer assay kits. For reverse transcription of total RNA, the RevertAidTM H Minus First Strand cDNA Synthesis Kit was used. The RT-qPCR reaction for NR1I2 and ABCB1 were performed with the Absolute QPCR SYBRGreen Mix; primer sequences were published previously [21]. RT-qPCR reactions were performed with the LightCycler® 480 via calibrator-normalized quantification with efficiency correction using the LightCycler® 480 software version 1.5 (Roche Applied Science, Mannheim, Germany). Ribosomal polymerase II (RPII) was used as a reference gene, as this gene was previously identified to be the most suitable gene in the used cell lines [11].