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https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#1
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29760470/breast-cancer-associated-germline-structural-variants-harboring-small-noncoding-rnas-impact-post-transcriptional-gene-regulation
#2
Mahalakshmi Kumaran, Preethi Krishnan, Carol E Cass, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Copy Number Variants (CNVs) are a class of structural variations of DNA. Germline CNVs are known to confer disease susceptibility, but their role in breast cancer warrants further investigations. We hypothesized that breast cancer associated germline CNVs contribute to disease risk through gene dosage or other post-transcriptional regulatory mechanisms, possibly through tissue specific expression of CNV-embedded small-noncoding RNAs (CNV-sncRNAs). Our objectives are to identify breast cancer associated CNVs using a genome wide association study (GWAS), identify sncRNA genes embedded within CNVs, confirm breast tissue (tumor and normal) expression of the sncRNAs, correlate their expression with germline copy status and identify pathways influenced by the genes regulated by sncRNAs...
May 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29749606/interactions-between-short-and-long-noncoding-rnas
#3
REVIEW
Igor Ulitsky
It is now evident that noncoding RNAs play key roles in regulatory networks determining cell fate and behavior, in a myriad of different conditions, and across all species. Among these noncoding RNAs are short RNAs, such as microRNAs, snoRNAs, and piRNAs, and the functions of those are relatively well understood. Other noncoding RNAs are longer, and their modes of action and functions are also increasingly explored and deciphered. Short RNAs and long noncoding RNAs (lncRNAs) interact with each other with reciprocal consequences for their fates and functions...
May 10, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29730207/sports1-0-a-tool-for-annotating-and-profiling-non-coding-rnas-optimized-for-rrna-and-trna-derived-small-rnas
#4
Junchao Shi, Eun-A Ko, Kenton M Sanders, Qi Chen, Tong Zhou
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1...
May 3, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29725044/nuclear-fate-of-yeast-snorna-is-determined-by-co-transcriptional-rnt1-cleavage
#5
Pawel Grzechnik, Sylwia A Szczepaniak, Somdutta Dhir, Anna Pastucha, Hannah Parslow, Zaneta Matuszek, Hannah E Mischo, Joanna Kufel, Nicholas J Proudfoot
Small nucleolar RNA (snoRNA) are conserved and essential non-coding RNA that are transcribed by RNA Polymerase II (Pol II). Two snoRNA classes, formerly distinguished by their structure and ribonucleoprotein composition, act as guide RNA to target RNA such as ribosomal RNA, and thereby introduce specific modifications. We have studied the 5'end processing of individually transcribed snoRNA in S. cerevisiae to define their role in snoRNA biogenesis and functionality. Here we show that pre-snoRNA processing by the endonuclease Rnt1 occurs co-transcriptionally with removal of the m7 G cap facilitating the formation of box C/D snoRNA...
May 3, 2018: Nature Communications
https://www.readbyqxmd.com/read/29712923/activity-dependent-lona-regulates-translation-by-coordinating-rrna-transcription-and-methylation
#6
Dingfeng Li, Juan Zhang, Ming Wang, Xiaohui Li, Huarui Gong, Huiping Tang, Lin Chen, Lili Wan, Qiang Liu
The ribosome is indispensable for precisely controlling the capacity of protein synthesis. However, how translational machinery is coordinated to meet the translational demands remains elusive. Here, we identify a nucleolar-specific lncRNA (LoNA), its 5' portion binds and sequesters nucleolin to suppress rRNA transcription, and its snoRNA like 3' end recruits and diminishes fibrillarin activity to reduce rRNA methylation. Activity-dependent decrease of LoNA leads to elevated rRNA and ribosome levels, an increased proportion of polysomes, mRNA polysome loading, and protein translation...
April 30, 2018: Nature Communications
https://www.readbyqxmd.com/read/29696996/a-technical-assessment-of-the-porcine-ejaculated-spermatozoa-for-a-sperm-specific-rna-seq-analysis
#7
Marta Gòdia, Fabiana Quoos Mayer, Julieta Nafissi, Anna Castelló, Joan Enric Rodríguez-Gil, Armand Sánchez, Alex Clop
The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPureTM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing...
April 26, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29693772/expression-of-granulosa-cell-micrornas-aven-and-atrx-are-associated-with-human-blastocyst-development
#8
A M O'Doherty, Y M O'Brien, J A Browne, M Wingfield, L C O'Shea
A greater understanding of the key molecules associated with embryo development during human assisted reproduction is imperative for the development of advanced diagnostics. Previous studies have shown that follicular microRNAs (miRNAs) are reliable markers of polycystic ovarian syndrome (PCOS). Leveraging the utility of miRNAs in PCOS, the aim of this study was to identify miRNAs in human granulosa cells that may be indicative of blastocyst development. Granulosa cells and oocytes were collected from the first follicle aspirated from patients undergoing oocyte retrieval for in-vitro fertilisation (IVF) or intra-cytoplasmic sperm injection (ICSI)...
April 25, 2018: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29691221/small-ncrna-seq-results-of-human-tissues-variations-depending-on-sample-integrity
#9
Nicole Ludwig, Tobias Fehlmann, Valentina Galata, Andre Franke, Christina Backes, Eckart Meese, Andreas Keller
BACKGROUND: Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. METHODS: Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data...
April 24, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29618798/differential-expression-of-micrornas-and-other-small-rnas-in-muscle-tissue-of-patients-with-als-and-healthy-age-matched-controls
#10
Anja Kovanda, Lea Leonardis, Janez Zidar, Blaž Koritnik, Leja Dolenc-Groselj, Stanislava Ristic Kovacic, Tomaž Curk, Boris Rogelj
Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29617896/an-evaluation-of-function-of-multicopy-non-coding-rnas-in-mammals-using-encode-fantom-data-and-comparative-genomics
#11
Marc P Hoeppner, Elena Denisenko, Paul P Gardner, Sebastian Schmeier, Anthony M Poole
Mammalian diversification has coincided with a rapid proliferation of various types of non-coding RNAs, including members of both snRNAs and snoRNAs. The significance of this expansion however remains obscure. While some ncRNA copy-number expansions have been linked to functionally tractable effects, such events may equally likely be neutral, perhaps as a result of random retrotransposition. Hindering progress in our understanding of such observations is the difficulty in establishing function for the diverse features that have been identified in our own genome...
April 3, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29596364/non-coding-rnas-and-endometrial-cancer
#12
REVIEW
Cristina Vallone, Giuliano Rigon, Caterina Gulia, Alberto Baffa, Raffaella Votino, Giulia Morosetti, Simona Zaami, Vito Briganti, Francesco Catania, Marco Gaffi, Roberto Nucciotti, Fabio Massimo Costantini, Roberto Piergentili, Lorenza Putignani, Fabrizio Signore
Non-coding RNAs (ncRNAs) are involved in the regulation of cell metabolism and neoplastic transformation. Recent studies have tried to clarify the significance of these information carriers in the genesis and progression of various cancers and their use as biomarkers for the disease; possible targets for the inhibition of growth and invasion by the neoplastic cells have been suggested. The significance of ncRNAs in lung cancer, bladder cancer, kidney cancer, and melanoma has been amply investigated with important results...
March 29, 2018: Genes
https://www.readbyqxmd.com/read/29579705/lncrna-snhg6-acts-as-a-prognostic-factor-to-regulate-cell-proliferation-in-glioma-through-targeting-p21
#13
Gang Cai, Qing Zhu, Liqun Yuan, Qing Lan
It has been certified that long noncoding RNAs (lncRNAs) are crucial regulators in the progression of various human cancers. snoRNA host gene 6 (SNHG6) has been uncovered to affect the initial stage and tumorigenesis of hepatocellular carcinoma. Nevertheless, the expression pattern and biological role of SNHG6 in glioma still need to be investigated. The study aims to investigate the expression pattern, biological role and the potential mechanism of SNHG6 in glioma. In this study, the high expression of SNHG6 was tested in both glioma tissues and glioma cells...
March 23, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29554660/c-d-box-snord105b-promotes-tumorigenesis-in-gastric-cancer-via-aldoa-c-myc-pathway
#14
Cong Zhang, Lian-Mei Zhao, Hao Wu, Guo Tian, Su-Li Dai, Ri-Yang Zhao, Bao-En Shan
BACKGROUND/AIMS: Small nucleolar RNAs (snoRNAs) play an important role in carcinogenesis. In this study, we identified a C/D box snoRNA, snord105b, and further investigated the function and mechanism of the snord105b in gastric cancer (GC). METHODS: The expression level of snord105b in GC tissures, sera and cell lines were detected by qRT-PCR. Cell viability was assessed using MTS assay. Transwell and wound healing assay were performed to evaluate migration and invasion, and protein expression was examined by western blotting...
2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29541452/clinical-significance-and-biological-roles-of-small-nucleolar-rnas-in-hepatocellular-carcinoma
#15
Dilip Baral, Long Wu, Gaurav Katwal, Xiong Yan, Yanfeng Wang, Qifa Ye
Hepatocellular carcinoma (HCC) is among the most common and fatal cancers. It is a multistage and multifactorial carcinoma, in which a number of factors serve roles in its initiation and progression. Small nucleolar RNAs (snoRNAs), considered to serve a role in various cancers, have recently been identified to have significant contributions to HCC tumorigenesis. Recent studies suggest that snoRNAs have a critical role in the pathogenesis of HCC. Moreover, detailed studies have demonstrated that various snoRNAs are involved in a range of biological processes associated with HCC, including initiation, proliferation, tumor growth, the cell cycle, apoptosis and metastasis...
April 2018: Biomedical Reports
https://www.readbyqxmd.com/read/29537884/current-status-of-sperm-functional-genomics-and-its-diagnostic-potential-of-fertility-in-bovine-bos-taurus
#16
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29534966/next-generation-sequencing-based-mirna-expression-analysis-in-parp1-deficient-embryonic-stem-cell-derived-exosomes
#17
Tadashige Nozaki, Yuka Sasaki, Itsuko Fukuda, Mayu Isumi, Keitaro Nakamoto, Takae Onodera, Mitsuko Masutani
Poly (ADP-ribose) polymerase family, member 1 (Parp1) has pleiotropic and disparate functions in multiple cellular signaling pathways through post-translational protein modification. It contributes to the regulation of various cellular processes, including DNA damage repair, cell death, and cell differentiation, genetically or epigenetically. Meanwhile, the functions of Parp1 in intercellular signaling remain to be established. To examine the functions of Parp1 in intercellular signaling, we examined microRNA (miRNA) regulation in exosomes derived from Parp1-deficient (Parp1-/- ) embryonic stem (ES) cells...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29529031/large-scale-profiling-of-noncoding-rna-function-in-yeast
#18
Steven Parker, Marcin G Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogerio Alves de Almeida, Edith Invernizzi, Tim Burgis, Walid Omara, Sam Griffiths-Jones, Daniela Delneri, Raymond T O'Keefe
Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media...
March 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29505615/circulating-mirnas-isomirs-and-small-rna-clusters-in-human-plasma-and-breast-milk
#19
Mercedes Rubio, Mariona Bustamante, Carles Hernandez-Ferrer, Dietmar Fernandez-Orth, Lorena Pantano, Yaris Sarria, Maria Piqué-Borras, Kilian Vellve, Silvia Agramunt, Ramon Carreras, Xavier Estivill, Juan R Gonzalez, Alfredo Mayor
Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and compare small RNA profiles in human biofluids. For this purpose, RNA was extracted from plasma and breast milk samples from 15 healthy postpartum mothers. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform...
2018: PloS One
https://www.readbyqxmd.com/read/29494516/the-unforeseen-non-coding-rnas-in-head-and-neck-cancer
#20
REVIEW
Alexandra Iulia Irimie, Alina-Andreea Zimta, Cristina Ciocan, Nikolay Mehterov, Diana Dudea, Cornelia Braicu, Ioana Berindan-Neagoe
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other "pieces of the RNA puzzle". These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis...
March 1, 2018: Genes
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