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small rna discovery short read sequencing

Anja Pecman, Denis Kutnjak, Ion Gutiérrez-Aguirre, Ian Adams, Adrian Fox, Neil Boonham, Maja Ravnikar
Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families...
2017: Frontiers in Microbiology
Daniel Dar, Maya Shamir, J R Mellin, Mikael Koutero, Noam Stern-Ginossar, Pascale Cossart, Rotem Sorek
Riboswitches and attenuators are cis-regulatory RNA elements, most of which control bacterial gene expression via metabolite-mediated, premature transcription termination. We developed an unbiased experimental approach for genome-wide discovery of such ribo-regulators in bacteria. We also devised an experimental platform that quantitatively measures the in vivo activity of all such regulators in parallel and enables rapid screening for ribo-regulators that respond to metabolites of choice. Using this approach, we detected numerous antibiotic-responsive ribo-regulators that control antibiotic resistance genes in pathogens and in the human microbiome...
April 8, 2016: Science
Spyros Karaiskos, Ammar S Naqvi, Karl E Swanson, Andrey Grigoriev
BACKGROUND: Development of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers. While the focus in the analysis of small RNA libraries has been primarily on microRNAs (miRNAs), recent studies have reported findings of fragments of transfer RNAs (tRFs) across a range of organisms. RESULTS: Here we describe Drosophila melanogaster tRFs, which appear to have a number of structural and functional features similar to those of miRNAs but are less abundant...
2015: Biology Direct
Craig Monger, Paul S Kelly, Clair Gallagher, Martin Clynes, Niall Barron, Colin Clarke
High throughput, cost effective next generation sequencing (NGS) has enabled the publication of genome sequences for Cricetulus griseus and several Chinese hamster ovary (CHO) cell lines. RNA-Seq, the utilization of NGS technology to study the transcriptome, is expanding our understanding of the CHO cell biological system in areas ranging from the analysis of transcription start sites to the discovery of small noncoding RNAs. The analysis of RNA-Seq data, often comprised of several million short reads, presents a considerable challenge...
July 2015: Biotechnology Journal
S Rhee, H Chae, S Kim
miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear, especially when microarray data is used. Fortunately, due to the low sequencing cost, small RNA and RNA sequencing are routinely processed and we may be able to infer regulation relationships between miRNAs and mRNAs more accurately by using sequencing data...
July 15, 2015: Methods: a Companion to Methods in Enzymology
Mark S Menor, Kyungim Baek, Guylaine Poisson
The discovery of novel microRNA (miRNA) and piwi-interacting RNA (piRNA) is an important task for the understanding of many biological processes. Most of the available miRNA and piRNA identification methods are dependent on the availability of the organism's genome sequence and the quality of its annotation. Therefore, an efficient prediction method based solely on the short RNA reads and requiring no genomic information is highly desirable. In this study, we propose an approach that relies primarily on the nucleotide composition of the read and does not require reference genomes of related species for prediction...
2015: International Journal of Molecular Sciences
Andrea Pauli, Eivind Valen, Alexander F Schier
Over the past decade, high-throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non-coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens...
January 2015: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
Marissa G Daniels, Rayleen V Bowman, Ian A Yang, Ramaswamy Govindan, Kwun M Fong
Lung cancer is a disease with a dismal prognosis and is the biggest cause of cancer deaths in many countries. Nonetheless, rapid technological developments in genome science promise more effective prevention and treatment strategies. Since the Human Genome Project, scientific advances have revolutionized the diagnosis and treatment of human cancers, including thoracic cancers. The latest, massively parallel, next generation sequencing (NGS) technologies offer much greater sequencing capacity than traditional, capillary-based Sanger sequencing...
October 2013: Journal of Thoracic Disease
Almut Mentz, Armin Neshat, Katharina Pfeifer-Sancar, Alfred Pühler, Christian Rückert, Jörn Kalinowski
BACKGROUND: Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C...
2013: BMC Genomics
Lijuan Wei, Meili Xiao, Alice Hayward, Donghui Fu
Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products...
December 2013: Planta
Zhen-hua Dang, Lin-lin Zheng, Jia Wang, Zhe Gao, Shu-biao Wu, Zhi Qi, Ying-chun Wang
BACKGROUND: Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress imposed by semi-desert saline soil. However, it is impossible to explore the mechanisms underlying this tolerance without detailed genomic information. Fortunately, newly developed high-throughput sequencing technologies are powerful tools for de novo sequencing to gain such information for this species...
2013: BMC Genomics
Anjing Ge, Lingfei Shangguan, Xi Zhang, Qinghua Dong, Jian Han, Hong Liu, Xicheng Wang, Jinggui Fang
In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new miRNAs in cultivated strawberry (Fragaria×ananassa)...
July 2013: Physiologia Plantarum
Chong-Jian Chen, Nicolas Servant, Joern Toedling, Alexis Sarazin, Antonin Marchais, Evelyne Duvernois-Berthet, Valérie Cognat, Vincent Colot, Olivier Voinnet, Edith Heard, Constance Ciaudo, Emmanuel Barillot
SUMMARY: Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions...
December 1, 2012: Bioinformatics
Gang Liu, Bin Lei, Yan Li, Keya Tong, Yi Ding, Lifan Luo, Xuanyan Xia, Siwen Jiang, Changyan Deng, Yuanzhu Xiong, Fenge Li
Piwi-interacting RNAs (piRNAs), a new class of small RNAs discovered from mammalian testes, are involved in transcriptional silencing of retrotransposons and other genetic elements in germ line cells. In order to identify a full transcriptome set of piRNAs expressed in the sexually mature porcine testes, small RNA fractions were extracted and were subjected to a Solexa deep sequencing. We cloned 6,913,561 clean reads of Sus Scrofa small RNAs (18-30 nt) and performed functional characterization. Sus Scrofa small RNAs showed a bimodal length distribution with two peaks at 21 nt and 29 nt...
2012: PloS One
Ransom L Baldwin, Robert W Li, Cong-jun Li, Jennifer M Thomson, Brian J Bequette
Development of management paradigms that enhance the rate of gain and qualitative characteristics of beef carcass development has the potential to impact production and nutrient use efficiency but also mitigate losses to the environment. We used eight Black Angus beef steers (272.5 ± 17.6 kg initial body wt) fed a forage-based pelleted diet alone (n = 4) or supplemented with sodium propionate included (n = 4) for 42 days. High-quality RNA was extracted from the longissimus lumborum and subjected to transcriptome sequencing using RNA-seq technology...
May 1, 2012: Physiological Genomics
Noha Youssef, Brandi L Steidley, Mostafa S Elshahed
The utilization of high-throughput sequencing technologies in 16S rRNA gene-based diversity surveys has indicated that within most ecosystems, a significant fraction of the community could not be assigned to known microbial phyla. Accurate determination of the phylogenetic affiliation of such sequences is difficult due to the short-read-length output of currently available high-throughput technologies. This fraction could harbor multiple novel phylogenetic lineages that have so far escaped detection. Here we describe our efforts in accurate assessment of the novelty and phylogenetic affiliation of selected unclassified lineages within a pyrosequencing data set generated from source sediments of Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma...
April 2012: Applied and Environmental Microbiology
Yuji Kageyama, Takefumi Kondo, Yoshiko Hashimoto
Genome analysis has identified a number of putative non-protein-coding transcripts that do not contain ORFs longer than 100 codons. Although evidence strongly suggests that non-coding RNAs are important in a variety of biological phenomena, the discovery of small peptide-coding mRNAs confirms that some transcripts that have been assumed to be non-coding actually have coding potential. Their abundance and importance in biological phenomena makes the sorting of non-coding RNAs from small peptide-coding mRNAs a key issue in functional genomics...
November 2011: Biochimie
Yu Zhang, Kashmir Singh, Ravneet Kaur, Wenping Qiu
A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively...
September 2011: Phytopathology
Chong-Jian Chen, Qing liu, Yu-Chan Zhang, Liang-Hu Qu, Yue-Qin Chen, Daniel Gautheret
Small RNAs constitute a new and unanticipated layer of gene regulation present in the three domains of life. In plants, all organs are ultimately derived from a few pluripotent stem cells localized in specialized structures called apical meristems. The development of meristems involves a coordinated balance between undifferentiated growth and differentiation, a phenomenon requiring a tight regulation of gene expression. We used in vitro cultured embryogenic calli as a model to investigate the roles of meristem-associated small RNAs...
May 2011: RNA Biology
Xiaohan Yang, Timothy J Tschaplinski, Gregory B Hurst, Sara Jawdy, Paul E Abraham, Patricia K Lankford, Rachel M Adams, Manesh B Shah, Robert L Hettich, Erika Lindquist, Udaya C Kalluri, Lee E Gunter, Christa Pennacchio, Gerald A Tuskan
Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences...
April 2011: Genome Research
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