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small RNA sequencing

Ahmed S Bayoumi, Tatsuya Aonuma, Jian-Peng Teoh, Yao-Liang Tang, Il-Man Kim
Recent advancements in genome-wide analyses and RNA-sequencing technologies led to the discovery of small noncoding RNAs, such as microRNAs (miRs), as well as both linear long noncoding RNAs (lncRNAs) and circular long noncoding RNAs (circRNAs). The importance of miRs and lncRNAs in the treatment, prognosis and diagnosis of cardiovascular diseases (CVDs) has been extensively reported. We also previously reviewed their implications in therapies and as biomarkers for CVDs. More recently, circRNAs have also emerged as important regulators in CVDs...
March 22, 2018: Acta Pharmacologica Sinica
Lorrayne Serra, Dennis Z Chang, Marissa Macchietto, Katherine Williams, Rabi Murad, Dihong Lu, Adler R Dillman, Ali Mortazavi
Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as well as embryos , the protocol should be adaptable for other nematode species and small invertebrates. In addition, we describe how to analyze the RNA-seq results using the Galaxy online environment...
February 20, 2018: Bio-protocol
Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
BACKGROUND: Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss...
March 19, 2018: BMC Systems Biology
Xiaoyan Liu, Wen Yuan, Lei Yang, Jing Li, Jun Cai
The role and miRNA expression profile of exosomes in hypertension remain largely unknown. Therefore, next-generation sequencing was used to define the miRNA expression profile of plasma exosomes in spontaneously hypertensive rats (SHRs), the most widely used animal model of human essential hypertension, and their controls, normotensive Wistar-Kyoto rats (WKYs). Results revealed that percentages of miRNA in the total small RNA isolated from SHRs and WKYs were not significantly different. Twenty-seven miRNAs were significantly differentially expressed (DE) between SHR and WKY exosomes, including 23 up-regulated and four down-regulated in SHR exosomes as compared to WKY exosomes...
March 20, 2018: Journal of Cardiovascular Translational Research
Keunsub Lee, Kan Wang
During the last decade, small noncoding RNAs (ncRNAs) have emerged as essential post-transcriptional regulators in bacteria. Nearly all important physiological and stress responses are modulated by ncRNA regulators, such as riboswitches, trans-acting small RNAs (sRNAs), and cis-antisense RNAs. Recently, three RNA-seq studies identified a total of 1534 candidate ncRNAs from Agrobacterium tumefaciens, a pathogen and biotechnology tool for plants. Only a few ncRNAs have been functionally characterized in A. tumefaciens, and some of them appear to be involved in virulence...
March 20, 2018: Current Topics in Microbiology and Immunology
Radhey S Gupta, Sahil Sawnani, Mobolaji Adeolu, Seema Alnajar, Aharon Oren
The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences...
March 20, 2018: Antonie Van Leeuwenhoek
Anson V Koehler, Tao Wang, Shane R Haydon, Robin B Gasser
Cryptosporidium viatorum is a globally distributed pathogenic species of Cryptosporidium that has only ever been recorded from humans, until now. For the first time, we molecularly characterised a novel subtype of C. viatorum (subtype XVbA2G1) from the endemic Australian swamp rat ( Rattus lutreolus ) using the small subunit of nuclear ribosomal RNA ( SSU ) gene and then subtyped it using the 60-kilodalton glycoprotein ( gp60 ) gene. In total, faecal samples from 21 swamp rats (three were positive for C. viatorum ), three broad toothed rats ( Mastacomys fuscus ) and two bush rats ( Rattus fuscipes ) were tested for Cryptosporidium ...
April 2018: International Journal for Parasitology. Parasites and Wildlife
Shanrong Zhao, Ying Zhang, Ramya Gamini, Baohong Zhang, David von Schack
To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification...
March 19, 2018: Scientific Reports
Po-Chia Chen, Pawel Masiewicz, Vladimir Rybin, Dmitri I Svergun, Janosch Hennig
We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information of biomolecular interactions independent of prior knowledge, so as to complement affinity-based screening and provide leads for further exploration. This protocol categorizes ligand titrations by computing pair-wise agreement between curves, and separately estimates affinities by quantifying complex formation as a departure from the linear sum properties of solution SAXS. The protocol is validated by sparse sequence search around the native poly-uridine RNA motifs of the two-RRM domain Sex-lethal protein (Sxl)...
March 19, 2018: ACS Combinatorial Science
Legang Sun, Ling Liu, Tingting Yu, Qiuqin Wang, Honghai Fu
In the present study, RNA interference (RNAi) was used to investigate the effect of vascular cell adhesion molecule 1 ( VCAM1 ) silencing on the proliferation of human oral squamous carcinoma HN12 cells. HN12 cells were divided into three groups: The untreated blank control cell group (CK), the negative control group transfected with non-homologous vector (NC) and the positive group transfected with the target sequence VCAM1 small hairpin RNA (KD). Reverse-transcription polymerase chain reaction and western blot analysis were used to examine the effects of VCAM1 -knockdown on the mRNA expression of VCAM1 and subsequent protein expression...
April 2018: Oncology Letters
Winston X Yan, Shaorong Chong, Huaibin Zhang, Kira S Makarova, Eugene V Koonin, David R Cheng, David A Scott
Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c...
March 9, 2018: Molecular Cell
Cristina Hoehener, Iris Hug, Mariusz Nowacki
Dicer proteins are known to produce small RNAs (sRNAs) from long double-stranded RNA (dsRNA) templates. These sRNAs are bound by Argonaute proteins, which select the guide strand, often with a 5' end sequence bias. However, Dicer proteins have never been shown to have sequence cleavage preferences. In Paramecium development, two classes of sRNAs that are required for DNA elimination are produced by three Dicer-like enzymes: Dcl2, Dcl3, and Dcl5. Through in vitro cleavage assays, we demonstrate that Dcl2 has a strict size preference for 25 nt and a sequence preference for 5' U and 5' AGA, while Dcl3 has a sequence preference for 5' UNG...
March 1, 2018: Cell
Sathish Kumar T, Navaneeth Krishnan A, Joseph Sahaya Rajan J, Makesh M, Jithendran K P, Alavandi S V, Vijayan K K
The emerging microsporidian parasite Enterocytozoon hepatopenaei (EHP), the causative agent of hepatopancreatic microsporidiosis, has been widely reported in shrimp-farming countries. EHP infection can be detected by light microscopy observation of spores (1.7 × 1 μm) in stained hepatopancreas (HP) tissue smears, HP tissue sections, and fecal samples. EHP can also be detected by polymerase chain reaction (PCR) targeting the small subunit (SSU) ribosomal RNA (rRNA) gene or the spore wall protein gene (SWP)...
March 17, 2018: Parasitology Research
Raymond Yokomi, Vijayanandraj Selvaraj, Yogita Maheshwari, Michela Chiumenti, Maria Saponari, Annalisa Giampetruzzi, Ziming Weng, Zhongguo Xiong, Subhas Hajeri
Strain differentiating marker profiles of citrus tristeza virus (CTV) isolates from California have shown the presence of multiple genotypes. To better define the genetic diversity involved, full-length genome sequences from four California CTV isolates were determined by small-interfering RNA sequencing. Phylogenetic analysis and nucleotide sequence comparisons differentiated these isolates into the genotypes VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new strain called S1 (CA-S1-L and CA-S1-L65). S1 isolates had three common recombination events within portions of genes from VT, T36 and RB strains and were transmissible by Aphis gossypii...
March 17, 2018: Archives of Virology
Sarinthip Preedagasamzin, Tiwaporn Nualkaew, Tanjitti Pongrujikorn, Natini Jinawath, Ryszard Kole, Suthat Fucharoen, Natee Jearawiriyapaisarn, Saovaros Svasti
Repair of a splicing defect of β-globin pre-mRNA harboring hemoglobin E (HbE) mutation was successfully accomplished in erythroid cells from patients with β-thalassemia/HbE disorder by a synthetic splice-switching oligonucleotide (SSO). However, its application is limited by short-term effectiveness and requirement of lifelong periodic administration of SSO, especially for chronic diseases like thalassemias. Here, we engineered lentiviral vectors that stably express U7 small nuclear RNA (U7 snRNA) carrying the splice-switching sequence of the SSO that restores correct splicing of βE -globin pre-mRNA and achieves a long-term therapeutic effect...
March 14, 2018: Biochemical and Biophysical Research Communications
Mikhail A Moldovan, Svetlana A Petrova, Mikhail S Gelfand
Riboswitches are conserved RNA structures located in non-coding regions of mRNA and able to bind small molecules (e.g. metabolites) changing conformation upon binding. This feature enables them to function as regulators of gene expression. The thiamin pyrophosphate (TPP) riboswitch is the only type of riboswitches found not only in bacteria, but also in eukaryotes - in plants, green algae, protists, and fungi. Two main mechanisms of fungal TPP riboswitch action, involving alternative splicing, have been established so far...
March 13, 2018: Fungal Genetics and Biology: FG & B
Shiqi Luo, Feng He, Junjie Luo, Shengqian Dou, Yirong Wang, Annan Guo, Jian Lu
Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By analyzing 495 public small RNA libraries, we demonstrate that most tsRNAs are conserved, prevalent and abundant in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition...
March 14, 2018: Nucleic Acids Research
Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Cristian De Gregorio, Paula Díaz, Rodrigo López-Leal, Patricio Manque, Felipe A Court
Exosomes are small (30-150 nm) vesicles of endosomal origin secreted by most cell types. Exosomes contain proteins, lipids, and RNA species including microRNA, mRNA, rRNA, and long noncoding RNAs. The mechanisms associated with exosome synthesis and cargo loading are still poorly understood. A role for exosomes in intercellular communication has been reported in physiological and pathological conditions both in vitro and in vivo. Previous studies have suggested that Schwann cell-derived exosomes regulate neuronal functions, but the mechanisms are still unclear...
2018: Methods in Molecular Biology
Veronika L Flöter, Anne-Kathrin Lorenz, Benedikt Kirchner, Michael W Pfaffl, Stefan Bauersachs, Susanne E Ulbrich
Porcine conceptuses synthesize estrogens between day 11 and 12 as signal for maternal recognition of pregnancy. A preimplantational estrogen exposure to pregnant gilts has been associated with embryonic losses and changes in endometrial mRNA expression. MicroRNAs (miRNAs) play a key role in the mRNA regulation by modulating the expression. Effects of estrogens on endometrial miRNAs have not been investigated in this context so far. Thus, we studied the endometrial expression profile of miRNAs in the pig at gestational day 10 after daily estradiol-17β (E2) application starting at fertilization using either 0, 0...
March 15, 2018: Molecular Reproduction and Development
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