scholarly journals High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

2016 ◽  
Author(s):  
Rafal Gumienny ◽  
Dominik Jedlinski ◽  
Georges Martin ◽  
Arnau Vina-Villaseca ◽  
Mihaela Zavolan
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Ribonucleoprotein Complexes ◽  
Short Rnas ◽  
Genome Wide ◽  
The Many ◽  
Nucleolar Rnas ◽  
Comprehensive Characterization

Identification of long and short RNAs, their processing and expression patterns have been greatly facilitated by high-throughput sequencing. Frequently, these RNAs act as guides for ribonucleoprotein complexes that regulate the expression or processing of target RNAs. However, to determine the targets of the many newly discovered regulatory RNAs in high-throughput remains a challenge. To globally assign guide small nucleolar RNAs to site of 2'-O-ribose methylation in human cells, we here developed novel computational methods for the analysis of data that was generated with protocols designed to capture direct small RNA-target interactions and to identify the sites of 2'-O-ribose methylation genome-wide. We thereby determined that many "orphan" snoRNAs appear to guide 2'-O-ribose methylation at sites that are targeted by other snoRNAs and that snoRNAs can be reliably captured in interaction with many mRNAs, in which a subsequent 2'-O-methylation cannot be detected. Our study provides a reliable approach to the comprehensive characterization of snoRNA-target interactions in species beyond those in which these interactions have been traditionally studied and contribute to the rapidly developing field of "epitranscriptomics".

scholarly journals Identification and characterization of salt-tolerance relative miRNAs in Procambarus clarkii by high-throughput sequencing

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Yuling Sun
Keyword(s):  
Salt Tolerance ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Economic Losses ◽  
Srna Library ◽  
Genome Wide ◽  
A Genome

Abstract Procambarus clarkii is one of the important economic species in China and has been served as tasty food in recent years after being introduced to Nanjing. Significant problems of environment factors, such as salinity, pH and temperature, especially salinity, has the potential to result in significant economic losses in many crayfish-producing farms in China. miRNAs are a kind of ~ 22 nucleotide small non coding RNAs which were encoded by plants, animals and some viruses with functions in RNA silencing or post-transcription regulation. We constructed four sRNA library of P. clarkia from different tissues and treatments by using high-throughput sequencing technology. A total of 101 conserved miRNAs and two novel pre-miRNAs were identified and RT-qPCR were further performed to confirm existence of part of identified miRNAs. A genome wide expression profile of salt-tolerance miRNAs was proved and three miRNAs were further validated by RT-qPCR with dynamic response to different salinity stages. The study of miRNAs in P. clarkia can help us better understanding the role of miRNAs in salt-tolerance in P. clarkia.

scholarly journals snoDB: an interactive database of human snoRNA sequences, abundance and interactions

2019 ◽  
Vol 48 (D1) ◽  
pp. D220-D225 ◽  
Author(s):  
Philia Bouchard-Bourelle ◽  
Clément Desjardins-Henri ◽  
Darren Mathurin-St-Pierre ◽  
Gabrielle Deschamps-Francoeur ◽  
Étienne Fafard-Couture ◽  
...  
Keyword(s):  
High Throughput ◽  
Ribosome Biogenesis ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Sequencing Data ◽  
Ribonucleoprotein Complexes ◽  
High Throughput Sequencing Data ◽  
Non Coding Rna ◽  
Rna Interaction

Abstract Small nucleolar RNAs (snoRNAs) are an abundant type of non-coding RNA with conserved functions in all known eukaryotes. Classified into two main families, the box C/D and H/ACA snoRNAs, they enact their most well characterized role of guiding site specific modifications in ribosomal RNA, through the formation of specific ribonucleoprotein complexes, with fundamental implications in ribosome biogenesis. However, it is becoming increasingly clear that the landscape of snoRNA cellular functionality is much broader than it once seemed with novel members, non-uniform expression patterns, new and diverse targets as well as several emerging non-canonical functions ranging from the modulation of alternative splicing to the regulation of chromatin architecture. In order to facilitate the further characterization of human snoRNAs in a holistic manner, we introduce an online interactive database tool: snoDB. Its purpose is to consolidate information on human snoRNAs from different sources such as sequence databases, target information, both canonical and non-canonical from the literature and from high-throughput RNA–RNA interaction datasets, as well as high-throughput sequencing data that can be visualized interactively.

scholarly journals Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

2013 ◽  
Vol 5 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Yue-Jian Hu ◽  
Qian Wang ◽  
Yun-Tao Jiang ◽  
Rui Ma ◽  
Wen-Wei Xia ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

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