Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

2013 ◽  
Vol 8 (5) ◽  
pp. 849-869 ◽  
Author(s):  
Yue Wan ◽  
Kun Qu ◽  
Zhengqing Ouyang ◽  
Howard Y Chang
Keyword(s):  
High Throughput ◽  
Rna Structure ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Nuclease Digestion

scholarly journals FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

2010 ◽  
Vol 7 (12) ◽  
pp. 995-1001 ◽  
Author(s):  
Jason G Underwood ◽  
Andrew V Uzilov ◽  
Sol Katzman ◽  
Courtney S Onodera ◽  
Jacob E Mainzer ◽  
...  
Keyword(s):  
High Throughput ◽  
Rna Structure ◽  
High Throughput Sequencing ◽  
Structure Probing

scholarly journals PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Juan Xie ◽  
Jinfang Zheng ◽  
Xu Hong ◽  
Xiaoxue Tong ◽  
Shiyong Liu
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Secondary Structures ◽  
Biological Processes ◽  
Genome Wide ◽  
Rna Interaction ◽  
Rna Complexes ◽  
Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing

2020 ◽  
Vol 20 (6) ◽  
pp. 825-838
Author(s):  
Xiaoqian Liu ◽  
Shanshan Chu ◽  
Chongyuan Sun ◽  
Huanqing Xu ◽  
Jinyu Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes
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