SMAtool reveals sequences and structural principles of protein-RNA interaction
Copyright © 2020 Elsevier Inc. All rights reserved..
Protein binding events on RNA are highly related to RNA secondary structure, which affects post-transcriptional regulation and translation. However, it remains challenging to describe the association between RNA secondary structure and protein binding events. Here, we present Structure Motif Analysis tool (SMAtool), a pipeline that integrates RNA secondary structure and protein binding site information to profile the binding structure preference of each protein. As an example of applying SMAtool, we extracted the RNA-structure and binding site information respectively from the DMS-seq and eCLIP-seq data of the K562 cell-line, and used SMAtool to analyze the structure motif of each RNA binding protein (RBP). This new approach provided results consistent with X-ray crystallography data from the protein data bank (PDB) database, demonstrating that it can help researchers investigate the structure preference of RBP, and understand the role of RNA secondary structure in gene expression. Availability and implementation: https://github.com/QuKunLab/SMAtool.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2020 |
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| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2020 |
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| Enthalten in: |
Biochemical and biophysical research communications - (2020) vom: 16. Feb. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Du, Pengcheng [VerfasserIn] |
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| Links: |
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| Themen: |
Journal Article |
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| Anmerkungen: |
Date Revised 27.02.2024 published: Print-Electronic Citation Status Publisher |
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| doi: |
10.1016/j.bbrc.2020.02.068 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM306644576 |
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| 520 | |a Copyright © 2020 Elsevier Inc. All rights reserved. | ||
| 520 | |a Protein binding events on RNA are highly related to RNA secondary structure, which affects post-transcriptional regulation and translation. However, it remains challenging to describe the association between RNA secondary structure and protein binding events. Here, we present Structure Motif Analysis tool (SMAtool), a pipeline that integrates RNA secondary structure and protein binding site information to profile the binding structure preference of each protein. As an example of applying SMAtool, we extracted the RNA-structure and binding site information respectively from the DMS-seq and eCLIP-seq data of the K562 cell-line, and used SMAtool to analyze the structure motif of each RNA binding protein (RBP). This new approach provided results consistent with X-ray crystallography data from the protein data bank (PDB) database, demonstrating that it can help researchers investigate the structure preference of RBP, and understand the role of RNA secondary structure in gene expression. Availability and implementation: https://github.com/QuKunLab/SMAtool | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Pipeline | |
| 650 | 4 | |a RBP regulation | |
| 650 | 4 | |a RNA secondary structure preference | |
| 650 | 4 | |a SMAtool | |
| 650 | 4 | |a Structure-sequencing | |
| 700 | 1 | |a Cai, Pengfei |e verfasserin |4 aut | |
| 700 | 1 | |a Huang, Beibei |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Chen |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Quan |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Bin |e verfasserin |4 aut | |
| 700 | 1 | |a Qu, Kun |e verfasserin |4 aut | |
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