Method for predicting RNA binding protein based on circRNA position information

A position information and protein-binding technology, applied in the field of genetic engineering, can solve constraints and other problems, and achieve the effect of convenient and fast operation and clear process

Active Publication Date: 2021-07-09
SOUTH CHINA AGRI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] Among the known public databases, only the circinteractome database can predict the RBP of circRNAs. However, due to the limitation of its database, only 20 circRNAs can be

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  • Method for predicting RNA binding protein based on circRNA position information
  • Method for predicting RNA binding protein based on circRNA position information
  • Method for predicting RNA binding protein based on circRNA position information

Examples

Experimental program
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Example Embodiment

[0051] Example 1

[0052] See figure 1 This embodiment provides a method of predicting the RNA binding protein based on CIRCRNA position information, comprising the steps of:

[0053] (1) Extraction of total RNA of tissue, cells or blood, and perform high-throughput ciRCRNA sequencing to obtain CiRCRNA chromosome position information, based on circRNA chromosome position information, the Bed file of all CircRNA chromosome position information is the suffix .bed Bed file ( Such as figure 2 Disted), named CircRNA_Location.bed. This file has a total of 6 columns, which are chromosomes belonging to Chrom: CircRNA, Start: CircRNA start position coordinates, end: CircRNA termination coordinates, name: CircRNA sequencing ID, Score: default is 0, strand: CircRNA in chromosome , Where + represents the positive chain, - represents the anti-chain;

[0054] (2) Based on the circrna_location.bed file obtained by step (1), run the location_change.py file by software Python, get files named Circ...

Example Embodiment

[0071] Example 2

[0072] This embodiment provides a method of predicting RNA binding proteins based on CircRNA location information, based on CircRNA location information, comprising the steps of:

[0073] (1) Extraction of the total RNA of the inner membrane samples in Chuanzhong Montenesty, performing high-throughput ciRCRNA sequencing to obtain CiRCRNA chromosome position information, other operations with Example 1 (1);

[0074] (2) Step (2) in Example 1 (2);

[0075] (3) From the NCBI, the goat reference genomic nucleotide sequence document (GCF_001704415.1_ARS1_GENOMIC.FNA), other operations with Example 1 Step (3);

[0076] (4) Specific operation with Example 1 Step (4), where a total of 15 MOTIF is obtained by screening.

[0077] (5) From the Jaspar Core database, the MOME format file jaspar2020_core_vertebrates_non-redundant_pfms.meme is downloaded from the Jaspar Core database, and other operations are used as in Example 1 (5), and 140 RBPs (including RBP USF1, etc.) ar...

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Abstract

The invention belongs to the technical field of gene engineering and relates to a method for predicting RNA binding protein based on circRNA position information. The method comprises the following steps of: based on circRNA chromosome position information, obtaining chromosome position information of first 100 basic groups at a starting position in the same direction of circRNA, then obtaining a front side position sequence in the same direction of the circRNA on a Linux system by utilizing bioinformatics software bedtools, and further obtaining motif of the front side position sequence in the same direction of the circRNA; downloading a meme format file of the motif of a known protein from a known database, and comparing and matching the meme format file of the motif with the motif of the front position sequence in the same direction of the circRNA to obtain the RNA binding protein of the circRNA. According to the method, the RBP of circRNA can be predicted in batches, and the method is not limited by the number and species.

Description

technical field [0001] The invention relates to the technical field of genetic engineering, in particular to a method for predicting RNA-binding proteins based on circRNA position information. Background technique [0002] Circular RNA, referred to as circRNA, is called circular RNA. It is a non-coding RNA with a covalent closed loop structure, neither 5' to 3' polarity, nor polyadenylation tail. It is back-spliced ​​by pre-mRNA Production requires the canonical splicing machinery, and both complementary sequences and specific protein factors can facilitate this splicing. Studies have shown that circRNAs are ubiquitous in the development of various tissues and organs, participate in some specific biological processes, including transcriptional regulation, information transmission between cells, etc., and play an important role in the occurrence and development of human diseases. [0003] RNA binding protein (RNA binding protein), referred to as RBP, plays a key role in the ...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16B30/00
CPCG16B20/30G16B30/00
Inventor 洪林君吴珍芳蔡更元臧旭鹏刘德武李紫聪顾婷徐铮黄思秀
Owner SOUTH CHINA AGRI UNIV
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