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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

AI Technical Summary

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 input at a time, and only human circRNAs with public circRNA IDs can be predicted. , such as pigs, cattle, sheep and other scientific research workers have caused great constraints

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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

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Embodiment 1

[0052] see figure 1 , the present embodiment provides a method for predicting RNA-binding proteins based on circRNA position information, comprising the following steps:

[0053] (1) Extract total RNA from samples such as tissues, cells, or blood, perform high-throughput circRNA sequencing, and obtain circRNA chromosome location information. Based on the circRNA chromosome location information, organize all circRNA chromosome location information into bed files with the suffix .bed ( Such as figure 2 shown), named circRNA_location.bed. The file has 6 columns, which are chrom: the chromosome to which the circRNA belongs, start: the coordinates of the starting position of the circRNA, end: the coordinates of the end position of the circRNA, name: the ID obtained by circRNA sequencing, score: the default is 0, strand: the direction of the circRNA on the chromosome , where + represents positive chain, - represents reverse chain;

[0054] (2) Based on the circRNA_location.bed f...

Embodiment 2

[0072] This embodiment provides a method for predicting RNA-binding proteins based on circRNA position information, taking Sichuan black goat as an example, including the following steps:

[0073] (1) Extract total RNA from the endometrium sample of black goat in central Sichuan, perform high-throughput circRNA sequencing, and obtain circRNA chromosome position information, and other operations are the same as step (1) in Example 1;

[0074] (2) with embodiment 1 step (2);

[0075] (3) Download the goat reference genome nucleotide sequence file (GCF_001704415.1_ARS1_genomic.fna) from NCBI, and other operations are the same as step (3) in Example 1;

[0076] (4) The specific operation is the same as step (4) of Example 1, wherein 15 motifs are obtained through p-value screening;

[0077] (5) Download the meme format file JASPAR2020_CORE_Vertebrates_non-redundant_pfms.meme of the motifs of known proteins from the JASPAR CORE database, and other operations are the same as step (...

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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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