Prediction method for target gene of long-fragment non-coding RNA of forest tree

A prediction method and target gene technology, applied in the field of molecular genetics, can solve the problems of false positives of target genes, low threshold parameters of prediction methods, etc., and achieve the effect of improving accuracy

Active Publication Date: 2017-08-01
BEIJING FORESTRY UNIVERSITY
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Problems solved by technology

[0003] In the prior art, the prediction of plant lncRNA target genes only takes into account the principle of sequence complementarity, and the threshold parameter of...

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  • Prediction method for target gene of long-fragment non-coding RNA of forest tree
  • Prediction method for target gene of long-fragment non-coding RNA of forest tree
  • Prediction method for target gene of long-fragment non-coding RNA of forest tree

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Embodiment 1

[0048] The target gene of populus tomentosa lncRNA lnc-CK is predicted by using the method for predicting the target gene of forest long fragment non-coding RNA of the present invention.

[0049] 1. Obtaining lnc-CK sequence. The leaves of the Populus tomentosa clone "LM50" were collected, and the total RNA of the leaves of Populus tomentosa was extracted by using the CTAB method. After the quality assessment, it was sent to the company for sequencing analysis, and the sequence data of lncRNA expressed in the leaves of Populus tomentosa were obtained. Then the sequence of Populus tomentosa lncRNA lnc-CK, SEQ ID NO.1, was obtained.

[0050]2. Preliminary prediction of the target gene of the lncRNA obtained in step 1 by using the prediction method of blast and RNAplex in combination. First, use the method of blast to compare lnc-CK with the sequences from the cDNA library of Populus tomentosa leaf tissue (E-valuefigure 1 shown. Preliminary screening obtained Pto-CKX6 as its pr...

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Abstract

The invention relates to a prediction method for a target gene of long-fragment non-coding RNA of forest tree, and belongs to the technical field of molecular genetics. The prediction method for the target gene of the long-fragment non-coding RNA of the forest tree, provided by the invention, comprises the following steps of 1) obtaining a lncRNA sequence of the forest tree; 2) obtaining a target gene of the lncRNA subjected to preliminary screening by utilizing a blast prediction method; 3) obtaining a target gene of the lncRNA subjected to secondary screening by utilizing an RNAplex prediction method; and 4) detecting tissue specific expression modes of the lncRNA and the target gene of the IncRNA subjected to the secondary screening in the step 3), calculating expression correlation of the lncRNA and the target gene of the lncRNA, and determining an interaction relationship between the lncRNA and the target gene of the lncRNA. According to the prediction method, the action fragments of the lncRNA and the target gene of the lncRNA can be efficiently and stably detected, and the accuracy of predicting the target gene of the lncRNA of the forest tree can be remarkably improved.

Description

technical field [0001] The invention relates to the technical field of molecular genetics, in particular to a method for predicting long-segment non-coding RNA target genes of forest trees. Background technique [0002] Long non-coding RNA (lncRNA) is a class of RNA transcripts longer than 200 nucleotides with no or very low protein-coding ability. Studies have shown that lncRNA can affect gene expression at the transcriptional, post-transcriptional and epigenetic levels, thereby affecting the physiological and biochemical processes of plants, such as the regulation of plant flowering time. Found in plants, lncRNA mainly binds to its target genes in the form of sequence complementarity, thereby promoting or inhibiting gene expression. For example, Arabidopsis lncRNA HID 1 (HIDDEN TREASURE 1) inhibits the expression of PIF3 by base pairing with the PIF 3 (PHYTOCHROME-INTERACTING FACTOR 3) promoter region. Due to the high degree of heterozygosity and rich DNA sequence polymo...

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Application Information

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IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 张德强权明洋肖亮
Owner BEIJING FORESTRY UNIVERSITY
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