A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin .
Introduction to transcriptome sequencing
- Transcriptome （Transcriptome） Is a single or group of cells in a tissue in a certain state DNA All transcribed RNA aggregate , all RNA Can be divided into code RNA（mRNA） and Non coding RNA（miRNA , piRNA, SiRNA, SnRNA,lncRNA, NAT, eRNA, circ RNA, ceRNAs wait ）, The following figure clearly shows RNA Family classification （ The figure below The red circle mark is the part that this article wants to focus on ）;
- Generally speaking Transcriptome sequencing Only mRNA Sequence , In practical research, transcriptome sequencing will be subdivided according to different purposes , Such as mRNA Sequence （Messenger RNAs）、miRNA Sequence （microRNAs,small RNA One of the most studied in ）、lncRNA Sequence （Long noncoding RNAs）、circRNA Sequence （Circular RNAs）、【 Single cell transcriptome 、 Space transcriptome 、 Three generations of sequenced full-length transcriptome 、 Unparalleled nonparametric transcriptome of the reference genome 、 Comparative transcriptome and pan transcriptome sequencing related to species evolution 、 Environment specific macro transcriptome, etc , Brackets are outside the scope of this article ~~】;
- according to sequencing strategy Differences can be divided into short-read cDNA ( Measure the short cDNA)、 long-read cDNA（ Length measurement cDNA）、long-read RNA（ Direct measurement RNA）, The comparison is as follows ：.
- short-read cDNA, High throughput , Good at studying Gene differential expression ;
- long-read cDNA, Long reading and long reading , Good at New isomer Find out 、 New transcripts Find out 、 New gene fusion Transcript discovery, etc ;
- long-read RNA, Long reading and long reading , Good at discovering new isomers 、 New transcripts found 、 Discovery of new gene fusion transcripts 、 Research Transcript modification Information .
- A detailed comparison of the three is as follows
- Transcriptome sequencing Mainly in the following aspects ：
- Gene differential expression （differential gene expression）
- mRNA Differential splicing （differential splicing of mRNAs）
- Single cell gene expression （single-cell gene expression）
- RNA Protein interactions （the translatome）
- RNA structure （the structurome）
- Transcriptional heterogeneity （spatialomics）
mRNA|miRNA|lncRNA|circRNA Introduction to analysis
Introduce the mechanism of each group in transcriptional regulation , Analysis process of Shengxin .
mRNA Group is to measure… In the figure above under certain conditions mature mRNA, As can be seen from the figure above mRNA There is one Poly-A tail,mRNA When the sequencing library is constructed , utilize oligo(dT) Magnetic beads can specifically bind Poly-A tail Principle , Specifically will mRNA From total RNA To achieve enrichment .
mRNA Shengxin analysis focuses on case Group and control Between groups Differentially expressed genes , Also do gene protein interaction 、 New transcripts predict 、 Variable shear 、 Analysis of gene fusion , The following figure can be referred to ：
- miRNA Mechanism of action Mainly silence mRNA In order to realize the Regulate gene expression , The mechanisms of action in plants and animals are different , The picture above shows miRNA The mechanism of action （ Shear to degrade mRNA Or inhibit translation ）.
- miRNA How to build database Different from other omics , Mainly by using its length distribution in 20 nt about , When building the library Glue cutting and recycling The band of this range , The strip also contains rRNA,siRNA,piRNA,tRNA And so on RNA, All subsequent analyses will use Rfame database ,miRBASE To pick unless miRNA.
- miRNA Shengxin analysis focuses on case Group and control Between groups Differential expression miRNA, Differential expression miRNA The target of mRNA forecast , Also functional analysis , The following figure can be referred to ：
Some key databases and software that will be used are as follows
- lncRNA（Long non-coding RNAs） Means greater than 200nt Non coding RNA, Can and DNA, RNA Even proteins .
- lncRNA Mechanism of action It can be divided into several categories as shown in the figure below ,
- lncRNA When the sequencing database is built , Will use the kit to remove total RNA Medium rRNA（ therefore lncRNA There will also be… In the library mRNA, Shengxin analysis will also be accompanied by analysis mRNA）.
- lncRNA Shengxin analysis focuses on case Group and control Between groups lncRNA Differential expression ,lncRNA along / Trans target gene prediction , Others will analyze miRNA、lncRNA And its target genes mRNA Correlation analysis of , The following figure introduces the analysis process .
- circRNA The synthesis and action mechanism are shown in the figure below .
- circRNA Shengxin analysis
mRNA|miRNA|lncRNA|circRNA Correlation analysis
according to mRNA、miRNA、lncRNA、circRNA The interaction between them can be analyzed by correlation , To further study the mechanism of transcriptional regulation , The following figure shows various coding and non coding RNA The interaction mechanism between .
Correlation analysis means something like that
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