阅读说明：本技术 microRNA感受器序列的设计方法与装置 (Design method and device of microRNA receptor sequence ) 是由 汪小我 魏磊 于 2021-07-27 设计创作，主要内容包括：本申请提出一种microRNA感受器序列的设计方法和装置,其中,方法包括：获得microRNA感受器所处于的细胞环境内的microRNA和RNA,根据microRNA和RNA获得竞争性RNA；其中,竞争性RNA是基于microRNA和RNA相互作用的强度,计算出每一种microRNA所调控的RNA在不同相互作用强度的数量；按照RNA所含竞争性RNA的相互作用强弱,从RNA中确定出不同强度的竞争性RNA,计算获得microRNA的噪声调控能力值；根据预期获得表达噪声的第一预设阈值,以根据第二预设阈值选取具有特定噪声调控能力值的microRNA设计靶位点,并对microRNA调控的靶位点进行设计,以定向调整所述表达噪声。本发明可以准确地基于细胞的状态和需求的基因表达值调高或调低基因表达噪声,在合成生物学中具有广泛的工程应用价值。(The application provides a method and a device for designing a microRNA receptor sequence, wherein the method comprises the following steps: obtaining microRNA and RNA in a cell environment where a microRNA receptor is positioned, and obtaining competitive RNA according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated; determining competitive RNAs with different strengths from RNAs according to the strength of the interaction of competitive RNAs contained in the RNAs, and calculating to obtain the noise regulation and control capability value of the microRNA; according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise. The invention can accurately adjust the gene expression noise up or down based on the state and the demand of the cell, and has wide engineering application value in synthetic biology.)

1. A method for designing a microRNA receptor sequence, the method comprising the steps of:

obtaining microRNA and RNA in a cell environment where a microRNA receptor is positioned, and obtaining competitive RNA according to the microRNA and the RNA; wherein the competitive RNA calculates the number of RNA regulated by each microRNA in different interaction strengths based on the interaction strengths of the microRNA and the RNA;

determining competitive RNAs with different strengths from the RNAs according to the strength of the interaction of the competitive RNAs contained in the RNAs, and calculating to obtain the noise regulation and control capability value of the microRNA;

according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise.

2. The method for designing the microRNA receptor sequence according to claim 1, wherein the step of determining competitive RNAs with different strengths from the RNAs according to the strength of the interaction of the competitive RNAs contained in the RNAs and calculating the noise regulation and control capability value of the microRNA comprises the following steps:

determining the number of said competitive RNA contained in said RNA;

judging whether the interaction strength of the competitive RNA is greater than or equal to a third preset threshold value;

if so, taking the competitive RNA as strong competitive RNA;

if not, taking the competitive RNA as weak competitive RNA;

and subtracting the number of the weak competitive RNA from the number of the strong competitive RNA to obtain the noise regulation and control capability value of the microRNA.

3. The method for designing a microRNA receptor sequence according to claim 1, wherein the obtaining of microRNA and RNA of a microRNA receptor in a cellular environment comprises one of high throughput sequencing or public database search.

4. The method for designing the microRNA receptor sequence according to claim 1, wherein the step of obtaining a first preset threshold of expression noise according to expectation, selecting a microRNA design target site with a specific noise regulation capability value according to a second preset threshold, and designing the microRNA regulation target site to directionally regulate the expression noise comprises the following steps:

determining the number of the strong competitive RNA and the weak competitive RNA contained in the microRNA;

if the expected obtained expression noise is larger than a first preset threshold value, selecting the microRNA with the specific noise regulation and control capability value larger than or equal to a second preset threshold value to design a target site;

and when the gene inhibition efficiency regulated by the required microRNA receptor is greater than the fourth preset threshold, simultaneously designing a plurality of microRNA target sites.

5. The method for designing a microRNA receptor sequence according to claim 4, further comprising:

if the expected expression noise is smaller than a first preset threshold, selecting a microRNA with a specific noise regulation and control capability value smaller than a second preset threshold to design a target site;

and when the gene inhibition efficiency regulated by the microRNA receptor is larger than the fourth preset threshold, combining a plurality of target sites regulated by different microRNAs to form the microRNA receptor.

6. A device for designing a microRNA receptor sequence, which is characterized by comprising:

the calculation module is used for obtaining microRNA and RNA in a cell environment where the microRNA receptor is located and obtaining competitive RNA according to the microRNA and the RNA; wherein the competitive RNA calculates the number of RNA regulated by each microRNA in different interaction strengths based on the interaction strengths of the microRNA and the RNA;

the determining module is used for determining competitive RNAs with different strengths from the RNAs according to the interaction strength of the competitive RNAs contained in the RNAs and calculating to obtain a noise regulation and control capability value;

the design module is used for selecting a microRNA with a specific noise regulation and control capability value according to a second preset threshold value to design a target site according to the first preset threshold value of expected acquired expression noise, and designing the microRNA regulated target site to directionally regulate the expression noise.

7. The apparatus for designing microRNA receptor sequences according to claim 6, wherein the determining module comprises:

determining the number of said competitive RNA contained in said RNA;

judging whether the interaction strength of the competitive RNA is greater than or equal to a third preset threshold value;

if so, taking the competitive RNA as strong competitive RNA;

if not, taking the competitive RNA as weak competitive RNA;

and subtracting the number of the weak competitive RNA from the number of the strong competitive RNA to obtain the noise regulation and control capability value of the microRNA.

8. The apparatus for designing microRNA receptor sequences according to claim 6, wherein the calculation module comprises one of high throughput sequencing or public database search methods.

9. The apparatus for designing microRNA receptor sequences according to claim 6, wherein the design module comprises:

determining the number of the strong competitive RNA and the weak competitive RNA contained in the microRNA;

if the expected obtained expression noise is larger than the first preset threshold, selecting microRNA with the specific noise regulation and control capability value larger than or equal to the second preset threshold to design a target site;

and when the gene inhibition efficiency regulated by the required microRNA receptor is greater than the fourth preset threshold, simultaneously designing a plurality of microRNA target sites.

10. The apparatus for designing microRNA receptor sequences according to claim 6, wherein the design module further comprises:

if the expected expression noise is smaller than a first preset threshold value, selecting the microRNA with the specific noise regulation and control capability value smaller than a second preset threshold value to design a target site;

and when the gene inhibition efficiency regulated by the microRNA receptor is larger than the fourth preset threshold, combining a plurality of target sites regulated by different microRNAs to form the microRNA receptor.

Technical Field

The invention relates to the technical field of biology, in particular to a method and a device for designing a microRNA receptor sequence.

Background

microRNA (microRNA) is a small RNA and is an important regulatory molecule in synthetic biology. The expression quantity of the microRNA has obvious difference in different cell types, so that the microRNA is a good marker for characterizing the cell state. In synthetic biology, decisions can be made by sensing the amount of micrornas, and sequences that sense the amount of micrornas are called microRNA receptors.

The microRNA receptor is a sequence on a class of RNA molecules, and the partial sequence is in complementary pairing with all or part of microRNA, so that the microRNA receptor is called a microRNA target site. The microRNA target site can be combined with specific microRNA, so that the degradation of RNA molecules is induced or the expression of protein is inhibited, and the effect of inhibiting the expression level of genes is achieved. The invention provides a design method of a microRNA receptor, which can design the microRNA receptor with a specific gene expression noise regulation function according to the quantity of microRNA and RNA in a cell.

The wide existence and unavoidable existence of gene expression noise in organisms affect the stability of synthetic gene circuits in synthetic biology and further affect the functions of the synthetic gene circuits. Therefore, it is important to design and construct a synthetic gene line to reasonably control the expression noise of the gene.

Disclosure of Invention

The present invention is directed to solving, at least to some extent, one of the technical problems in the related art.

Therefore, one objective of the present invention is to provide a method for designing a microRNA receptor sequence, which can accurately adjust up or down gene expression noise based on the state and demand of cells, and has a wide engineering application value in synthetic biology.

The invention also aims to provide a device for designing the microRNA receptor sequence.

In order to achieve the above purpose, an embodiment of an aspect of the present invention provides a method for designing a microRNA receptor sequence, including the following steps:

obtaining microRNA and RNA in a cell environment where a microRNA receptor is positioned, and obtaining competitive RNA according to the microRNA and the RNA; wherein the competitive RNA calculates the number of RNA regulated by each microRNA in different interaction strengths based on the interaction strengths of the microRNA and the RNA;

determining competitive RNAs with different strengths from the RNAs according to the strength of the interaction of the competitive RNAs contained in the RNAs, and calculating to obtain a noise regulation and control capability value;

according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise.

According to the design method of the microRNA receptor sequence, the microRNA and the RNA in the cellular environment where the microRNA receptor is located are obtained, and competitive RNA is obtained according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated; determining competitive RNAs with different strengths from RNAs according to the strength of the interaction of competitive RNAs contained in the RNAs, and calculating to obtain a noise regulation and control capability value; according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise. The invention can accurately adjust the gene expression noise up or down based on the state and the demand of the cell, and has wide engineering application value in synthetic biology.

In addition, the method for designing the microRNA receptor sequence according to the embodiment of the invention can also have the following additional technical characteristics:

further, in an embodiment of the present invention, the determining competitive RNAs with different strengths from the RNAs according to the strength of the interaction between the competitive RNAs contained in the RNAs, and calculating to obtain the noise control capability value of the microRNA includes:

determining the number of said competitive RNA contained in said RNA;

judging whether the interaction strength of the competitive RNA is greater than or equal to a third preset threshold value;

if so, taking the competitive RNA as strong competitive RNA;

if not, taking the competitive RNA as weak competitive RNA;

and subtracting the number of the weak competitive RNA from the number of the strong competitive RNA to obtain the noise regulation and control capability value of the microRNA.

Further, in one embodiment of the present invention, the obtaining of micrornas and RNAs of microRNA receptors in a cellular environment comprises one of high-throughput sequencing or public database search methods.

Further, in an embodiment of the present invention, the obtaining a first preset threshold of expression noise according to expectation, selecting a microRNA with a specific noise regulation capability value according to a second preset threshold, and designing the microRNA-regulated target site to directionally adjust the expression noise includes:

determining the number of the strong competitive RNA and the weak competitive RNA contained in the microRNA;

if the expected obtained expression noise is larger than a first preset threshold value, selecting the microRNA with the specific noise regulation and control capability value larger than or equal to a second preset threshold value to design a target site;

and when the gene inhibition efficiency regulated by the required microRNA receptor is greater than the fourth preset threshold, simultaneously designing a plurality of microRNA target sites.

Further, in an embodiment of the present invention, the method further includes:

if the expected expression noise is smaller than a first preset threshold value, selecting the microRNA with the specific noise regulation and control capability value smaller than a second preset threshold value to design a target site;

and when the gene inhibition efficiency regulated by the microRNA receptor is larger than the fourth preset threshold, combining a plurality of target sites regulated by different microRNAs to form the microRNA receptor.

In order to achieve the above object, another embodiment of the present invention provides a device for designing a microRNA receptor sequence, including:

the calculation module is used for obtaining microRNA and RNA in a cell environment where the microRNA receptor is located and obtaining competitive RNA according to the microRNA and the RNA; wherein the competitive RNA calculates the number of RNA regulated by each microRNA in different interaction strengths based on the interaction strengths of the microRNA and the RNA;

the determining module is used for determining competitive RNAs with different strengths from the RNAs according to the interaction strength of the competitive RNAs contained in the RNAs and calculating to obtain a noise regulation and control capability value;

the design module is used for selecting a microRNA with a specific noise regulation and control capability value according to a second preset threshold value to design a target site according to the first preset threshold value of expected acquired expression noise, and designing the microRNA regulated target site to directionally regulate the expression noise.

According to the design device of the microRNA receptor sequence, the microRNA and the RNA in the cellular environment where the microRNA receptor is located are obtained, and competitive RNA is obtained according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated; determining competitive RNAs with different strengths from RNAs according to the strength of the interaction of competitive RNAs contained in the RNAs, and calculating to obtain a noise regulation and control capability value; according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise. The invention can accurately adjust the gene expression noise up or down based on the state and the demand of the cell, and has wide engineering application value in synthetic biology.

Additional aspects and advantages of the invention will be set forth in part in the description which follows and, in part, will be obvious from the description, or may be learned by practice of the invention.

Drawings

The foregoing and/or additional aspects and advantages of the present invention will become apparent and readily appreciated from the following description of the embodiments, taken in conjunction with the accompanying drawings of which:

FIG. 1 is a flow chart of a method for designing a microRNA receptor sequence according to one embodiment of the present invention;

fig. 2 is a schematic structural diagram of a device for designing a microRNA receptor sequence according to an embodiment of the present invention.

Detailed Description

Reference will now be made in detail to embodiments of the present invention, examples of which are illustrated in the accompanying drawings, wherein like or similar reference numerals refer to the same or similar elements or elements having the same or similar function throughout. The embodiments described below with reference to the drawings are illustrative and intended to be illustrative of the invention and are not to be construed as limiting the invention.

The method and the device for designing the microRNA receptor sequence provided by the embodiment of the invention are described below with reference to the accompanying drawings, and firstly, the design of the microRNA receptor sequence provided by the embodiment of the invention is described with reference to the accompanying drawings.

FIG. 1 is a flow chart of a method for designing a microRNA receptor sequence according to an embodiment of the present invention.

As shown in figure 1, the design method of the microRNA receptor sequence comprises the following steps:

step S1, obtaining microRNA and RNA in the cell environment where the microRNA receptor is located, and obtaining competitive RNA according to the microRNA and the RNA; wherein, the competitive RNA is based on the interaction strength of the microRNA and the RNA, and the quantity of the RNA regulated and controlled by each microRNA in different interaction strengths is calculated.

In particular, microRNA receptors need to function within cells. Firstly, the quantity of microRNAs and RNAs in a working cell environment is obtained, and then the quantity of the RNAs regulated and controlled by each microRNA under different interaction strengths is calculated based on the interaction strength of the microRNAs and the RNAs, and the number is named as competitive RNA.

It is understood that the microRNAs and the RNA quantity can be obtained by a high-throughput sequencing or public database retrieval method.

The strength of interaction between microRNA and RNA can be based on existing software (such as miRmap, targetScan and the like).

And step S2, determining competitive RNAs with different strengths from the RNAs according to the strength of the interaction of the competitive RNAs contained in the RNAs, and calculating to obtain the noise regulation and control capability value of the microRNA.

It is understood that, with a reasonable threshold of interaction strength, competing RNAs are classified into two categories: competitive RNA with an interaction strength above the threshold is named strong competitive RNA, and the other way round is named weak competitive RNA. Wherein:

the threshold value can be adjusted according to actual requirements. We have some thresholds for reference earlier, e.g., mircap score < -0.05 can be considered a strong competitive RNA when dividing strong and weak competitive RNAs by the predicted value of mircap, mircap score, and vice versa.

It can be understood that the noise regulation ability value of the microRNA is obtained by subtracting the number of the weak competitive RNA from the number of the strong competitive RNA.

Step S3, according to a first preset threshold of expected obtained expression noise, selecting a microRNA with a specific noise regulation and control ability value according to a second preset threshold to design a target site, and designing the microRNA regulated target site to directionally regulate the expression noise.

Specifically, if a higher expression noise regulation effect is expected, the microRNA receptor is designed according to the following whole or partial principles:

selecting microRNA with a large noise regulation and control capacity value to design a target site;

when the gene inhibition efficiency regulated by the required microRNA receptor is high, 2 or more than 2 microRNA target sites can be simultaneously designed.

If a regulatory effect with lower expression noise is expected, the microRNA receptor is designed according to the following whole or partial principles:

selecting microRNA with a smaller noise regulation and control capability value to design a target site;

when the gene inhibition efficiency regulated by the required microRNA receptor is higher, 2 or more than 2 target sites regulated by different microRNAs can be combined to form the microRNA receptor.

According to the design method of the microRNA receptor sequence provided by the invention, the microRNA and the RNA in the cellular environment where the microRNA receptor is located are obtained, and the competitive RNA is obtained according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated; determining competitive RNAs with different strengths from RNAs according to the strength of the interaction of competitive RNAs contained in the RNAs, and calculating to obtain a noise regulation and control capability value; according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise. The invention can accurately adjust the gene expression noise up or down based on the state and the demand of the cell, and has wide engineering application value in synthetic biology.

Next, a device for designing a microRNA receptor sequence according to an embodiment of the present invention is described with reference to the drawings.

FIG. 2 is a schematic structural diagram of a device for designing a microRNA receptor sequence according to an embodiment of the present invention.

As shown in fig. 2, the structural device 10 includes: a calculation module 100, a determination module 200, and a design module 300.

The calculation module 100 is used for obtaining microRNA and RNA of the microRNA receptor in a cell environment and obtaining competitive RNA according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated;

the determining module 200 is configured to determine competitive RNAs with different strengths from the RNAs according to the strength of interaction between competitive RNAs contained in the RNAs, and calculate to obtain a noise regulation capability value;

the design module 300 is configured to select a microRNA with a specific noise regulation and control capability value according to a first preset threshold of expected obtained expression noise to design a target site, and design the microRNA regulated target site to directionally regulate the expression noise.

Further, the determining module 200 includes:

determining the number of competitive RNAs contained in the RNA;

judging whether the interaction strength of the competitive RNA is greater than or equal to a third preset threshold value or not;

if so, using the competitive RNA as strong competitive RNA;

if not, the competitive RNA is taken as weak competitive RNA;

and subtracting the number of the weak competitive RNA from the number of the strong competitive RNA to obtain the noise regulation and control capability value of the microRNA.

Further, the computing module 100 includes one of a high throughput sequencing or a public database retrieval method.

Further, the design module 300 includes:

determining the quantity of strong competitive RNA and weak competitive RNA contained in microRNA;

if the expected expression noise is larger than a first preset threshold, selecting a microRNA with a specific noise regulation and control capability value larger than or equal to a second preset threshold to design a target site;

and when the gene inhibition efficiency regulated by the required microRNA receptor is greater than a fourth preset threshold value, simultaneously designing a plurality of microRNA target sites.

Further, the design module 300 further includes:

if the expected expression noise is smaller than a first preset threshold, selecting a microRNA with a specific noise regulation and control capability value smaller than a second preset threshold to design a target site;

and when the gene inhibition efficiency regulated by the required microRNA receptor is greater than a fourth preset threshold value, combining a plurality of target sites regulated by different microRNAs to form the microRNA receptor.

It should be noted that the explanation of the embodiment of the method for designing a microRNA receptor sequence is also applicable to the device for designing a microRNA receptor sequence of the embodiment, and is not repeated herein.

According to the device for designing the sequence of the microRNA receptor, provided by the embodiment of the invention, the microRNA and the RNA in the cellular environment where the microRNA receptor is located are obtained, and the competitive RNA is obtained according to the microRNA and the RNA; the competitive RNA is based on the interaction strength of microRNA and RNA, and the quantity of RNA regulated and controlled by each microRNA in different interaction strengths is calculated; determining competitive RNAs with different strengths from RNAs according to the strength of the interaction of competitive RNAs contained in the RNAs, and calculating to obtain a noise regulation and control capability value; according to a first preset threshold value of expected obtained expression noise, selecting microRNA with a specific noise regulation and control capacity value according to a second preset threshold value to design a target site, and designing the microRNA regulated and controlled target site to directionally regulate the expression noise. The invention can accurately adjust the gene expression noise up or down based on the state and the demand of the cell, and has wide engineering application value in synthetic biology.

Furthermore, the terms "first", "second" and "first" are used for descriptive purposes only and are not to be construed as indicating or implying relative importance or implicitly indicating the number of technical features indicated. Thus, a feature defined as "first" or "second" may explicitly or implicitly include at least one such feature. In the description of the present invention, "a plurality" means at least two, e.g., two, three, etc., unless specifically limited otherwise.

In the description herein, references to the description of the term "one embodiment," "some embodiments," "an example," "a specific example," or "some examples," etc., mean that a particular feature, structure, material, or characteristic described in connection with the embodiment or example is included in at least one embodiment or example of the invention. In this specification, the schematic representations of the terms used above are not necessarily intended to refer to the same embodiment or example. Furthermore, the particular features, structures, materials, or characteristics described may be combined in any suitable manner in any one or more embodiments or examples. Furthermore, various embodiments or examples and features of different embodiments or examples described in this specification can be combined and combined by one skilled in the art without contradiction.

Although embodiments of the present invention have been shown and described above, it is understood that the above embodiments are exemplary and should not be construed as limiting the present invention, and that variations, modifications, substitutions and alterations can be made to the above embodiments by those of ordinary skill in the art within the scope of the present invention.