Direct Interaction Between 5' UTR and 3' UTR Enhances miRNA Translation Repression

• US 20190325987A1
• Filed: 04/22/2019
• Published: 10/24/2019
• Est. Priority Date: 04/20/2018
• Status: Active Application

• Current Assignee: Inhan Lee
• Original Assignee: Inhan Lee
• Inventors: LEE, INHAN
• Application Number:
  US16/390,658
• Publication Number:
  US 20190325987A1
• Time in Patent Office: Days
• CPC Class Codes: C12N 2310/141 MicroRNAs, miRNAs
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/166 Oligonucleotides used as internal standards, controls or normalisation probes
• CPC Class Codes: G16B 15/10 Nucleic acid folding
• CPC Class Codes: G16B 15/30 Drug targeting using structural data; Docking or binding prediction
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A computer implemented method for evaluating if a mRNA nucleotide sequence can form a triBridge complex. The miRNA-mRNA triBridge complex is a complex formed from the mRNA nucleotide sequence and the miRNA nucleotide sequence that includes the UTR-UTR zipper and a miRNA bridge. A biological sample can be obtained from a subject to determine the presence of single nucleotide polymorphisms in the mRNA nucleotide sequence that forms UTR-UTR zipper and a miRNA bridge.

Claims

1. A method comprising:

a) executing by a computer a step of receiving into computer memory data identifying an mRNA nucleotide sequence representing a gene or portion thereof, the mRNA nucleotide sequence has an upstream UTR region that is upstream of translation start site, a downstream UTR region that is downstream of translation stop site, and an open reading frame;

b) executing by the computer a step of evaluating the upstream UTR region for a first nucleotide UTR subregion that can stably hybridize to a second nucleotide UTR subregion in the downstream UTR region such that if the first UTR nucleotide subregion can stably hybridizes the second UTR nucleotide subregion a first hybridization region is identified, the first hybridization region being a UTR-UTR zipper;

c) executing by the computer a step of receiving into computer memory data identifying a miRNA nucleotide sequence, the miRNA nucleotide sequence having a 5′

miRNA section and a 3′

miRNA section;

d) executing by the computer a step of evaluating the upstream UTR region for a third UTR nucleotide subregion that is capable of stably hybridizing to at least of a subregion of the 3′

miRNA section or at least a portion of the 5′

miRNA section such that if the third UTR nucleotide subregion can stably hybridizing to at least of a subregion of the 3′

miRNA section or at least a subregion of the 5′

miRNA section a second hybridization region is identified;

e) executing by the computer a step of evaluating the downstream UTR region for a fourth UTR nucleotide subregion that is capable of stably hybridizing to at least of a subregion of the 5′

miRNA section or at least a subregion of the 3′

miRNA section such that if the fourth UTR nucleotide subregion can stably hybridizing to at least of a subregion of the 3′

miRNA section or at least a subregion of the 5′

miRNA section a third hybridization region is identified; and

f) executing by the computer a step of identifying the mRNA nucleotide sequence as a candidate for forming a miRNA-mRNA triBridge complex, the miRNA-mRNA triBridge complex being a complex formed from the mRNA nucleotide sequence and the miRNA nucleotide sequence that includes the first hybridization region, the second hybridization region and the third hybridization region where the second hybridization region and the third hybridization region form a miRNA bridge.

2. The method of claim 1 wherein in the first hybridization region the first UTR nucleotide subregion in in an opposite direction to the second UTR nucleotide subregion with respect to 5′

to 3′

direction.

3. The method of claim 1 wherein in a miRNA interaction is upstream of the first hybridization region or downstream of the first hybridization region;

or upstream of the second hybridization region or downstream of the second region.

4. The method of claim 1 wherein the first hybridization region, the second hybridization region, and the third hybridization region each independently include from 5 to 15 nucleotide base pairs.

5. The method of claim 1 wherein stable hybridization is determine by a degree of complementariness.

6. The method of claim 5 wherein complementary sub-regions include at most 2 mismatches.

7. The method of claim 1 wherein stable hybridization is determined by thermodynamic criteria.

8. The method of claim 1 further comprising obtaining a biological sample form a subject and evaluating the mRNA nucleotide sequence for polymorphisms in the first nucleotide UTR subregion and/or the second nucleotide UTR subregion.

9. The method of claim 1 further comprising obtaining a biological sample form a subject and evaluating the mRNA nucleotide sequence for polymorphisms in the third nucleotide UTR subregion.

10. The method of claim 1 further comprising obtaining a biological sample from a subject and evaluating the mRNA nucleotide sequence for polymorphisms in the fourth nucleotide UTR subregion.