US 2014/0228556A1 Fukuda Et Al
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US 20140228556A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0228556A1 Fukuda et al. (43) Pub. Date: Aug. 14, 2014 (54) RBOZYME FOR IDENTIFYING Publication Classification MODIFICATION ON RNASEQUENCE AND RNA CLEAVAGE METHOD USING SAME (51) Int. Cl. CI2N IS/II3 (2006.01) (75) Inventors: Masatora Fukuda, Fukuoka (JP); (52) U.S. Cl. Masanobu Deshimaru, Fukuoka (JP); CPC .................................... CI2N 15/I 13 (2013.01) Kei Kurihara, Fukuoka (JP) USPC ......................................... 536/23.1; 536/25.3 (73) Assignee: Fukuoka University, Fukuoka (JP) (21) Appl. No.: 14/118,562 (57) ABSTRACT (22) PCT Fled: May 19, 2012 The hammerhead ribozyme according to the present inven tion produces a hammerhead ribozyme-target RNA con (86) PCT NO.: PCT/UP2012/062878 struct by base-pairing with an edited target RNA, and an S371 (c)(1), editing recognition site of the hammerhead ribozyme cleaves (2), (4) Date: Nov. 19, 2013 the modification site by forming a base pair with the target RNA modification site. The cleavage of the modification site Related U.S. Application Data is expected to be applicable to the research and development (60) Provisional application No. 61/488.345, filed on May of new drugs that can be used to prevent or treat diseases 20, 2011. caused by the edited target RNA. Patent Application Publication Aug. 14, 2014 Sheet 1 of 21 US 2014/0228556 A1 FIG. 1 R2C fia S-A&CAAA Gia--O f f f A SITE / ESTE R 8 S: On O-P-O S. F.G. 1 RNAEDITING AND 3. 2....Y.A38 KC 38ii, 2.O.Y.A38; {S:33:38.88: FIG 2 sk- SES / , C38.arm-Es PRES J/ Riggy, iaiti isS: Arg. , BEFOREE: 83 8:8; it is is &ERE86 was aškisserkrg.E. Patent Application Publication Aug. 14, 2014 Sheet 2 of 21 US 2014/0228556 A1 FIG 3 Recognition base X) = C (for A-to-I editing) = A (for C-to-U editing) Hammerhead Ribozyme Helix 5 Substrate RNA w Editing site \ (A-to-I or C-to-U) Cleavage site Patent Application Publication Aug. 14, 2014 Sheet 3 of 21 US 2014/0228556 A1 FIG. 4 Patent Application Publication Aug. 14, 2014 Sheet 4 of 21 US 2014/0228556 A1 FIG. 5A Patent Application Publication Aug. 14, 2014 Sheet 5 of 21 US 2014/0228556A1 FIG. 6A : 2: S - 38 - 8 Patent Application Publication Aug. 14, 2014 Sheet 6 of 21 US 2014/0228556 A1 : C C & O 2: Patent Application Publication Aug. 14, 2014 Sheet 7 of 21 US 2014/0228556 A1 FIG. 7 HRZ1E VSHRZ1C 0.8 HRZ1C 06 DHR21 3.. *:: . as s is 0.2 { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - for. 2 24 $8 time (h) R2E WS HRZ2C Patent Application Publication Aug. 14, 2014 Sheet 8 of 21 US 2014/0228556 A1 FIG. 9 EA 3: Kä: 3: x 822 : 8 & 3.C. R2C X Patent Application Publication Aug. 14, 2014 Sheet 9 of 21 US 2014/0228556 A1 Patent Application Publication Aug. 14, 2014 Sheet 10 of 21 US 2014/0228556 A1 FIG. 1 1A : & Patent Application Publication Aug. 14, 2014 Sheet 11 of 21 US 2014/0228556 A1 FIG 11 B Patent Application Publication Aug. 14, 2014 Sheet 12 of 21 US 2014/0228556 A1 FIG 12 : 8 :: 28 FIG 13 ;: i 3. i :E. s: 3. i-8- 88: Patent Application Publication Aug. 14, 2014 Sheet 14 of 21 US 2014/0228556 A1 **** 6 Patent Application Publication Aug. 14, 2014 Sheet 16 of 21 US 2014/0228556 A1 A ... HRHTR2C edit 2 & 10 20 40 6O 90 (min) HiR2C-ade hir-HTR2C edit O 2 5 10 20 40 60 90 (min) HTR2C-ino > 3. O 20 40 60 80 100 Time (min) Patent Application Publication Aug. 14, 2014 Sheet 17 of 21 US 2014/0228556 A1 FIG. 20 isozyme (Xs A(HR-APOBedi) Stott) No.5) 3 -GAAJAS . {X, AAACA-5' 5 -GCAGACAUAUAUGAUsaac AAUUUGAUCAG-3 is state y x editing side a CAPOE-cytic8:338):8:w x AO8-irises 3x866, 3. C 0.8 4a s: 04 3 - 2 APOB-cy APOEur did 8 ite ini Patent Application Publication Aug. 14, 2014 Sheet 18 of 21 US 2014/0228556 A1 FIG. 21 A. cata is. Y. s. (ribozyme) Gayley)x.yiw £88 {x&X 8: six-: r Fixia-8cifist:}}}x}: -88 ($3:33:: &3:33 3. : ''Y w 2 S ( 2 : 8 it iii.338 in an as the tie on iriikii-8i ( 2 5 ( 20 & 8 90 init 8 ( 20 40 60 80 00 i8 is Patent Application Publication Aug. 14, 2014 Sheet 19 of 21 US 2014/0228556 A1 FIG. 22 A. ribozyne catalytic... ---a cose- {X}1. : CHR-FiM. r. -- e. NA-edits:o&: 38.3: 3 -AAGAYGGGAA: ; ; ; ; ; ; ; ; ; (XCCUGAGC-5; ; ; ; ; ; ; 5 JuCUAGCCUU-CAGGAGJCAGGGC-3 {substrate . editing scies: A Fixia-ade $83838-3 & fixiário is: 3 x8-67; 8 *-i-iii-ei ( 2 8 20 & 8 & fit iii.33:8 in a won eace de Y R-fixi£-8dii 2 20 - 80 S3 is Fijiaic { 3.8- : 06: s: 0.4 s: ...5 (.2 3, 20 40 80 80 00 ise it Patent Application Publication Aug. 14, 2014 Sheet 20 of 21 US 2014/0228556 A1 FIG. 23A Tet-ADAR2 Cell (Cultured with DOX) V Extraction of total RNA 1N/N1 N. ?\//N. 9. A-S unedited-FLNA mRNA MS R edited-FLNA mRNA 1N/N/N N/NYN M \, M Physiological RNAs V Cleavage reaction ( ; V Direct Sequencing Quantifying the editing ratio Patent Application Publication Aug. 14, 2014 Sheet 21 of 21 US 2014/0228556 A1 FIG. 23B HR-FLNA-edit FIG. 24 3 6 24 jeaction time (h) US 2014/0228556 A1 Aug. 14, 2014 RBOZYME FOR IDENTIFYING phrenia and autism; however, a mechanism to control normal MODIFICATION ON RNASEQUENCE AND regulation has not yet been revealed. RNA CLEAVAGE METHOD USING SAME 0007 Serotonin 2C receptor (HTR2CR), when serotonin is bound to the extracellular loop of HTR2CR, transmits TECHNICAL FIELD impulses to coupled G protein, then causes changes in prop erties of nerve cells via intracellular signal transduction path 0001. This application claims priority on U.S. Provisional way and eventually controls cerebral functions such as Application No. 61/488.345 filed on May 20, 2011. The memory, learning and emotion. When serotonin 20 receptor present invention relates to a ribozyme for identifying modi (HTR2CR) is subjected to RNA editing, the amino acid fication on an RNA sequence and an RNA cleavage method sequence in the G protein-binding region of a receptor protein using the same. More specifically, the present invention is changed and the signal transduction ability of the receptor relates to a hammerhead ribozyme for identifying modifica is changed. As shown in FIG. 2, in HTR2CR, up to 24 types tion on an RNA sequence by RNA editing and the like and an (mainly 8 types) of receptor proteins with different amino RNA cleavage method using the same. acid sequences and different transmitting abilities are gener ated from a single gene by combining sites Subjected to RNA BACKGROUND ART editing (shown by Solid-white letters in the drawing) among the base sequence of HTR2CR and amino acids to be encoded 0002. It is known that RNA in a living organism is chemi (Non-Patent Documents 4 and 5, FIG. 2). cally modified, and noncoding RNA such as rRNA and tRNA 0008. In the pre-mRNA of glutamate receptor subunit B is functionalized by modification. Meanwhile, mRNA is also (GRIA2), desensitization kinetics of the receptor and an ion modified and, for example, modification Such as RNA editing channel, Ca2++ permeability, are controlled by RNA editing Such as A-to-I editing in which adenosine (A) is substituted by (Non-Patent Document 6). inosine (I) in the nucleotides of mRNA and C-to-U editing in 0009. As another form of RNA modification by substitu which cytosine (C) is substituted by uracil (U) is known. tion, C-to-U editing in which cytosine (C) is substituted by 0003. Among these, RNA editing is a mechanism to con uracil (U) and cytosine is converted to uridine by deamination Vert genetic information after transcription and a phenom is known (Non-Patent Document 7). It is reported that the enon to alter the base at a specific site in the base sequence of nucleus transcriptional body encoding intestinal apolipopro pre-mRNA generated by transcription of a gene into another tein B (ApoB) is subjected to C-to-U RNA editing to convert base by enzyme action, and appears in various forms such as a CAA codon to a UAA stop codon and a shorter protein than insertions, deletions or substitutions of bases (Non-Patent that before editing is generated (Non-Patent Document 8). Document 1). This phenomenon is generally a mechanism 0010. As described above, RNA editing such as A-to-I programmed in living organisms to change gene products editing and C-to-U editing is involved in an important mecha depending on changes in physiological conditions and envi nism to control genetic adaptability by generating a protein ronments. In higher eukaryotes, it is believed that A-to-I different from a protein to be generated when editing does not editing in which the adenosine (A) base at a specific site in occur. RNA modification by Substitution in a coding region pre-mRNA is substituted by the inosine (I) base by the action plays a definitive role in biological process control, and thus of adenosine deaminase (ADAR) has a physiologically the development of abnormal modification is a cause of a important meaning (Non-Patent Document 2). When A-to-I serious disease (Non-Patent Document 9), and, in particular, base Substitution occurs in an mRNA sequence encoding a the relation of RNA modification by substitution to mental protein, since the inosine (I) is read as guanosine by ribo disorders such as Schizophrenia, bipolar disorder and major Somes during translation, codons are changed, thereby depressive disorder attracts attention.