KR102477906B1 - 유도만능 줄기세포 분화 특이적 lncRNA, 및 이의 용도 - Google Patents
유도만능 줄기세포 분화 특이적 lncRNA, 및 이의 용도 Download PDFInfo
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Abstract
Description
도 2는 lncRNA 유전자 중 NPC 특이적 유전자를 규명한 것이다.
도 3은 발명의 일 실시예에 따른 신경 분화 특이적 lncRNA 후보군을 ZENBU browser에서 개별적으로 확인한 것이다.
도 4는 RT-qPCR을 이용하여 20개의 후보군에 대한 실험적 검증을 진행한 것이다.
NPC 특이적 lncRNA 개수 | 1차 분석(LNCipedia) | 2차 분석( FANTOM CAT) |
분석 결과 | 60 | 51 |
공통으로 발견된 lncRNA | 18 | |
확인 후 선별된 lncRNA | 36 | 14 |
구분 | 단계 | 내용 |
1 | 데이터 다운로드 | RNA-seq & CAGE-seq 데이터 ZENBU browser에서 내려 받음(binning size: 128bp) |
2 | 파일 intersection | LncRNA발현 데이터와 annotation 파일 intersection(bedtools) |
3 | strand 유형 정리 | LncRNA strand(Sense, Anti-sense) 정리 |
4 | 유전자 grouping | LncRNA 유전자별로의 grouping(bedtools) |
5 | 데이터 표준화 | 각 샘플 값 normalization |
6 | Fold change 값 계산 | RNA-seq 및 CAGE-seq 공통으로 iPSC와 NPC fold-change값이 4배 이상 차등발현 보이는 lncRNA 규명 |
7 | ZENBU browser에서 선별 | NPC 특이적인 lncRNA 후보를 개별적으로 ZENBU browser에서 확인함으로 high-confidence list 선별 |
서열
번호 |
후보
이름 |
유전자명 | 발현량 | 위치 | |||
NPC | hiPSC | 염색체 | start | end | |||
1 | npc1 | lnc-TRAFD1-4 | 1088.89 | 236.96 | chr12 | 112267077 | 112267394 |
2 | npc2 | lnc-LRRTM4-6 | 895.776 | 189.466 | chr2 | 76445079 | 76445410 |
3 | npc3 | lnc-TMEM135-8 | 683.198 | 6.39425 | chr11 | 86800544 | 86937818 |
4 | npc4 | lnc-ENC1-5 | 293.456 | 15.3835 | chr5 | 74627406 | 74641424 |
5 | npc5 | lnc-PYGO1-2 | 238.96 | 0.709 | chr15 | 55611552 | 55614422 |
6 | npc6 | lnc-SLC10A6-4 | 221.71 | 19.0565 | chr4 | 86164446 | 86594119 |
7 | npc7 | lnc-CDH11-12 | 171.95 | 6.7045 | chr16 | 65004642 | 65126112 |
8 | npc8 | lnc-SIX2-3 | 134.825 | 1.058 | chr2 | 44920193 | 44939206 |
9 | npc9 | lnc-TDP1-3 | 113.702 | 24.6073 | chr14 | 89712511 | 89712823 |
10 | npc10 | lnc-WDR25-6 | 104.141 | 0.13625 | chr14 | 100726893 | 100728690 |
11 | npc11 | lnc-STBD1-3 | 91.0335 | 8.0185 | chr4 | 76436146 | 76559576 |
12 | npc12 | lnc-COL2A1-1 | 78.06 | 0.331 | chr12 | 47997615 | 48004486 |
13 | npc13 | SPON1 | 69.5095 | 4.6435 | chr11 | 13962723 | 14280155 |
14 | npc14 | lnc-GLIS3-2 | 65.9525 | 4.04975 | chr9 | 3824127 | 4348392 |
15 | npc15 | lnc-SS18-7 | 59.472 | 3.47475 | chr18 | 25227587 | 25352190 |
16 | npc16 | lnc-CHD2-4 | 36.6095 | 1.82425 | chr15 | 93312557 | 93569483 |
17 | npc17 | FEZF1-AS1 | 33.5945 | 0.95975 | chr7 | 122303658 | 122310077 |
18 | ipsc1 | lnc-C8orf83-8 | 0.214 | 38.0028 | chr8 | 92005166 | 92103228 |
19 | ipsc2 | lnc-POM121L2-2 | 0.9175 | 10.7953 | chr6 | 27357823 | 27375374 |
20 | ipsc3 | lnc-HS3ST5-7 | 0.1655 | 45.5813 | chr6 | 114408889 | 114456194 |
Claims (6)
- 서열번호 18 내지 20으로 이루어진 군에서 선택된 하나 이상의 염기서열을 가지는 유전자로부터 전사되고, 유도만능 줄기세포가 신경으로 분화할 때 유도만능 줄기세포에서 발현이 증가되는 유도만능 줄기세포 신경 분화 특이적 lncRNA(long non-coding RNA).
- 제1항의 lncRNA 염기서열, 상기 lncRNA에 대한 안티센스 염기서열, 또는 상기 lncRNA 염기서열의 단편인 유도만능 줄기세포의 분화 예측용 바이오 마커.
- 제1항의 염기서열, 상기 lncRNA 염기서열의 단편, 상기 lncRNA 염기서열에 특이적으로 결합하는 프라이머 또는 프로브를 포함하는 유도만능 줄기세포의 분화 예측용 키트.
- 제3항에 있어서,
마이크로어레이, 유전자 증폭 키트, RNA 시퀀싱(RNA sequencing) 또는 면역분석(immunoassay)용 키트인 유도만능 줄기세포의 분화 예측용 키트. - (a) 유도만능 줄기세포 및 시험 제제를 접촉시키는 단계;
(b) 서열번호 18 내지 20으로 이루어진 군에서 선택된 하나 이상의 염기서열을 가지는 유전자로부터 전사된 lncRNA의 발현에 대한 조절 효과를 결정하는 단계; 및
(c) 상기 시험 제제와 접촉된 세포 및 상기 시험 제제와 접촉되지 않은 대조군에서 상기 lncRNA의 발현 수준을 비교하는 단계;를 포함하는 유도만능 줄기세포의 분화 조절제 스크리닝 방법. - 제1항의 신경 분화 특이적 lncRNA의 발현을 증가 또는 억제시키는 단계;를 포함하는 유도만능 줄기세포의 분화 제어 방법.
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WO2012018881A2 (en) | 2010-08-03 | 2012-02-09 | Alnylam Pharmaceuticals, Inc. | Methods and compositions for the regulation of rna |
CN105238784A (zh) | 2015-10-16 | 2016-01-13 | 上海交通大学 | 长非编码rna及在作为调控神经干细胞增殖和分化中的应用 |
US9441224B1 (en) | 2013-06-27 | 2016-09-13 | California Institute Of Technology | Long noncoding RNAS and cell reprogramming and differentiation |
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WO2012018881A2 (en) | 2010-08-03 | 2012-02-09 | Alnylam Pharmaceuticals, Inc. | Methods and compositions for the regulation of rna |
US9441224B1 (en) | 2013-06-27 | 2016-09-13 | California Institute Of Technology | Long noncoding RNAS and cell reprogramming and differentiation |
CN105238784A (zh) | 2015-10-16 | 2016-01-13 | 上海交通大学 | 长非编码rna及在作为调控神经干细胞增殖和分化中的应用 |
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