Bioinformatics Analysis of hMTERF3 Gene Promoter Region

Abstract

Abstract:

Objective: To investigate the characters, transcription factors and their binding sites of human mitochondrial transcription
termination factor 3（hMTERF3）gene promoter by different bioinformatics tools. Methods: Promoter 2.0, NNPP, Proscan, and FirstEF
softwares were used to analyze the numbers and distributions of hMTERF3 gene promoter; CpG Islander and CpG Plot softwares were
used to analyze the GpG island of hMTERF3 gene promoter; P-match 1.0 protocol and TRANSFAC database were used to analyze the
transcription factors and their binding sites of hMTERF3 gene promoter. Results: hMTERF3 gene was located on 8q21.2. The full
length of hMTERF3 gene was 22 216 bp, consisting of 11 exons and 10 introns. There were at least two promoters in the 5' unconding
region of hMTERF3 gene. The core promoter of hMTERF3 gene was located between 1 733-2 302 bp, containing TATA box. In
hMTERF3 gene promoter region, a 1 145 bp CpG island could be found. In addition, 1 055 transcription factor binding sites were
predicted by P-Match 1.0 protocol, and only 19 transcription factor binding sites were found in conserved core promoter region of
human and mouse homologous MTERF3 genes by phylogenetic foot- printing analysis. Conclusion: Gene promoter related
bioinformatics analysis can improve the efficiency of hMTERF3 gene promoter research, and provide significant information for the
construction of promoter expression vector, also for the further study of promoter function.

Key words: hMTERF3, bioinformatics, promoter, transcription factor, CpG island

CLC Number:

Q71：Q811.4

Sun Meitao, Wang Yun, Li Yue, Zhang Xiaojuan, Yang Yongqin, Yang Zefang, Xiong W. Bioinformatics Analysis of hMTERF3 Gene Promoter Region[J]. , 2017, 2(2): 40-45.

References

〔1〕HYVÄRINEN A K，POHJOISMÄKI J L，HOLT I J，et al.
Overexpression of MTERFD1 or MTERFD3 impairs the
completion of mitochondrial DNA replication〔J〕. Mol Biol
Rep，2011，38（2）：1321-1328.
〔2〕PARK C B，ASIN- CAYUELA J，CÁMARA Y，et al.
MTERF3 is a negative regulator of mammalian mtDNA
transcription〔J〕. Cell，2007，130（2）：273-285.
〔3〕WREDENBERG A，LAGOUGE M，BRATIC A，et al.
MTERF3 regulates mitochondrial ribosome biogenesis in
invertebrates and mammals〔J〕. PLoS Genet，2013，9（1）：
e1003178.
〔4〕ANDERSSON D C，FAUCONNIER J，PARK C B，et al.
Enhanced cardiomyocyte Ca（2+）cycling precedes terminal
AV- block in mitochondrial cardiomyopathy Mterf3 KO
mice〔J〕. Antioxid Redox Signal，2011，15（9）：2455-
2464.
〔5〕熊伟，余敏，左绍远. 线粒体转录终止因子蛋白家族在线粒体基因表达中的调节作用〔J〕. 中国生物化学与分
子生物学报，2015，31（3）：223-231.
〔6〕XIONG W，LUO Y，ZHANG C，et al. Expression，purifi?
cation of recombinant human mitochondrial transcription
termination factor 3（hMTERF3）and preparation of poly?
clonal antibody against hMTERF3〔J〕. Appl Biochem
Biotechnol，2012，167（8）：2318-2329.
〔7〕熊伟，张晓娟，张海洋，等. 基于生物信息学方法预测
人线粒体转录终止因子3蛋白的结构与功能〔J〕. 生物技
术通讯，2015，26（3）：367-373.
〔8〕孙勇，王良喜，孙曙光，等. 人三叶因子3基因启动子区
的生物信息学分析〔J〕. 医学研究生学报，2013，26（4）：
340-342.
〔9〕唐亮，王燕，陈碧峰. 人Toll样受体9基因启动子区的生物
信息学分析〔J〕. 生物技术通讯，2014，25（2）：210-212.
〔10〕杨树德，曹奇志，冯小英，等. 人LAIR-1/CD305基因
启动子的生物信息学分析〔J〕. 细胞与分子免疫学杂
志，2010，26（8）：826-828.
〔11〕KLINGENHOFF A，FRECH K，QUANDT K，et al. Func?
tional promoter modules can be detected by formal models
independent of overall nucleotide sequence similarity〔J〕.
Bioinformatics，1999，15（3）：180-186.
〔12〕管晓翔，陈巍魏，陈龙邦，等. p27Kip1基因启动子区
的生物信息学分析〔J〕. 医学研究生学报，2010，23
（10）：1029-1032.
〔13〕TAKAI D，JONES P A. Comprehensive analysis of CpG
islands in human chromosomes 21 and 22〔J〕. Proc Natl
Acad Sci USA，2002，99（6）：3740-3745.
〔14〕WINGENDER E. TRANSFAC：a database on transcrip?
tion factors and their DNA binding sites〔J〕. Nucleic Acids
Research，1996，24（1）：238-241.
〔15〕PORTALES-CASAMAR E，THONGJUEA S，KWON A T，
et al. JASPAR 2010：the greatly expanded open-access
database of transcription factor binding profiles〔J〕. Nucle?
ic Acids Res，2010，38：105-110.
〔16〕王佐广，牛秋丽，刘雅，等. 线粒体融合基因2启动子
的生物信息学研究〔J〕. 中国动脉硬化杂志，2013，21
（2）：97-104.
〔17〕HOFFMAN M M，BUSKE O J，WANG J，et al. Unsuper?
vised pattern discovery in human chromatin structure
through genomic segmentation〔J〕. Nat Methods，2012，9
（5）：473-476.
〔18〕ERNST J，KELLIS M. ChromHMM：automating chroma?
tin-state discovery and characterization〔J〕. Nat Methods，
2012，9（3）：215-216.
〔19〕卢一鸣，屈武斌，张成岗. 基于表观基因组学的DNA
元件鉴定方法研究进展〔J〕. 生物化学与生物物理进
展，2014，41（7）：640-648.

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