|本期目录/Table of Contents|

果蝇基因组功能区域组蛋白修饰的协同模式(PDF)

《内蒙古大学学报(自然科学版)》[ISSN:1000-9035/CN:22-1262/O4]

期数:
2015年06期
页码:
619-629
栏目:
研究论文
出版日期:
2015-11-20

文章信息/Info

Title:
Combinatorial Patterns of Histone Modifications in Functional Regions of Drosophila Melanogaster Genome
作者:
张砚 张利绒 曹艳妮
内蒙古大学物理科学与技术学院物理系, 呼和浩特 010021
Author(s):
ZHANG Yan ZHANG Li-Rong CAO Yan-Ni
School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
关键词:
组蛋白修饰功能区域组合模式
Keywords:
histone modificationfunctional regioncombinatorial pattern
分类号:
Q61
DOI:
-
文献标识码:
-
摘要:
基于"组蛋白密码"假设,以黑腹果蝇(Drosophila melanogaster)为研究对象,应用CoSBI(coherent and shifted bicluster identification)算法对黑腹果蝇Oregon-R细胞株培养14-16h的胚胎细胞,在全基因组范围、RNA聚合酶Ⅱ结合区域、绝缘子结合蛋白的结合区域的22种组蛋白修饰的分布情况进行CoSBI聚类分析,发现了果蝇基因组的功能区域所具有的一些"核心组蛋白修饰",说明果蝇基因组的组蛋白修饰具有成簇出现、相互协同的调控模式.另外,将黑腹果蝇处于14-16h胚胎细胞的基因分为表达与不表达两类,分析了两类基因所在区域组蛋白修饰的组合模式.
Abstract:
Based on histone code hypothesis,a scalable subspace clustering algorithm,coherent and shifted bicluster identification (CoSBI) is applied to analyze the distribution features of histone modifications in order to study its regulational function in the biological processes.Genome-wide maps of 22 histone modifications have been generated using ChIP-seq of 14-16h embryos for Oregon-R strain of Drosophila melanogasters.Considering the distribution of 22 histone modifications on the whole genome,genomic regions binding by RNA polymeraseⅡand seven distinct insulators binding proteins,a significant correlation feature is analyzed between histone modifications and some core combinatorial patterns are found out.Furthermore,the algorithm is applied on two groups with different activities (expressed genes and non-expressed genes) respectively and combinational patterns of histone modifications associated with gene expression level are analyzed.

参考文献/References

[1] Strahl Brian D,Allis C David.The language of covalent histone modifications[J].Nature,2000,403(6765):41-45.
[2] Rando Oliver J.Combinatorial complexity in chromatin structure and function:revisiting the histone code[J].Current opinion in genetics & development,2012,22(2):148-155.
[3] Benevolenskaya Elizaveta V.Histone H3K4 demethylases are essential in development and differentiation[J].Biochemistry and cell biology,2007,85(4):435-443.
[4] Rosenfeld Jeffrey A,Wang Zhibin,Schones Dustin E,et al.Determination of enriched histone modifications in non-genic portions of the human genome[J].BMC genomics,2009,10:143.
[5] Elsheikh Somaia E,Green Andrew R,Rakha Emad A,et al.Global histone modifications in breast cancer correlate with tumor phenotypes,prognostic factors,and patient outcome[J].Cancer research,2009,69(9):3802-3809.
[6] Wang Zhong,Gerstein Mark,Snyder Michael.RNA-Seq:a revolutionary tool for transcriptomics[J].Nature Reviews Genetics,2009,10(1):57-63.
[7] Park Peter J.ChIP-seq:advantages and challenges of a maturing technology[J].Nature Reviews Genetics,2009,10(10):669-680.
[8] Ucar Duygu,Hu Qingyang,Tan Kai.Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering[J].Nucleic acids research,2011,39(10):4063-4075.
[9] modENCODE Consortium.Identification of functional elements and regulatory circuits by Drosophila modENCODE[J].Science,2010,330(6012):1787-1797.
[10] Langmead Ben,Salzberg Steven L.Fast gapped-read alignment with Bowtie 2[J].Nature methods,2012,9(4):357-359.
[11] Li Heng,Handsaker Bob,Wysoker Alec,et al.The sequence alignment/map format and SAMtools[J].Bioinformatics,2009,25(16):2078-2079.
[12] Quinlan Aaron R,Hall Ira M.BEDTools:a flexible suite of utilities for comparing genomic features[J].Bioinformatics,2010,26(6):841-842.
[13] Kubicek Stefan,O’Sullivan Roderick J,August E Michael,et al.Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase[J].Molecular cell,2007,25(3):473-481.
[14] Barski Artem,Cuddapah Suresh,Cui Kairong,et al.High-resolution profiling of histone methylations in the human genome[J].Cell,2007,129(4):823-837.
[15] Himanen Kristiina,Woloszynska Magdalena,Boccardi Tommaso M,et al.Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis[J].The Plant Journal,2012,72(2):249-260.
[16] Hwang William W,Venkatasubrahmanyam Shivkumar,Ianculescu Alexandra G,et al.A conserved RING finger protein required for histone H2B monoubiquitination and cell size control[J].Molecular cell,2003,11(1):261-266.
[17] Burgess-Beusse Bonnie,Farrell Catherine,Gaszner Miklos,et al.The insulation of genes from external enhancers and silencing chromatin[J].Proceedings of the National Academy of Sciences of the United States of America,2002,99(Z4):16433-16437.
[18] Gurudatta B V,Corces Victor G.Chromatin insulators:lessons from the fly[J].Briefings in functional genomics,2009,8(4):276-282.
[19] Amartya Sanyal,Bryan R Lajoie,Gaurav Jain,et al.The long-range interaction landscape of gene promoters[J].Nature,2012,489(7414):109-113.
[20] Portoso Manuela,Cavalli Giacomo.Weinheim:Germany WILEY-VCH Verlag GmbH & Co. KGaA[M].RNA and the regulation of gene expression:a hidden layer of complexity,2008:29-44.
[21] Zeng Jia,Kirk Brian D,Gou Yufeng,et al.Genome-wide polycomb target gene prediction in Drosophila melanogaster[J].Nucleic acids research,2012,40(13):5848-5863.
[22] Kondo Yutaka,Shen LanLan,Issa Jean-Pierre J.Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer[J].Molecular and cellular biology,2003,23(1):206-215.
[23] Phillips Jennifer E,Corces Victor G.CTCF:master weaver of the genome[J].Cell,2009,137(7):1194-1211.
[24] Kharchenko Peter V,Alekseyenko Artyon A,Schwartz Yuri B,et al.Comprehensive analysis of the chromatin landscape in Drosophila melanogaster[J].Nature,2011,471(7339):480-485.
[25] Wilkins R Chris,Lis John T.GAGA factor binding to DNA via a single trinucleotide sequence element[J].Nucleic acids research,1998,26(11):2672-2678.
[26] Mohan Man,Bartkuhn Marek,Herold Martin,et al.The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning[J].The EMBO journal,2007,26(19):4203-4214.
[27] Zhi-Liang Hu,Bao J,Reecy J M.CateGOrizer:a web-based program to batch analyze gene ontology classification categories[J].Online J Bioinformatics,2008,9(2):108-112.
[28] Xu Han,Wei Chia-Lin,Lin Feng,et al.An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data[J].Bioinformatics,2008,24(20):2344-2349.

备注/Memo

备注/Memo:
收稿日期:2015-04-20;改回日期:2015-09-09。
基金项目:国家自然科学基金资助项目(61462068,31106188);内蒙古自治区自然科学基金资助项目(2014MS0103)
作者简介:张砚(1985-),女(蒙古族),内蒙古呼和浩特人,硕士.
通讯作者:张利绒(1972-),女,内蒙古乌兰察布人,副教授,博士.E-mail:pyzlr@imu.edu.cn.
更新日期/Last Update: 1900-01-01