水稻基因组核小体定位分析

Nucleosome Positioning Analysis In Rice

黎圆圆

11749074

硕士

生物学

侯春晖

2019-05-22

2019-06-20

哈尔滨工业大学

深圳

水稻(Oryza sativa L.)作为重要的高等真核模式植物，具有重大研究意义。真核生物遗传物质染色质的基本结构单位是核小体，它是由组蛋白八聚体和~147bp的核心DNA组成，其中组蛋白八聚体是由组蛋白H2A/H2B，H3/H4各两个拷贝组成，核心DNA围绕组蛋白八聚体盘绕1.75圈，组蛋白H1结合在连接DNA上，锁住核小体DNA的进出端，稳定核小体的状态。核小体在压缩染色质形成高级结构和基因调控中发挥重要作用，分析水稻基因组中核小体在DNA序列上的精确位置，即核小体定位，对于基因调控机制的研究具有重要的意义。核小体定位与顺式调节元件的位置相关。例如，有研究发现核小体位于真核基因的转录起始位点(TSS, transcription start stie)附近，然而关于核小体定位的动态模式及其与转录调节间关联的研究较少。本课题采用微球菌核酸酶(MNase, micrococcal nuclease)消化水稻染色质，获得单核小体大小的DNA片段，经纯化后扩增，通过Illumina高通量测序获得DNA序列，运用生物信息学分析手段，对水稻日本晴根、茎、叶三种不同组织全基因组核小体定位进行分析；通过核小体与TSSs附近区域不同的结合情况对水稻基因进行分类，揭示了与不同功能类别基因相关的核小体定位模式；寻找核小体定位不同的开放基因，并对每个组织的不同核小体定位的开放基因做GO (gene ontology)分析，发现核小体的定位差异与基因表达具有很强的关联性。通过整合MNase-seq数据分析，我们初步在水稻中揭示了核小体定位模式与基因结构、功能以及表达调控之间的关系。

Rice (Oryza sativa L.) is an important higher eukaryotic model plant with great research significance. The basic structural unit of chromatin in eukaryotic is nucleosome, a histone octamer wrapped around by DNA by 1.75 laps. Each histone octamer contains two copies of histone H2A/H2B and H3/H4 dimers. DNA wrapped around a nucleosome is ~147 bp . Histone protein H1 locks the entry and exit ends of nucleosome DNA to stabilize nucleosomes. Nucleosomes play an important role in the compression of chromatin, formation of high order chromatin structure and gene transcription regulation. Studies have shown that nucleosome localization is correlated with the location of cis-regulatory elements. For example, nucleosomes are found well positioned near the transcription start site (TSSs) of eukaryotic gene. However, there are very limited studies on the dynamic patterns of nucleosome localization and occupancy and their association with transcriptional regulation. In this project, we digested the rice genome with micrococcal nuclease (MNase) to obtain the DNA fragments wrapping around single nucleosomes for Illumina high-throughput sequencing. We carried out bioinformatic analysis and reveal the global occupancy of nucleosomes in three different rice tissues: roots, stems and leaves. The pattern of nucleosome occupancy at TSSs was found different in three tissues. GO analysis was performed on the genes with differential nucleosome occupancy in different tissue and revealed that the differential occupancy of nucleosome is correlated with the gene expression level. By integrating MNase-seq data analysis, we initially revealed the relationship between nucleosome localization patterns and gene structure, function, and expression regulation in rice.

核小体定位 水稻 高通量测序 GO分析

nucleosome positioning rice high-throughput sequencing GO analysis MNase-seq

中文

联合培养

南方科技大学

黎圆圆. 水稻基因组核小体定位分析[D]. 深圳. 哈尔滨工业大学,2019.