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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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CpG甲基化和基因表达之间的相关性是由序列变异驱动的.

Olafur Andri Stefansson1, Brynja Dogg Sigurpalsdottir2,3, Solvi Rognvaldsson2

  • 1deCODE genetics/Amgen Inc., Reykjavik, Iceland. olafurs@decode.is.

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概括

在CpG位点中的DNA甲基化模式调节基因表达. 由DNA序列变异驱动的基因特异甲基化定量特征位点 (ASM-QTLs) 解释了基因表达和CpG甲基化之间的大部分联系.

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科学领域:

  • 基因组学就是基因组学.
  • 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
  • 分子生物学分子生物学

背景情况:

  • 基因促进剂和增强剂序列通常在CpG位点未甲基化,与基因表达相关.
  • 据了解,DNA甲基化在基因表达中起着调节作用.

研究的目的:

  • 在全血基因组中的数百万个CpG单元中调查单 haplotype 特定的甲基化率.
  • 识别甲基化枯竭序列及其与遗传变异的关联.
  • 确定DNA序列变异在等位基因特定甲基化和基因表达中的作用.

主要方法:

  • 利用纳米孔测序来确定7,179个全血基因组中的1530万个CPG单元的甲基化率.
  • 确定了189178个甲基化贫乏序列 (至少在一个单元型上有三个或更多的近端CpG未甲基化).
  • 在896个样本上进行RNA测序,以将甲基化模式与基因表达相关联.

主要成果:

  • 发现了77,789个甲基化枯竭序列,与80,503个cis作用序列变异相关,称为等位基特异性甲基化定量特征位置 (ASM-QTLs).
  • 证明ASM-QTLs (DNA序列可变性) 驱动基因表达和CpG甲基化之间的相关性.
  • 发现ASM-QTLs在与血液学特征相关的变体中被显著丰富 (40.2倍丰富).

结论:

  • ASM-QTLs是非编码基因组中的关键功能元素,将DNA序列变异与表观遗传调节联系起来.
  • 通过ASM-QTLs捕获的DNA序列变异性是受DNA甲基化影响的等位基因特异性基因表达的主要驱动因素.
  • 这些发现强调了ASM-QTLs在理解复杂特征,特别是血液学特征的遗传和表观遗传基础方面的重要性.