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基于DNA自由能量和单核酸多态密度的棕油油调节元素的识别

Redi Aditama¹, Zulfikar Achmad Tanjung¹, Victor Aprilyanto¹

¹Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia.

Computational biology and chemistry

|July 23, 2023

概括

研究人员使用DNA自由能量和SNP密度在棕油中确定了cis-regulatory元素 (CREs). 这种方法准确地预测了CRE位置,这对于植物生物技术应用至关重要.

科学领域:

植物基因组学植物基因组学
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

基因表达受到cis调节元件 (CREs) 的调节.
在油棕 (Elaeis guineensis Jacq.) 中了解CREs. 对于其生物技术来说至关重要.
准确识别CREs是一个挑战.

研究的目的:

在油棕基因组中定位cis调节元件 (CREs).
开发一种使用DNA自由能量和SNP密度进行CRE预测的高效方法.
探索促进区域中DNA自由能量和SNP密度之间的关系.

主要方法:

从油棕的基因组中提取了促进子序列 (TSS的上游1500nT到下游1000nT).
用PromPredict软件计算了DNA自由能量概况.
通过59个棕油原产地的深度测序数据来确定SNP密度.

主要成果:

与下游相比,上游TSS地区的平均自由能量 (AFE) 较高.
使用DNA自由能量方法预测了16,281个CREs,主要位于TSS上游.
在预测的CREs中观察到自由能量和SNP密度之间的反相关性模式,并在EgMSP1基因促进体中得到验证.

结论:

结合DNA自由能量和SNP密度方法,为预测棕油中CREs提供了准确和有效的方法.
这种方法对植物生物技术和基因工程有重大影响.
这些发现增强了我们对棕油中基因调节的理解.

关键词:

关联监管要素关联监管要素 DNA是自由的能量.埃莱斯 (Elaeis guineensis) 是一个古尼的植物.在SNP密度.

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