为玉米建立一个优化的ATAC-seq协议
Jo-Wei Allison Hsieh1,2, Pei-Yu Lin1, Chi-Ting Wang1
1Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Frontiers in plant science
|June 12, 2024
概括
我们为玉米开发了一种简单的转化酶可访问染色体测试,具有高通量测序 (ATAC-seq) 协议. 这种方法有效地绘制了染色质景观,有助于作物改进和精确的基因控制策略.
科学领域:
- 基因组学就是基因组学.
- 植物生物学 植物生物学
- 分子生物学分子生物学
背景情况:
- 下一代测序提供了对染色质结构的洞察,这对于理解作物发育和适应中的基因活性至关重要.
- 玉米表现出与转录变异相关的动态色素结构,需要整合色素数据以精确控制育种中的基因.
研究的目的:
- 为玉米开发一种可访问和高效的转化酶可访问染色体检测与高通量测序 (ATAC-seq) 协议.
- 为了能够精确评估玉米染色质景观,用于作物改良应用.
主要方法:
- 为玉米开发了一种精简的四步ATAC-seq协议,需要更少的核和标准设备.
- 在没有细胞分类的情况下实现核净化,只使用标准的长板离心机.
- 生物信息分析包括通过阅读长度周期性,关键指标和与转录丰度的相关性进行验证.
主要成果:
- 展示了一种精确有效的方法来评估玉米染色质景观.
- 该协议成功地绘制了对作物改进至关重要的 cis-regulatory 元素.
- 通过全面的生物信息学分析验证了该协议的有效性.
结论:
- 开发的ATAC-seq协议对于玉米来说很容易实施,这有助于进行染色体结构研究.
- 这种方法支持在作物育种中精确的基因控制策略.
- 该协议的设计可以适应其他作物和组织,特别是那些样本大小有限的作物和组织.
相关概念视频
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...