在完整的植物基因组中,同时对染色质可访问性和DNA甲基化进行分析,使用长读测序
Basile Leduque1, Alejandro Edera1, Clémentine Vitte2
1Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche Scientifique, Institute National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, Orsay, France.
Nucleic acids research
|April 27, 2024
概括
同时可访问性和DNA甲基化测序 (SAM-seq) 在植物中提供高分辨率的表观遗传特征. 这种方法揭示了DNA甲基化和染色质可访问性在独特和重复的基因组区域之间的交叉声.
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:
- 诸如染色质可访问性和DNA甲基化等表观遗传因素对于基因组功能至关重要.
- 现有的短读测序方法在重复区域和同时多特征分析方面遇到了困难.
- 植物表观遗传学需要先进的技术来进行全面的分析.
研究的目的:
- 开发一种用于同时分析染色质可访问性和DNA甲基化的新方法.
- 在重复的基因组区域中克服短读测序的局限性.
- 以高分辨率研究植物表观遗传调节.
主要方法:
- 同时可访问性和DNA甲基化测序 (SAM-seq) 使用长读纳米孔测序.
- 用SAM-seq应用于从阿拉比多普西斯和玉米中净化的核.
- 对DNA甲基化中的序列偏好偏差的分析.
主要成果:
- SAM-seq提供高分辨率,全基因组的染色质可访问性和植物DNA甲基化的地图.
- 在基因,TEs和中心重复中发现了可访问性和甲基化之间的交叉声.
- 揭示了染色质域中的细胞异质性和潜在的细胞特异性调节.
结论:
- SAM-seq是一个强大的工具,可以在独特和重复的序列中同时进行表观遗传分析.
- 该方法增强了对植物表观遗传机制和基因组调节的理解.
- SAM-seq为研究复杂的表观遗传景观开辟了新的途径.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...