通过对植物泛基因组和泛转录组的贝叶斯分析揭示了调节代码的自然变异
Wei Wei1, Xing Wu2,3, Chandler A Sutherland1
1Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
bioRxiv : the preprint server for biology
|November 24, 2025
概括
我们开发了K-PROB,这是一个计算工具,用于在植物基因组中识别cis-regulatory元素 (CREs). K-PROB揭示了促进子变异如何驱动基因表达多样性,有助于作物特征工程.
科学领域:
- 植物基因组学 植物基因组学
- 计算生物学是一种计算生物学.
- 分子遗传学 分子遗传学
背景情况:
- 了解 cis 调节元件 (CREs) 对于作物基因表达工程和特征调节至关重要.
- 植物基因表达的快速进化通常与促进体的结构变异有关,这对单基因组分析提出了挑战.
研究的目的:
- 开发一种计算工具,K-PROB (K-mer-based in silico PROmoter Bashing),通过分析物种内促进子序列和基因表达变异来识别CREs.
- 研究促进体中的结构变异作为植物转录多样性的驱动因素的作用.
主要方法:
- K-PROB使用基于k-mer的贝叶斯变量选择框架来识别泛基因组和泛转录组的因果变量.
- 该工具应用于玉米和大豆,重点关注具有高度可变的促进子序列和多样化的表达模式的基因.
- 验证涉及识别与转录因子结合部位,开放色素区域和DAP-seq结合部位相关的k-mers,并通过光酶记者分析进一步确认.
主要成果:
- K-PROB成功地确定了为转录因子结合序列和重叠与调控区域丰富的k-mers.
- 在存在/缺失结构变异中发现了显著的k-mers,证实了它们在转录多样性中的作用.
- 路西法酶记者测定验证了已识别的k-mers对基因表达的监管影响.
结论:
- K-PROB提供了一种高吞吐量,泛基因的方法,用于发现新的cis元素和理解自然的物种内部监管多样性.
- 这些发现凸显了促进剂结构变异对于推动作物中的基因表达多样性的重要性.
- 这种方法促进了未来的表达工程,以改善作物特征.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
6.8K
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...
6.8K
02:02Cis-regulatory Sequences
11.5K
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...
11.5K
02:02Cis-regulatory Sequences
4.0K
4.0K
02:05Gene Evolution - Fast or Slow?
7.9K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.9K
01:25Genetic Variation
1.2K
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
Genes exist in different versions called alleles,...
1.2K
03:21Genome Size and the Evolution of New Genes
9.0K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
9.0K