在 silico 基因组移植和生物多样性的 cis 监管基础
Alexander L Starr1, Michael E Palmer1, Hunter B Fraser1
1Department of Biology, Stanford University, Stanford, CA, USA.
Trends in genetics : TIG
|November 29, 2025
概括
机器学习从DNA序列中预测cis-regulatory活动,从而使基因组移植成为可能. 这种强大的新方法为生物多样性的遗传基础提供了洞察力.
科学领域:
- 进化生物学是进化的生物学.
- 基因组学就是基因组学.
- 计算生物学是一种计算生物学.
背景情况:
- 转录的 cis-regulation 驱动着表型多样性的演化.
- 目前研究cis调节的实证方法受到混因素和可扩展性的限制.
研究的目的:
- 开发一种基于机器学习的方法,从DNA序列中预测cis-regulatory活动.
- 为了使基因组移植能够用于研究cis-regulatory分歧.
- 为了提供一种更强大,更可扩展的方法来推断自然选择对ciss-regulatory元素的推断.
主要方法:
- 利用机器学习模型根据DNA序列预测cis调节活动.
- 在基因组移植中进行基因移植,以评估跨物种的 cis 调控特征.
- 编目全基因组的 cis 调节分歧.
主要成果:
- 拟议的方法允许在跨物种背景下预测cis-regulatory特征.
- 在基因组移植可以揭示cis-regulatory分歧的模式.
- 这种方法可以更容易地推断出自然选择是如何作用于ciss-regulatory元素的.
结论:
- 基于机器学习的Cis-regulatory活动预测为实证方法提供了一个可扩展和强大的替代方案.
- 在 silico 基因组移植为生物多样性的遗传基础提供了前所未有的见解.
- 这种方法可以显著提升我们对生命树上的进化过程的理解.
相关概念视频
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
02:13Overview of Transposition and Recombination
18.7K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
18.7K
02:08Gene Conversion
10.5K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.5K
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
02:51Multi-species Conserved Sequences
4.6K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.6K