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相关概念视频

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
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...
9.9K
DNA as a Genetic Template02:05

DNA as a Genetic Template

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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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...
3.9K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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...
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Bacterial Transcription01:53

Bacterial Transcription

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RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
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相关实验视频

Updated: Jun 29, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

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具有物种意识的DNA语言模型捕捉了调节元素及其演变.

Alexander Karollus1,2, Johannes Hingerl1, Dennis Gankin1

  • 1School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

Genome biology
|April 2, 2024
PubMed
概括

具有物种意识的DNA语言模型通过分析进化模式,在各种物种中有效地识别基因调节元素. 这些模型在预测功能序列和理解动机演变方面优于传统方法.

更多相关视频

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

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相关实验视频

Last Updated: Jun 29, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.6K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 大规模的多物种基因组测序推进了对基因调节的理解.
  • 需要新的算法来识别使用进化保护的监管元素.

研究的目的:

  • 引入对物种有意识的DNA语言模型,用于监管元素的识别.
  • 评估它们在跨越进化距离的过程中捕获保存的调节元素的能力.

主要方法:

  • 在800多种物种上训练了DNA语言模型.
  • 评估模型在预测掩盖核酸和区分功能性图案方面的性能.
  • 对比模型功能与序列对齐,以捕捉遥远的进化保护.

主要成果:

  • DNA语言模型区分了转录因子和RNA结合蛋白质图案与非编码序列.
  • 模型捕捉了比序列对齐更大的进化距离上保存的调节元素.
  • 模型准确地重建了体内结合的动图实例,并解释了动图演变.

结论:

  • 具有物种意识的DNA语言模型是整合来自高度分化的基因组数据的强大工具.
  • 这些模型为分析基因组监管信息提供了灵活和可扩展的方法.
  • 这些模型展示了对基因调节中的序列和进化背景的复杂理解.