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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.6K
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...
9.6K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.3K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.3K
Combinatorial Gene Control02:33

Combinatorial Gene Control

8.2K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.2K
Master Transcription Regulators02:23

Master Transcription Regulators

6.8K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
6.8K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

5.9K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
5.9K
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

4.5K
4.5K

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相关实验视频

Updated: May 21, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

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创建:通过离散嵌入来识别特定细胞类型的cis-regulatory元素.

Xuejian Cui1, Qijin Yin1, Zijing Gao1

  • 1Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, China.

Nature communications
|May 17, 2025
PubMed
概括

CREATE是一个新的深度学习框架,通过整合多种基因组数据类型来识别和表征cis-regulatory元素 (CREs). 这促进了对健康和疾病中的基因调节的理解.

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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

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科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 分子生物学分子生物学

背景情况:

  • 对基因调节至关重要,但目前的识别方法有限.
  • 现有的方法往往侧重于单个CRE类型,缺乏细胞类型的特异性.

研究的目的:

  • 开发一个全面的框架,用于CRE的识别和表征.
  • 为了能够对CREs及其调节功能进行细胞类型特定的分析.

主要方法:

  • 介绍了CREATE,这是一个使用矢量量量化变量自动编码器的多式深度学习框架.
  • 综合基因组序列,染色质可访问性和染色质相互作用数据.
  • 为多个类别的分类和表征生成了离散的CRE嵌入.

主要成果:

  • CREATE准确地识别了特定于细胞类型的CREs.
  • 该框架提供了对CRE特征和监管代码的定量和可解释的见解.
  • 促进了在特定细胞类型中大规模预测CREs.

结论:

  • CREATE增强了对基因调节场景的理解.
  • 该框架有助于识别疾病或表型相关的CRE变异性.
  • 在健康和疾病背景下推进基因调节的研究.