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Transcription Factors02:16

Transcription Factors

82.2K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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General Transcription Factors01:30

General Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
6.7K
Combinatorial Gene Control02:33

Combinatorial Gene Control

9.5K
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...
9.5K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

12.1K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
12.1K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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...
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Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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STAN：空間情報を考慮した転写因子活性を推定するための計算フレームワーク

Linan Zhang1, April Sagan2, Bin Qin3

  • 1Department of Applied Mathematics, School of Mathematics and Statistics, Ningbo University, Ningbo, Zhejiang 315211, China.

Nucleic acids research
|January 12, 2026
PubMed
まとめ

STANは、空間トランスクリプトミクスを使用して組織内の転写因子（TF）活性をマッピングする計算手法を開発した。これにより、TFネットワークがさまざまな疾患や生物学的文脈における細胞アイデンティティと空間組織にどのように影響するかを明らかにする。

キーワード:
空間トランスクリプトミクス転写因子活性計算フレームワーク細胞アイデンティティ組織構造

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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科学分野:

  • 計算生物学
  • ゲノミクス
  • システム生物学

背景:

  • 転写因子（TF）は細胞応答を調節し、微小環境の影響を受けます。
  • 空間トランスクリプトミクス（ST）は組織微小環境に関する洞察を提供しますが、TF活性の推定には十分に活用されていません。
  • 細胞アイデンティティと空間組織におけるTFの役割を理解することは重要です。

研究 の 目的:

  • STデータから空間的に解決されたTF活性を推定するための計算アプローチを開発すること。
  • TF活性、細胞アイデンティティ、および組織構造の関係を調査すること。
  • 生物学的発見のためのSTデータの分析能力を強化すること。

主な方法:

  • STAN（Spatially informed Transcription factor Activity Network）を導入しました。これは線形混合効果モデルです。
  • TF-ターゲット遺伝子プライア、mRNA発現、空間座標、および組織学的特徴を統合しました。
  • Lymph node、脳、乳がん、神経膠芽腫の多様なSTデータセットにSTANを適用しました。

主要な成果:

  • STANは、スポット固有のTF活性を正常に予測しました。
  • 異なる細胞タイプ、空間領域、および病理学的ゾーンに関連するTFを特定しました。
  • 組織微小環境内のリガンド-受容体相互作用におけるTFの関与を明らかにしました。

結論:

  • STANはSTデータからTF活性を効果的に推定し、空間的コンテキストを提供します。
  • このアプローチは、細胞機能と組織組織におけるTFの役割を理解するためのSTの有用性を高めます。
  • さまざまな生物学的システムにわたるTFネットワークと空間生物学の間の複雑な相互作用を強調しています。