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Related Concept Videos

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...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.4K
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...
6.4K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.2K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.2K
Master Transcription Regulators02:23

Master Transcription Regulators

6.9K
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...
6.9K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

7.3K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Transcription01:17

Transcription

21.6K
Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
21.6K

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Updated: Jun 28, 2025

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
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Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

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Deep Learning Sequence Models for Transcriptional Regulation.

Ksenia Sokolova1, Kathleen M Chen1, Yun Hao2

  • 1Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA; email: sokolova@princeton.edu, kc31@princeton.edu, ogt@cs.princeton.edu.

Annual Review of Genomics and Human Genetics
|April 10, 2024
PubMed
Summary
This summary is machine-generated.

Deep learning models analyze DNA sequences to understand gene expression regulation and the impact of genetic variations. These models predict functional consequences of genomic variants, offering insights into biological mechanisms.

Keywords:
AIdeep learninggenomicsmachine learningsequence modelstranscriptional regulation

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Understanding gene expression regulation and the impact of genetic variations is crucial in human genetics.
  • Abundant data from experimental technologies enables advanced computational approaches.

Purpose of the Study:

  • To develop sequence-based deep learning models for deciphering the regulatory code of gene expression.
  • To interpret the transcriptional effects of genome variation and predict functional consequences of noncoding variants.

Main Methods:

  • Utilizing sequence-based deep learning models to link DNA patterns to regulatory properties.
  • Modeling epigenetic marks, 3D genome organization, and gene expression with tissue/cell-type specificity.
  • Applying interpretability approaches to identify key sequence patterns and biological mechanisms.

Main Results:

  • Models can predict the functional consequences of any noncoding variant, including rare or novel ones.
  • Systematic characterization of variant consequences beyond experimental tractability.
  • Identification of key sequence patterns driving regulatory predictions.

Conclusions:

  • Deep learning models offer powerful tools for understanding gene regulation and genome variation.
  • Interpretability methods provide biological insights and guide future model development.
  • These approaches advance the systematic characterization of genetic variant effects.