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Related Concept Videos

Combinatorial Gene Control02:33

Combinatorial Gene Control

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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Related Experiment Video

Updated: Jun 5, 2026

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Published on: April 21, 2023

Informational blueprints reveal condition-dependent gene regulatory architectures.

Doruk Efe Gökmen1,2, Rosalind Wenshan Pan3, Tom Röschinger3

  • 1NSF-Simons National Institute for Theory and Mathematics in Biology, Chicago, IL 60611, USA.

Biorxiv : the Preprint Server for Biology
|June 4, 2026
PubMed
Summary

This study introduces an "information blueprint" algorithm to identify transcription factor binding sites in non-coding DNA. The method uses hyperletters to represent active binding sites under specific conditions, improving gene expression analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Non-coding DNA plays crucial roles in biological functions, but identifying regulatory elements like transcription factor (TF) binding sites remains challenging.
  • Existing methods often focus on local sequence information, lacking a comprehensive understanding of global regulatory mechanisms.

Purpose of the Study:

  • To develop a novel algorithm for accurately identifying transcription factor binding sites in genomic sequences.
  • To distill complex sequence data into actionable 'hyperletters' representing condition-specific TF binding.
  • To advance the understanding of gene regulation by analyzing global information within promoter sequences.

Main Methods:

  • Developed an 'information blueprint' algorithm inspired by renormalisation-group techniques.
  • Distilled nucleotide sequences into collective coordinates (hyperletters) to represent TF binding sites.
  • Optimised filters to scan entire promoter sequences, capturing global information and correlated mutations.

Main Results:

  • Successfully identified transcription factor binding sites active under specific environmental conditions.
  • Validated the approach using experimental data from *E. coli*.
  • Discovered novel regulatory elements, demonstrating the algorithm's scalability and effectiveness.

Conclusions:

  • The 'information blueprint' algorithm provides a powerful new method for identifying regulatory elements in non-coding DNA.
  • This approach enhances our ability to understand gene regulation across diverse conditions and organisms.
  • The findings open avenues for large-scale analysis of regulatory networks and their impact on biological functions.