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Related Concept Videos

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...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
Euchromatin01:01

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Published on: May 31, 2011

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.

Sebastian J Schultheiss1, Wolfgang Busch, Jan U Lohmann

  • 1Friedrich Miescher Laboratory of the Max Planck Society, and Max Planck Institute for Developmental Biology, Tübingen, Germany. sebi@tuebingen.mpg.de

Bioinformatics (Oxford, England)
|April 25, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel algorithm for identifying degenerate transcription factor (TF) binding motifs, improving the modeling of regulatory modules. The new method enhances the recognition of TF targets in gene regulatory networks.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Genomics

Background:

  • Transcriptional regulation is a key challenge in computational biology.
  • Identifying transcription factor (TF) binding sites in gene promoter regions is crucial for understanding gene regulation.
  • Existing motif identification algorithms struggle with degenerate binding sites common in cis-regulatory modules.

Purpose of the Study:

  • To develop a new algorithm for identifying degenerate TF binding motifs.
  • To improve the modeling of cis-regulatory modules by combining existing motif-finding techniques with Support Vector Machines (SVMs).
  • To enhance the recognition of TF targets.

Main Methods:

  • Developed a novel algorithm integrating traditional motif finding with Support Vector Machines (SVMs).
  • Applied the algorithm to analyze microarray data from Arabidopsis thaliana.
  • Focused on identifying combinations of degenerate TF binding sites.

Main Results:

  • The proposed algorithm significantly improves the recognition of TF targets compared to existing methods.
  • Demonstrated improved modeling of regulatory modules through the identification of degenerate motifs.
  • Experimental validation on Arabidopsis thaliana microarray data confirmed the strategy's effectiveness.

Conclusions:

  • The new algorithm offers a significant advancement in identifying degenerate TF binding motifs.
  • This approach enhances the understanding of transcriptional regulation and cis-regulatory module function.
  • The method provides a more accurate way to identify TF targets, particularly in complex regulatory scenarios.