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Related Concept Videos

Global Regulatory Systems01:28

Global Regulatory Systems

Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
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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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Kernel-based identification of regulatory modules.

Sebastian J Schultheiss1

  • 1Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany. sebi@umich.edu

Methods in Molecular Biology (Clifton, N.J.)
|September 10, 2010
PubMed
Summary
This summary is machine-generated.

Identifying cis-regulatory modules (CRMs) is crucial for understanding gene regulation. A new method, KIRMES, combines motif finding with machine learning to accurately identify CRMs, even complex ones, aiding biological research.

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DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Identifying cis-regulatory modules (CRMs) is vital for understanding transcriptional regulation in eukaryotes.
  • Existing motif-finding algorithms struggle with degenerate binding sites common in CRMs.

Purpose of the Study:

  • To develop a robust method for identifying CRMs that combines motif finding with machine learning.
  • To create software, KIRMES, for identifying key CRMs in co-regulated gene sets and predicting regulation in other genes.

Main Methods:

  • Developed KIRMES software integrating motif finding with machine learning.
  • Applied KIRMES to sets of co-regulated genes to identify CRMs.
  • Utilized gene sets from microarrays and ChIP-seq experiments.

Main Results:

  • KIRMES accurately identifies key CRMs responsible for co-regulation.
  • The software can predict if unlisted genes share the same regulatory mechanism.
  • Provides interpretable visualizations for biological analysis.

Conclusions:

  • KIRMES offers a fast, robust, and interpretable approach to CRM identification.
  • The method aids in understanding complex regulatory relationships and designing experiments.