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Covalently Linked Protein Regulators

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.

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Cis-regulatory Sequences

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 Regulators

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.

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Cis-regulatory Sequences

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...

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Related Experiment Video

Updated: Jun 27, 2026

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Published on: July 30, 2011

A gene-centered C. elegans protein-DNA interaction network.

Bart Deplancke¹, Arnab Mukhopadhyay, Wanyuan Ao

¹Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.

|June 17, 2006

Summary

This summary is machine-generated.

This study maps transcription factor (TF) interactions in C. elegans using a gene-centered yeast one-hybrid assay. It reveals a highly connected protein-DNA interaction network, identifying novel TFs and providing insights into gene regulation.

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Large-scale Gene Knockdown in C. elegans Using dsRNA Feeding Libraries to Generate Robust Loss-of-function Phenotypes

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Area of Science:

Molecular Biology
Genomics
Systems Biology

Background:

Transcription regulatory networks govern gene expression through interactions between transcription factors (TFs) and target genes.
Mapping these interactions is challenging in metazoan systems compared to unicellular organisms.
Existing TF-centered methods are less suitable for complex multicellular organisms.

Purpose of the Study:

To systematically map transcription factor-target gene interactions in C. elegans using a gene-centered approach.
To construct a protein-DNA interaction (PDI) network for the C. elegans digestive tract.
To identify novel TFs and gain insights into metazoan gene regulation.

Main Methods:

Utilized high-throughput yeast one-hybrid (Y1H) assays.
Employed a gene-centered strategy focusing on gene promoters.
Investigated interactions between 72 C. elegans digestive tract gene promoters and 117 proteins.

Main Results:

Identified 283 protein-DNA interactions, forming a highly connected PDI network.
The network is enriched for TFs expressed in the C. elegans digestive tract.
Provided functional annotations for previously uncharacterized TFs and identified ten novel putative TFs.
Generated in vivo evidence supporting multiple PDIs.

Conclusions:

A gene-centered approach is powerful for dissecting metazoan transcription regulatory networks.
The constructed PDI network offers valuable insights into differential gene expression at a systems level.
This study expands the functional annotation of C. elegans TFs and reveals new regulatory components.