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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...

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.

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.

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

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 dimers that...

Regulation of the Unfolded Protein Response

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...

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Related Experiment Video

Updated: May 21, 2026

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

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

Published on: July 21, 2014

A common ancestry for BAP1 and Uch37 regulators.

Luis Sanchez-Pulido¹, Lesheng Kong, Chris P Ponting

¹MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK. luis.sanchezpulido@dpag.ox.ac.uk

Bioinformatics (Oxford, England)

|May 31, 2012

Summary

Computational analysis revealed new domains in ASXL1, a component of the polycomb repressive-deubiquitinase (PR-DUB) complex. This finding clarifies substrate specificity and suggests a shared ancestry with other protein complexes.

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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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Published on: July 21, 2014

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

Molecular Biology
Genomics
Structural Biology

Background:

The polycomb repressive-deubiquitinase (PR-DUB) complex plays a crucial role in epigenetic regulation.
Understanding the components of PR-DUB, such as ASXL1 and BAP1, is key to deciphering its functions.
Previous studies have not fully elucidated the structural domains and evolutionary relationships within the PR-DUB complex.

Purpose of the Study:

To investigate the structural basis of substrate selection specificity within the PR-DUB complex.
To identify novel domains within the ASXL1 protein.
To explore the evolutionary connections between PR-DUB components and other protein complexes.

Main Methods:

Detailed computational sequence analysis of ASXL1 and BAP1 proteins.
Bioinformatic analysis to identify protein domains and evolutionary relationships.
Comparative genomics to assess protein ancestry across different complexes.

Main Results:

Discovery of two previously unrecognized domains in ASXL1: a forkhead (winged-helix) DNA-binding domain and a deubiquitinase adaptor domain.
Identification of shared domains between ASXL1 and regulators of ubiquitin carboxyl-terminal hydrolase 37 (Uch37), including ADRM1 and NFRKB.
Demonstration of a common evolutionary origin for BAP1 and Uch37 regulators within PR-DUB, INO80 chromatin remodeling, and proteasome complexes.

Conclusions:

The identified domains in ASXL1 provide new insights into the substrate selection mechanisms of the PR-DUB complex.
ASXL1 and BAP1 share evolutionary links with Uch37 regulators, suggesting conserved functional roles.
This study enhances our understanding of the structural and evolutionary landscape of epigenetic regulatory complexes.