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Internal Receptors

Internal Receptors

Many cellular signals are hydrophilic and therefore cannot pass through the plasma membrane. However, small or hydrophobic signaling molecules can cross the hydrophobic core of the plasma membrane and bind to internal, or intracellular, receptors that reside within the cell. Many mammalian steroid hormones use this mechanism of cell signaling, as does nitric oxide (NO) gas.

Types of Receptors: Internal Receptors

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Many cellular signals are hydrophilic and cannot pass through the plasma membrane. However, small or hydrophobic signaling molecules can cross the hydrophobic core of the plasma membrane and bind intracellular receptors that reside within the cell cytoplasm or nucleus. Many mammalian steroid hormones and nitric oxide (NO) gas use this cell signaling mechanism.
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Identification and characterization of androgen response elements.

Reinhilde De Bruyn¹, Rita Bollen, Frank Claessens

¹Department of Molecular Cell Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA. hilde.debruyn@med.kuleuven.be

Methods in Molecular Biology (Clifton, N.J.)

|July 29, 2011

Summary

Identifying androgen response elements (AREs) is challenging. This study introduces an in silico method using a weight matrix to find AREs in genomic fragments, followed by experimental validation using electrophoretic mobility shift and transactivation assays.

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Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

The androgen receptor (AR) binds to specific DNA sequences called androgen response elements (AREs).
AREs are crucial for regulating androgen-responsive genes and can be located at varying distances from gene promoters.
Identifying AREs has traditionally been difficult, with methods like DNA cellulose competition assays and in vitro footprinting being used.

Purpose of the Study:

To develop an efficient in silico method for identifying potential AREs within large genomic fragments.
To outline the experimental validation methods necessary for confirming identified AREs.

Main Methods:

Development of an in silico weight matrix approach based on known ARE sequences.
Utilizing chromatin immunoprecipitation (ChIP) assays to identify AR-binding genomic fragments.
Experimental validation using electrophoretic mobility shift assays (EMSAs) and transactivation assays.

Main Results:

An in silico weight matrix was created to predict candidate AREs in genomic regions bound by AR.
The study highlights the necessity of experimental validation for computationally identified AREs.
Electrophoretic mobility shift and transactivation assays are presented as key methods for ARE validation.

Conclusions:

The developed in silico approach aids in the initial localization of AREs within genomic fragments.
Experimental validation remains critical to confirm the functional significance of predicted AREs.
Electrophoretic mobility shift and transactivation assays are the most suitable methods for describing AREs.