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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...

Master Transcription Regulators

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

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...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Reporter Genes

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

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TFM-Explorer: mining cis-regulatory regions in genomes.

Laurie Tonon¹, Hélène Touzet, Jean-Stéphane Varré

¹INRIA Lille-Nord Europe, 40 av Halley, 59650 Villeneuve d'Ascq, d'Ascq Cedex, France.

Nucleic Acids Research

|June 5, 2010

Summary

TFM-Explorer is a new web server that helps researchers find DNA binding sites for transcription factors (TFs) in gene regulatory sequences. It aids in understanding gene regulation across multiple species.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

Genomics and Bioinformatics
Molecular Biology
Computational Biology

Background:

Transcription factors (TFs) are crucial for regulating gene transcription.
Understanding TF binding mechanisms is essential for deciphering gene regulation.
Computational tools can aid in analyzing complex regulatory networks.

Purpose of the Study:

To introduce TFM-Explorer, a web server designed to identify TF binding sites.
To provide a toolbox for analyzing upstream regulatory sequences of co-regulated genes.
To facilitate the discovery of cis-regulatory modules.

Main Methods:

The TFM-Explorer server identifies overrepresented TF binding sites in local genomic regions.
It accepts regulatory sequences from human, mouse, rat, chicken, and Drosophila.
Features include visualization of binding sites and selection of cis-regulatory modules.

Main Results:

The TFM-Explorer server successfully identifies putative TF binding sites within specified gene sets.
It enables the analysis of TF binding site overrepresentation in regulatory sequences.
The tool supports data analysis across multiple model organisms.

Conclusions:

TFM-Explorer provides a valuable computational resource for TF binding site identification.
The web server aids researchers in elucidating gene regulatory mechanisms.
It facilitates the study of cis-regulatory elements and their organization.