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Related Concept Videos

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...
Cooperative Binding of Transcription Regulators02:13

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...
Reporter Genes02:11

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.
Commonly used reporter...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

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

Published on: August 9, 2019

Discovering sequences with potential regulatory characteristics.

Minou Bina1, Phillip Wyss, Sheryl A Lazarus

  • 1Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. Bina@Purdue.edu

Genomics
|December 17, 2008
PubMed
Summary
This summary is machine-generated.

We created a computational model to decode regulatory instructions in human genomic DNA. This model identifies potential transcription factor binding sites and epigenetic signals within both coding and regulatory DNA sequences.

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Last Updated: Jun 27, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Published on: August 9, 2019

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Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • Genomic DNA contains regulatory instructions crucial for gene expression.
  • Understanding these instructions is complex due to their context-dependent nature.
  • Specific DNA sequences, or 'codes', are hypothesized to convey these regulatory instructions.

Purpose of the Study:

  • To develop and validate a computational model for decoding regulatory instructions in human genomic DNA.
  • To test the hypothesis that regulatory information is context-dependent and encoded in specific DNA sequences.
  • To identify potential transcription factor binding sites and epigenetic signals within genomic DNA.

Main Methods:

  • Development of a computational model to analyze human genomic DNA sequences.
  • Correlation of computational predictions with experimentally mapped DNase I hypersensitive segments in the HOXA locus.
  • Statistical analysis of sequence patterns (9-mers) in promoter, intronic, intergenic, and coding regions.

Main Results:

  • The computational model identified statistically significant 9-mers in various genomic regions, including promoter-proximal, intronic, and intergenic areas.
  • A subset of 9-mers from coding sequences was found to frequently cluster in noncoding regulatory regions.
  • Computational predictions showed correlation with mapped DNase I hypersensitive segments, supporting the model's validity.

Conclusions:

  • The developed computational model shows potential for decoding regulatory instructions within human genomic DNA.
  • The findings suggest that regulatory codes can be found in diverse genomic locations, including coding sequences.
  • The model can aid in discovering candidate transcription factor binding sites and epigenetic signals across the genome.