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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
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...
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...
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...

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Annotating the regulatory genome.

Stephen B Montgomery1, Katayoon Kasaian, Steven J M Jones

  • 1Wellcome Trust Sanger Institute, Cambridge, UK. stephen.montgomery@unige.ch

Methods in Molecular Biology (Clifton, N.J.)
|September 10, 2010
PubMed
Summary
This summary is machine-generated.

Understanding gene regulation is key to function and traits. Current models lack specificity, but efforts like ORegAnno database curation are defining the regulatory genome.

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Area of Science:

  • Genomics and Molecular Biology
  • Gene Regulation and Expression

Background:

  • Gene expression timing and molecular mechanisms are crucial for understanding gene function and heritable traits.
  • Existing models of gene regulation suffer from limited specificity and fail to fully capture biological context-dependent logic.
  • Defining the regulatory genome remains a significant challenge in molecular biology due to complexity and limited understanding.

Purpose of the Study:

  • To address limitations in current gene regulation models and define the regulatory genome.
  • To discuss ongoing efforts in annotating the regulatory genome through curation and text-mining.
  • To highlight information standards and curation processes within the ORegAnno database.

Main Methods:

  • Review and discussion of current efforts in defining and annotating the regulatory genome.
  • Focus on data curation and text-mining activities for regulatory element information.
  • Examination of the ORegAnno database's information types and curation processes.

Main Results:

  • Current research faces challenges due to regulatory complexity and context-dependency.
  • Curation and text-mining are vital for advancing the annotation of the regulatory genome.
  • The ORegAnno database serves as a key resource for cataloging regulatory elements.

Conclusions:

  • Defining the regulatory genome requires overcoming challenges in specificity and biological context.
  • Database curation and evolving information standards are essential for progress.
  • Continued efforts in annotation are critical for a comprehensive understanding of gene regulation.