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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics.

Soile V E Keränen1, Angel Villahoz-Baleta2,3, Andrew E Bruno2,3

  • 1Independent Research, Berkeley, CA 94705, USA.

Insects
|July 27, 2022
PubMed
Summary
This summary is machine-generated.

The REDfly database now offers enhanced annotation for insect transcriptional regulatory elements, including over 40,000 experimentally verified cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). This resource aids research in development, evolution, and insect control.

Keywords:
Drosophilacis-regulatory moduleenhancergene regulationgenome annotationinsectsregulatory genomics

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcriptional regulatory elements like cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs) are crucial for gene expression but are not comprehensively curated in major databases.
  • Understanding these elements is vital for studying development, disease, phenotypic variation, and evolution in insects.

Purpose of the Study:

  • To provide an updated description of the REDfly database, a specialized resource for insect transcriptional regulatory elements.
  • To highlight new features and improvements implemented in REDfly since 2020.
  • To demonstrate the utility of REDfly through common search use cases.

Main Methods:

  • Database curation of experimentally verified CRMs and TFBSs from insect genomes.
  • Development of a detailed data model for regulatory element annotation.
  • Implementation of new features and search functionalities since 2020.

Main Results:

  • REDfly contains over 40,000 experimentally verified CRMs and TFBSs for insects, including detailed genomic sequences, associated genes, and directed expression patterns.
  • The database provides the most comprehensive metazoan regulatory-element annotation available.
  • New features enhance the usability and scope of REDfly for researchers.

Conclusions:

  • REDfly is an indispensable resource for insect regulatory genomics, offering unparalleled annotation of CRMs and TFBSs.
  • The updated database supports diverse research areas, from basic developmental biology to applied insect control strategies.
  • REDfly facilitates deeper understanding of gene regulation and its impact on insect biology.