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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

Genome Annotation and Assembly

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.

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Related Experiment Video

Updated: Oct 30, 2025

Maintaining Biological Cultures and Measuring Gene Expression in Aphis nerii: A Non-model System for Plant-insect Interactions

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Published on: August 31, 2018

Annotating the Insect Regulatory Genome.

Hasiba Asma¹, Marc S Halfon^1,2,3,4,5

¹Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.

|July 2, 2021

Summary

This summary is machine-generated.

Scientists are improving insect genome annotation by identifying cis-regulatory modules (CRMs). Two developed tools, REDfly and SCRMshaw, offer accurate and efficient methods for this crucial task in diverse insect species.

Keywords:

arthropod cis-regulation enhancer genome annotation genomics

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Area of Science:

Genomics and Bioinformatics
Molecular Biology
Evolutionary Biology

Background:

Increasing availability of insect genome sequences necessitates comprehensive annotation.
Regulatory regions, particularly cis-regulatory modules (CRMs), are vital for understanding gene regulation.
Accurate identification of CRMs is essential for maximizing the utility of genomic data.

Purpose of the Study:

To review current methods for identifying CRMs in insect species.
To introduce and highlight the utility of the REDfly and SCRMshaw tools for insect regulatory annotation.
To demonstrate a powerful combination of tools for broad-spectrum insect regulatory annotation.

Main Methods:

Review of existing empirical and computational strategies for CRM discovery.
Description of the REDfly database and the SCRMshaw computational tool.
Evaluation of the combined use of REDfly and SCRMshaw for regulatory annotation.

Main Results:

Progress in identifying CRMs has been driven by advancements in sequencing and discovery strategies.
The REDfly and SCRMshaw tools provide a powerful combination for insect regulatory annotation.
This combined approach achieves accuracy comparable to or exceeding other state-of-the-art methods.

Conclusions:

Timely and comprehensive regulatory annotation of insect genomes remains a challenge.
REDfly and SCRMshaw offer a robust solution to facilitate broad insect regulatory annotation.
The developed tools enhance the ability to study gene regulation across diverse insect species.