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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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Cooperative Binding of Transcription Regulators02:13

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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...
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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SCRMshaw: Supervised cis-regulatory module prediction for insect genomes.

Hasiba Asma1, Luna Liu2, Marc S Halfon1,2,3

  • 1Departments of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY, United States of America.

Plos One
|December 5, 2024
PubMed
Summary
This summary is machine-generated.

SCRMshaw is a computational tool that efficiently predicts cis-regulatory modules (enhancers) in insect genomes. This updated protocol simplifies regulatory genome annotation for researchers with minimal computational resources.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The rapid increase in sequenced insect genomes necessitates efficient methods for annotating regulatory elements.
  • Identifying cis-regulatory modules (enhancers) is crucial for understanding gene regulation.

Purpose of the Study:

  • To present an updated protocol for SCRMshaw, a computational tool for predicting insect cis-regulatory modules.
  • To provide a user-friendly, resource-efficient pipeline for regulatory genome annotation.

Main Methods:

  • Utilizes a genome sequence and training data from known Drosophila regulatory sequences.
  • SCRMshaw can be applied using single or multiple training datasets for specific or broad annotation.
  • The protocol details an end-to-end pipeline from genome sequence to annotated regulatory genome.

Main Results:

  • SCRMshaw offers an accessible method for predicting enhancers in diverse insect species.
  • The tool requires minimal computational resources, suitable for desktop applications.
  • The updated protocol aligns with recent large-scale insect regulatory genome annotations.

Conclusions:

  • SCRMshaw provides a valuable and accessible tool for insect genome annotation.
  • This updated protocol facilitates the study of gene regulation across a wide range of insect species.
  • The availability of scripts and a living protocol enhances usability and reproducibility.