cRegions-a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Identifying cis-acting elements is vital for understanding gene regulation.
• Discovering novel cis-elements, particularly in viruses with divergent sequences, is difficult.
• Advancements in genome sequencing provide new opportunities for identifying these elements.

Purpose of the Study:

• To introduce cRegions, a web-based tool for identifying cis-acting elements.
• To detect regions of nucleotide conservation within protein-coding sequences that indicate functional cis-elements.
• To facilitate the discovery of novel regulatory sequences in diverse organisms, especially viruses.

Main Methods:

• Development of the cRegions web tool.
• Analysis of protein-coding sequences to identify regions where amino acid conservation is driven by nucleotide conservation.
• Application of cRegions to alphavirus polyproteins as a case study.

Main Results:

• cRegions successfully identified all known cis-acting elements in alphaviruses.
• The tool demonstrated efficacy in detecting various functional elements in DNA and RNA viruses.
• Detected elements include splice sites, stem-loops, overlapping reading frames, and internal promoters.

Conclusions:

• cRegions is an effective tool for discovering novel cis-acting sequences from diverged protein-coding genes.
• The tool aids in identifying functional elements in viruses, providing a basis for experimental validation.
• cRegions expands the capability to detect a wide range of embedded functional elements in viral genomes.