Question

Annotation involves identifying genes and gene-regulatory sequences in a genome. List and describe characteristics of a genome that are hallmarks for identifying genes in an unknown sequence. What characteristics would you look for in a bacterial genome? A eukaryotic genome?

Short answer

Answer: Some general characteristics of a genome that can be used to identify genes in an unknown sequence include open reading frames (ORFs), promoter sequences, conservation across species, and RNA secondary structure.

Step-by-step solution

General Characteristics of a Genome for Identifying Genes

When faced with an unknown sequence, the following features can often help identify genes: 1. Open reading frames (ORFs): An ORF is a continuous stretch of codons, without any stop codons, that begins with a start codon (AUG) and ends with a stop codon (UAA, UAG, or UGA). 2. Promoter sequences: These are regions of DNA that serve as binding sites for RNA polymerase and other necessary transcription factors. 3. Conservation across species: Genes that are conserved across different species are likely important for fundamental cellular processes, so finding regions with high sequence similarity to known genes in other organisms can indicate a potential gene. 4. RNA secondary structure: Functional RNA molecules (such as tRNA or rRNA) often have a specific structure necessary for their function, so examining possible secondary structures in the sequence can hint at the presence of a functional RNA-encoding gene.

Characteristics for Identifying Genes in a Bacterial Genome

In addition to the general characteristics mentioned above, there are features specific to bacterial genomes that can be useful for identifying genes: 1. Operons: Bacterial genes that are functionally related are often organized into operons, which are a cluster of genes arranged in a linear fashion and transcribed together. 2. Shine-Dalgarno sequence: This is a ribosome-binding site commonly found in bacterial mRNA, which helps recruit the ribosome for translation. Look for AGGAGG sequences located upstream of the start codon.

Characteristics for Identifying Genes in a Eukaryotic Genome

Eukaryotic genomes have their distinct features that can help reveal gene-encoding regions: 1. Introns and exons: Eukaryotic genes are often composed of coding regions (exons) interspersed with non-coding regions (introns). These sequences can be recognized by specific splicing signals at their boundaries, such as the 5' GU and 3' AG splice sites. 2. Enhancers and silencers: These are regulatory DNA sequences that can either increase or decrease the transcription of a gene, and are usually located upstream or downstream of the gene. 3. CpG islands: These are regions with high concentrations of CpG dinucleotides, often associated with gene promoters in eukaryotes. 4. Polyadenylation signals: Eukaryotic mRNAs are typically stabilized at the 3' end by the addition of a poly-A tail. The presence of the polyadenylation signal (AAUAAA or a similar sequence) near the 3' end of a transcript can help identify the gene.