Genome annotations and features

What is genome annotation?

Turning a raw genome sequence into a meaningful understanding of what all the parts might be doing.

In a eukaryotic genome annotation diagram, what do green boxes represent?

Introns.

In a eukaryotic genome annotation diagram, what do red blocks represent?

Non-functional regions.

In a eukaryotic genome annotation diagram, what do lines represent?

Introns.

What does alternative splicing involve, according to the genome annotation notes?

Sometimes skipping a middle exon; this is described as very common.

What is represented by a single coding transcript with no alternative splicing?

A single coding transcript is produced, with no alternative splicing.

What do grey ovals represent in the genome annotation diagram?

Promoters or enhancers.

What do long non-coding RNAs (lncRNAs) do according to the annotation notes?

They do not produce proteins; they remain as RNA, may bind to other RNA molecules or DNA, and may also be referred to as microRNA in the notes.

What do green and processed grey boxes represent in the genome annotation diagram?

Dead genes or pseudogenes; they are described as non-deleterious and do not make proteins, remaining in the genome with a stop codon in the middle.

What is an open reading frame (ORF)?

The part that encodes the protein.

What does UTR stand for?

Untranslated region.

What is the 5′ UTR?

A transcribed but untranslated region that is useful for the ribosome to bind to; it becomes RNA but is not translated.

Where can enhancers and silencers occur relative to a gene, according to the notes?

They can be a few base pairs away or very close.

What is found downstream of the coding region, according to the notes?

The 3′ UTR, which has some kind of terminator; enhancers and silencers may also occur there, and their distance still varies.

Where does mRNA start, and what regions are transcribed?

mRNA starts at the start of the UTR; the entire open reading frame and the 3′ UTR are transcribed.

What is the function of the poly-A tail?

It is a string of A's that gives mRNA stability, as the mRNA needs to remain in the cell for a while, and prevents the gene from decaying.

What is meant by finding genes using a long ORF?

Finding a long open reading frame.

How can codon usage bias help identify genes?

Coding sequences tend to use certain synonymous codons more frequently than others. Codon frequencies can be calculated in known genes from an organism and used as a pattern to identify potential coding regions that show similar bias.

What is codon usage bias?

The tendency for coding sequences to use certain synonymous codons more frequently than others.

How can a ribosome binding site (RBS) help identify genes in prokaryotes?

Look for Shine-Dalgarno sequences, such as AGGAGG in E. coli, located approximately 8 base pairs upstream of potential start codons. These sequences help recruit ribosomes for translation initiation.

How can promoter and regulatory element scanning help identify genes?

Search for conserved promoter sequences, such as TATA boxes approximately 25 bp upstream of the start codon in eukaryotes, or CAAT boxes in eukaryotes, or -10 and -35 boxes in prokaryotes.

What does the gene-finding note say about sequences encoding proteins shorter than 20 amino acids?

If something is less than 20 amino acids in length, it does not really have a chance of coding for a protein.

How can GC content analysis help identify genes?

In many organisms, coding regions have different GC content from intergenic regions. Sliding-window analysis can identify regions with GC content typical of genes.

What start codons should be considered when finding genes?

ATG, and sometimes GTG or TTG in prokaryotes.

What should follow a start codon when identifying a potential coding sequence?

In-frame stop codons: TAA, TAG or TGA, at appropriate distances.

How can periodicities in base composition help identify genes?

Coding sequences often show periodic patterns in nucleotide composition at codon positions 1, 2 and 3, with the third position showing the strongest bias.

How can comparative genomics help identify genes?

Find homologous sequences in related organisms. Using BLAST, conserved regions across species often indicate functional genes.

How can splice-site detection help identify genes in eukaryotes?

Look for canonical splice donor (GT) and acceptor (AG) sites, along with branch points, to identify intron–exon boundaries.

Exam-style MCQ: What is the main purpose of genome annotation? A. To turn a raw genome sequence into an understanding of what its parts do. B. To remove all introns from the genome. C. To translate every DNA region into protein. D. To identify only promoter sequences.

Correct answer: A. To turn a raw genome sequence into an understanding of what its parts do.

Exam-style MCQ: Which feature is described as a transcribed but untranslated region useful for ribosome binding? A. ORF. B. 5′ UTR. C. 3′ UTR. D. Poly-A tail.

Correct answer: B. 5′ UTR.

Exam-style multiple answer: Which methods are listed for finding genes? Select all that apply. A. Long ORF identification. B. Codon usage bias analysis. C. Ribosome binding site detection. D. Promoter and regulatory element scanning. E. GC content analysis. F. Start and stop codon patterns. G. Periodicity in base composition. H. Comparative genomics. I. Splice-site detection.

Correct answers: A, B, C, D, E, F, G, H and I.

Exam-style short answer: Describe how codon usage bias can be used to find genes.

Calculate codon frequencies in known genes from an organism, then use those frequencies as a pattern to identify potential coding regions with similar bias.

Exam-style short answer: Explain how Shine-Dalgarno sequences help identify prokaryotic genes.

Shine-Dalgarno sequences, such as AGGAGG in E. coli, are located approximately 8 base pairs upstream of potential start codons and help recruit ribosomes for translation initiation.

Exam-style MCQ: Which combination correctly describes start and stop codon patterns used in gene finding? A. Start codons ATG, sometimes GTG or TTG in prokaryotes, followed by in-frame TAA, TAG or TGA stop codons. B. Start codons TAA, TAG or TGA, followed by ATG. C. Start codons are only TATA boxes. D. Stop codons must occur before the start codon.

Correct answer: A.

Exam-style multiple answer: Which statements about regulatory sequences are supported by the notes? Select all that apply. A. TATA boxes are approximately 25 bp upstream of the start codon in eukaryotes. B. Prokaryotes have -10 and -35 boxes. C. CAAT boxes are mentioned in relation to eukaryotes. D. Enhancers and silencers can be a few base pairs away or very close. E. Regulatory sequences are never conserved.

Correct answers: A, B, C and D.

Exam-style short answer: How does splice-site detection identify gene boundaries in eukaryotes?

Look for canonical splice donor GT and acceptor AG sites, along with branch points, to identify intron–exon boundaries.

Exam-style MCQ: What does the poly-A tail do according to the notes? A. Encodes the protein. B. Gives mRNA stability and prevents the gene from decaying. C. Recruits ribosomes to Shine-Dalgarno sequences. D. Identifies the promoter.

Correct answer: B.

Exam-style multiple answer: Which statements about non-coding RNA are included in the notes? Select all that apply. A. Small RNAs include miRNA, siRNA and piRNA. B. Long non-coding RNAs are associated with gene-expression control. C. Long non-coding RNAs can act as molecular scaffolds. D. Long non-coding RNAs are involved in RNA processing and regulation. E. Long non-coding RNAs are involved in nuclear architecture. F. Long non-coding RNAs are involved in epigenetic regulation. G. Structural RNAs include rRNA, tRNA and snRNA.

Correct answers: A, B, C, D, E, F and G.

What small non-coding RNAs are listed in the notes?

miRNA, siRNA and piRNA.

What functions are listed for long non-coding RNAs?

Gene-expression control; molecular scaffolds; RNA processing and regulation; nuclear architecture; and epigenetic regulation.

Which RNAs are listed as structural RNAs?

rRNA, tRNA and snRNA.

What are the main categories of regulatory elements listed in the notes?

Promoters; enhancers and silencers; transcription-factor binding sites; epigenetic marks; repetitive elements; transposable elements; and tandem repeats.

What are promoters described as in the regulatory-elements notes?

Core and proximal elements.

What are enhancers and silencers associated with?

Long-range regulation.

What features of transcription-factor binding sites are highlighted?

Motifs and conservation.

Which regulatory features are described under epigenetic marks?

Histone methylation and histone modifications.

What topics are listed under repetitive elements?

Types and prevalence.

What distinction is listed under transposable elements?

DNA transposons versus retrotransposons.

Which types of tandem repeats are listed?

Microsatellites, minisatellites and satellites.

Exam-style MCQ: Which of the following is listed as a structural RNA? A. snRNA. B. TATA box. C. Poly-A tail. D. ORF.

Correct answer: A. snRNA.

Exam-style multiple answer: Which are listed as regulatory elements or regulatory-element categories? Select all that apply. A. Promoters. B. Enhancers and silencers. C. Transcription-factor binding sites. D. Epigenetic marks. E. Repetitive elements. F. Transposable elements. G. Tandem repeats.

Correct answers: A, B, C, D, E, F and G.

Exam-style short answer: List the categories of regulatory elements shown in the notes and give the detail associated with each where provided.

Promoters: core and proximal elements; enhancers and silencers: long-range regulation; transcription-factor binding sites: motifs and conservation; epigenetic marks: histone methylation and histone modifications; repetitive elements: types and prevalence; transposable elements: DNA transposons versus retrotransposons; tandem repeats: microsatellites, minisatellites and satellites.

What is intron splicing in eukaryotes?

The process shown in the notes in which snRNPs bind to an intron and the intron is removed, allowing the exons to be joined together.

What is the role of snRNPs in the eukaryotic intron-splicing diagram?

They bind to the intron and help bring the splice sites together so that the intron can be removed and the exons joined.

What happens during the first step of intron splicing, according to the diagram?

A group of five snRNPs, or ribonucleoproteins, is needed to bind to the intron of pre-mRNA to remove it and leave only the exons.

What happens during the second step of intron splicing, according to the diagram?

The snRNPs bind to the intron and cause it to fold, bringing the 5′ and 3′ ends of the intron together. The intron is then removed as the exons are joined together.

What happens during the third step of intron splicing, according to the diagram?

The intron detaches and the splice sites are connected to make a mature mRNA. The intron is removed, leaving the exons joined together.

What is alternative splicing?

The production of different mRNAs from the same pre-mRNA by splicing it in different ways.

What can alternative splicing produce?

Different alternatively spliced mRNAs that are translated into different protein isoforms.

Exam-style MCQ: What is a result of alternative splicing? A. Different mRNAs can produce different protein isoforms. B. All introns become proteins. C. All genes are removed from the genome. D. DNA is converted directly into protein without RNA.

Correct answer: A.

Exam-style short answer: Explain how alternative splicing can result in different protein isoforms.

The same pre-mRNA can be spliced in different ways to produce different mRNAs, which are then translated into different protein isoforms.

Exam-style multiple answer: Which statements about eukaryotic intron splicing match the diagram? Select all that apply. A. snRNPs bind to the intron. B. The intron folds so that its 5′ and 3′ ends come together. C. The intron is removed. D. The exons are joined to form mature mRNA. E. The intron is translated into a protein.

Correct answers: A, B, C and D.