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The state of play in higher eukaryote gene annotation

Nature Reviews Genetics volume 17, pages 758–772 (2016)Cite this article

Subjects

Key Points

  • Gene annotation is one of the core mechanisms through which we decipher the information that is contained in genome sequences.

  • Gene annotation is complicated by the existence of 'transcriptional complexity', which includes extensive alternative splicing and transcriptional events outside of protein-coding genes.

  • The annotation strategy for a given genome will depend on what it is hoped to achieve, as well as the resources available.

  • The availability of next-generation data sets has transformed gene annotation pipelines in recent years, although their incorporation is rarely straightforward.

  • Even human gene annotation is far from complete: transcripts are missing and existing models are truncated. Most importantly, 'functional annotation' — the description of what transcripts actually do — remains far from comprehensive.

  • Efforts are now under way to integrate gene annotation pipelines with projects that seek to describe regulatory sequences, such as promoter and enhancer elements.

  • Gene annotation is producing increasingly complex resources. This can present a challenge to usability, most notably in a clinical context, and annotation projects must find ways to resolve such problems.

Abstract

A genome sequence is worthless if it cannot be deciphered; therefore, efforts to describe — or 'annotate' — genes began as soon as DNA sequences became available. Whereas early work focused on individual protein-coding genes, the modern genomic ocean is a complex maelstrom of alternative splicing, non-coding transcription and pseudogenes. Scientists — from clinicians to evolutionary biologists — need to navigate these waters, and this has led to the design of high-throughput, computationally driven annotation projects. The catalogues that are being produced are key resources for genome exploration, especially as they become integrated with expression, epigenomic and variation data sets. Their creation, however, remains challenging.

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Figure 1: A modern view of the genomic landscape.
Figure 2: The core annotation workflows for different gene types.
Figure 3: High-level strategies for gene annotation projects.
Figure 4: Transcriptional complexity in the NRIP1 locus.

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Acknowledgements

The work performed by J.M.M. and J.H. on the GENCODE project is supported by the National Human Genome Research Institute of the National Institutes of Health (grant number U41 HG007234). The authors thank A. Frankish for informative discussions.

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Authors and Affiliations

  1. Department of Computational Genomics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK

    Jonathan M. Mudge & Jennifer Harrow

  2. Illumina Cambridge Ltd, Chesterford Research Park, Saffron Walden, CB10 1 XL, Little Chesterford, UK

    Jennifer Harrow

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  1. Jonathan M. Mudge
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Correspondence to Jonathan M. Mudge or Jennifer Harrow.

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PowerPoint slides

Glossary

Gene

Redefined for the modern era by Gerstein et al. (Ref. 1) as “a union of genomic sequences encoding a coherent set of potentially overlapping functional products” (that is, RNAs or proteins).

Genebuild

Used by GENCODE and Ensembl for a collection of transcript models generated by computational or manual annotation across an entire genome sequence. Protein-coding genes, long non-coding RNAs, small RNAs and pseudogenes may be included.

Transcript

Any form of RNA molecule that is transcribed from the genome sequence.

Functional annotation

The process of defining or predicting functional roles for transcript models during gene annotation.

Alternative splicing

Process by which a gene makes distinct transcripts through the use of different splice sites or exon combinations; these are known as alternative transcripts or transcript variants.

Pseudogenes

'Broken' genes that are derived from protein-coding loci. Can be formed by retrotransposition ('processed'), duplication ('unprocessed') or inactivation ('unitary', which may be polymorphic). All forms may be transcribed.

Long non-coding RNAs

(lncRNAs). Genes that do not contain protein-coding transcripts and that are not pseudogenes or small RNAs; a 200 bp size cut-off is typically applied to distinguish them from small RNAs.

Small RNA

A member of one of several known families of small RNA molecules. Includes the classic tRNA and rRNA families alongside more recent discoveries such as PIWI-interacting RNAs (piRNAs), microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs).

Coding sequences

(CDSs). The regions of a transcript that are translated, that is, contain the information that encodes a protein sequence.

Manual annotation

When a person constructs a transcript model de novo after appraising the available evidence (typically using software tools), or examines and potentially validates ('curates') a model that has been created computationally.

Computational annotation

The process of generating genebuilds through entirely in silico processes, that is, by the use of computational algorithms.

Transcription start site

(TSS). The base pair on the genome where transcription begins.

Polyadenylation tail

A sequence of adenosine monophosphates attached to the 3′ end of an RNA as transcription terminates, beginning at the polyA site.

Translation initiation site

(TIS). The codon that is translated to give the first amino acid of a peptide; almost always ATG; also known as a START codon.

STOP codon

The final codon of a protein translation; almost always TAG, TAA or TGA; also known as a translation termination site or codon.

Isoforms

Protein molecules that differ in their amino acid composition from other translations made from the same gene, for example, owing to alternative splicing.

Intron retention

Occurs when a transcript does not splice out one or more introns, that is, this sequence is left incorporated into the mature RNA.

Nonsense-mediated decay

(NMD). Cellular 'surveillance' mechanism that targets transcripts for destruction. Imprecisely understood, although transcripts featuring termination codons more than 50 bp upstream of splice junctions are thought likely to be substrates.

Poison exon

An exon that prevents correct coding sequence translation when incorporated into the transcript of a protein-coding gene, either by causing a frameshift or through the introduction of a premature termination codon.

Untranslated region

(UTR). Non-coding sequence on coding sequence transcripts found between the transcription start site and the translation initiation site (5′ UTR), and the STOP codon and polyA site (3′ UTR).

Enhancer

Sequence that regulates a promoter from a distal site on the chromosome, probably brought into close proximity through DNA looping.

Promoters

Regions immediately upstream of the transcription start site where the RNA polymerase complex attaches in order to initiate transcription.

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Mudge, J., Harrow, J. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17, 758–772 (2016). https://doi.org/10.1038/nrg.2016.119

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