Gene and Genome Annotation Concepts

• Annotation provides meaning to a given sequence, which significantly enhances understanding and helps researchers to analyze its contents.

Gene and Genome Annotation Concepts

• Includes gene annotation, sequence elements, bioinformatics, structural and functional annotations, cDNA and splice signals.
• Addresses the underlying challenge of gene and genome annotation and its applications.
• Lists five categories of biological information that can be annotated in the DNA of a gene and a genome.
• Explains how cDNA cloning facilitates the annotation of genes in eukaryotic genomes.
• The six possible reading frames for any DNA fragment are illustrated through a drawing.
• Briefly summarizes the NCBI procedure for accessing gene and genome annotation levels.
• Explains how bioinformatics may contribute to gene and genome annotation.
• Describes the principle behind annotation of transmembrane helices in protein sequences that encode transmembrane receptors.
• Provides a procedure to tentatively identify and annotate promoters in a genome.

Genome Annotation

• All biological information required to build and maintain a living organism is contained within the genome.
• Molecular history of an organism is encapsulated in its genome.
• Genome annotation involves decoding biological information encoded within genes and genomes.
• The genome annotation process enhances biology understanding significantly.
• The process of locating and designating individual genes and features on raw DNA sequences, known as assemblies.

Informative Value and Usefulness of DNA

• Functional elements are identified along a DNA sequence through genome annotation.
• Genome annotation has improved over the past three decades because:
  • The build up of a reference dataset of sequence elements.
  • Exponential growth in computational power for data processing.
• Genome annotation is a multi-step process using specialized algorithms identifying sequence element categories.

Annotation Framework

• Structural and functional gene and genome annotation serve different purposes.
• Structural annotation identifies the "what" and "where" of genomic elements, involving identification of physical gene and genome components like genes, exons, introns, and regulatory elements, including sequencing, mapping and identifying gene features.
• Functional annotation explores the "how" and "why" of the roles and interactions, focuses on understanding roles and interactions of genes and genomic elements, it studies gene expression, protein functions, and interactions using high-throughput methods determining how genes contribute.
• The Gene Ontology (GO) database provides a structured framework defining functions of genes and gene products across different species.
• Focus is on three main aspects:
  • Molecular function, such as enzymatic activity (activities performed by gene products).
  • Biological process, like the cell cycle or metabolic pathways (biological objectives or processes that gene products contribute to).
  • Cellular component, such as the nucleus or ribosome (locations within cells where gene products are active).
• The GO database underlies functional annotation through:
  • Comparing gene functions across different organisms.
  • Integrating knowledge from various biological databases.

Eucaryotic Genomes

• Eukaryotic gene organization complexity can cause problems in gene identification, as genes are separated by large intergenic regions and contain numerous introns, many of which are long.
• Coding regions form a minor portion of the gene, making eukaryotic gene annotation challenging.

cDNA Cloning

• Complementary DNA (cDNA) is DNA synthesized from a messenger RNA (mRNA) template via reverse transcription.
• Introns are spliced out of cDNA, leaving protein-coding exons with short 5'UTR and 3'UTR regions; making it simpler than genomic DNA.
• cDNA cloning facilitates gene annotation of genomic DNA via a precise depiction of expressed genes and less intronic interference.
• Eukaryotic gene annotation in genomic DNA is performed through searches for DNA sequence elements controlling transcriptional, translational, and splicing biological functions.
• The GeneBuilder performs gene annotation with parameters including splicing site data, CpG islands, and repetitive elements.
• GeneBuilder performs searches of its predicted genes against the NCBI protein database to refine boundaries of predicted exons.
• The Al Splice Site Prediction to submit up to 100,000 bps from the human chromosome 1 is accessible.
• Splice annotators can identify approximately 95% of true splicing signals, with a false-positive rate of one signal per 150-250 bases.

Procaryotic Genomes

• A prokaryotic gene typically lacks introns and is defined as the longest open reading frame (ORF) in a DNA region.
• Translating a DNA sequence in all six reading frames can be easily done online.
• Additional evidence for an ORF encoding a protein can be via:
  • The ORF codes for a similar protein already described.
  • The ORF has an upstream promoter and a typical ribosome-binding site such as the Shine-Dalgarno sequence element.

Central Servers Data

• A centralized platform for genomic data is provided from various sources, which can be stored, accessed and managed, ensuring data standardization and annotation purposes accessibility.
• Different algorithms and tools can be integrated seamlessly because NCBI utilizes a modular framework for annotation pipelines.
• NCBI employs specilized algorithms for various annotation aspects, such as the Prokaryotic Genome Annotation Pipeline combining ab initio gene prediction algorithms with homology-based methods, enhancing annotations accuracy.

Bioinformatics and Genome Annotation

• Bioinformatics involves using computer technology to collect, store, analyze, and disseminate biological data and information.
• Bioinformatics provides necessary tools and methods for genome annotation.
• Bioinformatics algorithms find where genes are within a genome, by identifying coding regions and other elements.
• Bioinformatics tools can align DNA or protein sequences and compare genetic material by identifying similarites.
• Functional annotation links genes to their biological functions analysing gene expression.
• Data Integration: integrates data from multiple sources for a comprehensive view of gene function and regulation.
• Automated Annotation: high-throughput tools automate the process for faster and more accurate annotations.

Predicting Protein 2D/3D Stucture

• Significant portions of the human genome, along with even more of non-model organisms, lack any form of annotations.
• Systems using forms of AI can prove helpful in gene annotation.
• Most conclusions have emerged through applying computational techniques based on established biological concepts.
• Early Protein secondary structure prediction using Machine Learning was carried out in mid-1980's, with AI systems designed to predict remarkable structures since.

CpG Islands to Identify Promoters

• BRCA1 gene, which is associated with breast cancer susceptibility, is one example of a gene with long CpG islands.
• CpG islands are present in its promoter region helps regulate its expression and ensures proper functioning.
• To search follow this procedure:
  • Search for CpG islands within BRCA1 gene.
  • Use human chromosome 17 on which BRCA1 gene is located.

Recombination Analysis

• Recombination analysis involving Sordaria fimicola, is useful in annotating the distance between a gene associated with the color of ascospores and the centromere.
• Estimating the gene responsible for a specific trait's crossing over frequency can help estimate and map where the centromere is located on its chromosome.