Lesson 19: Genomics

Genomics

study of the genome, mapping, annotation, and analysis. medicine (heredity, infectious disease), agriculture (GMOs), and evolutionary studies

Genetic Maps

Abstract maps derived from recombination frequency and linkage analysis, providing relative locations of genes or genetic markers. Distances are measured in centimorgans.

Physical Maps

Maps that provide precise positions, nucleotide level, using landmarks like STS sites. Distances are measured in base pairs (bp) or kilobase pairs (kbp).

STSs (Sequence Tagged Sites)

Small, unique DNA stretches amplified using PCR occur only one location in genome. Researchers use to identify DNA fragment locations and piece together fragments by analyzing overlapping, organizing them into a contiguous sequence (contig).

DNA Sequencing Principles

All methods rely on polymerase chain reaction (PCR), electrophoresis, and chain-terminating nucleotides (e.g., dideoxynucleotides), which prevent further DNA synthesis by lacking a 3’ hydroxyl group.

Dideoxynucleotides

Chain-terminating nucleotides that lack the 3’ hydroxyl group, preventing further phosphodiester bond formation, terminating DNA synthesis.

Automated Sequencing

Involves a template strand subjected to PCR with four different dideoxynucleotides, each labeled with a different color fluorescent tag. DNA fragments are separated in a single capillary tube by electrophoresis, and a laser and photo-detector identify the fluorescent dideoxynucleotides to determine the sequence.

Next-Generation Sequencing (NGS)

A technology offering speed and affordability, where DNA is fragmented and single-stranded fragments are attached to a solid surface. Multiple copies are created via PCR, and synthesis begins with DNA polymerase incorporating special reversible chain-terminating nucleotides that fluoresce, allowing each fragment to be sequenced multiple times.

Clone-Contig Method

A genome assembly method that requires a physical map. The genome is fragmented into large DNA pieces, ordered based on physical mapping landmarks (e.g., STS sites). These clones are then broken into smaller, sequenceable fragments, which are sequenced and assembled and then combined into a large segment

Shotgun Method

genome assembly method does not rely on genetic/physical maps. randomly fragmented into manageable pieces for sequencing, and computer software assembles all pieces based on overlapping nucleotide regions.

Genome Annotation

The process of assigning information (e.g., number, location, type of genes, contribution to phenotype) to genomic sequences, typically stored in searchable online databases.

Open Reading Frame (ORF)

A potential gene sequence, characterized by a start codon, a series of amino acids, and a stop codon.

GenBank

A prominent online database that serves as an annotated collection of publicly available DNA sequences.

BLAST (Basic Local Alignment Search Tool)

used by researchers to compare an unknown gene sequence to those in databases, providing insights into its potential function if similar known sequences are found.

Non-coding DNA

significant portion of DNA, does not code for proteins or functional RNAs. It can comprise as much as 99\%of the human genome (includes introns, structural DNA, simple sequence repeats, pseudogenes, and transposable elements)

ENCODE Project (Encyclopedia of DNA Elements)

aimed to identify all functional elements in the human genome, concluding that 80% of DNA is functional based on 'reproducible biological activity,' including DNA methylation, chromatin modification, and DNase cut sites.

Comparative Genomics

An approach in genome analysis that uses information from one genome to learn about a second genome, predicting gene function, locating similar genes, or inferring evolutionary relatedness (e.g., through synteny).

Synteny

The conserved arrangements of segments of DNA in related genomes, derived from comparing physical maps and sequence data, used in comparative genomics to infer evolutionary relationships or gene function.

Functional Genomics

An approach in genome analysis that uses biotechnology to highlight the connection between genotype and phenotype by characterizing RNA products (the transcriptome) and proteins (the proteome) encoded by genes.

Transcriptome Analysis

The study of all RNA molecules. Techniques include DNA Microarrays (RNA Microarrays) and RNA Sequencing (RNA-seq).

RNA Microarrays

Tools enabling researchers to determine which known genes are expressed at a particular location or time. Each dot on a chip represents a known gene, with colors indicating expression levels.

RNA-seq

A technique that uses next-generation sequencing to capture all mRNA transcripts at a given time, providing comprehensive information on gene expression beyond just suspected genes, without prior knowledge of genes.

Proteomics

The study of the proteome, or the collection of proteins encoded in the genome. It is more challenging to analyze than the transcriptome due to alternative splicing and post-transcriptional modifications.

Mass-spec

technique used in proteomics, proteins are isolated, separated, and cut into peptides by protease enzymes. Peptides are then separated, ionized, and their charge-to-mass ratio is calculated and compared to databases for protein identification.

Protein Microarrays

antibodies are applied to the chip to identify specific proteins in a sample.

Bioinformatics

The application of computer programming, mathematics, and modeling to analyze large amounts of biological data, used in proteomics for rapid protein identification and predicting protein structure from DNA and amino acid sequences.

Applications of Genomics

Include synthetic biology (engineering organisms for specific problems), diagnostics (identifying genes responsible for genetic disorders), and forensics (identifying unknown remains or pathogens, such as viruses).

Ethical Concerns in Genomics

misuse of genomic technology and issues surrounding the ownership of gene sequences