OMICs and Genomics Overview

OMICs

• OMICs is the study of complete sets of molecules within a biological system.
• They include genomics, transcriptomics, proteomics, and metabolomics.
• They identify genetic factors and metabolic pathways important for growth and development.
• By combining datasets, researchers understand molecular mechanisms for cell growth, development, and responses to stress.

Genomics

• Genomics is the study of an organism's entire genome, including gene identification and function.
• It involves techniques for analyzing DNA.
• Some of these techniques are DNA sequencing, genome assembly, genome annotation, comparative genomics, metagenomics, functional genomics, and phylogenomics.

DNA Sequencing

• Sanger sequencing is traditional.
• Next-generation sequencing (NGS) is a high-throughput technique.

Genome Assembly

• De novo assembly creates a genome sequence from scratch without a reference.
• Reference-based assembly uses a known reference genome to align and assemble reads.

Genome Annotation

• Tools like GeneMark, AUGUSTUS, and BLAST predict genes and annotate functional elements.

Comparative Genomics

• Whole-genome alignment compares genomes to find similarities and differences.
• Synteny analysis studies conserved genomic arrangements across species.

Metagenomics

• It studies genomes of microbial communities in environmental samples.

Functional Genomics

• Gene knockout/knockdown disrupts gene function to study its effects.

Phylogenomics

• Phylogenetic analysis uses genomic data to study evolutionary relationships between species.

Transcriptomics

• Transcriptomics is the analysis of an organism's transcriptome including identifying all expressed genes and their expression levels.
• It identifies genes and pathways linked to diseases and environmental conditions.
• It focuses on RNA expression patterns to understand gene expression levels, alternative splicing, and regulatory mechanisms.

RNA Sequencing

• It quantifies gene expression by measuring RNA transcript abundance.
• It also identifies alternative splicing events by detecting different isoforms of genes.

Microarray Analysis

• It profiles gene expression and measures the expression levels of multiple genes simultaneously.
• It also helps with comparative expression studies by comparing gene expression across different conditions or tissues.

Quantitative Real-Time PCR

• It validates gene expression patterns observed in RNA-Seq or microarray studies.

Proteomics

• Proteomics studies the proteome of an organism, including protein identification and functions.
• It identifies proteins associated with stress responses.
• It studies protein structure, function, and interactions.

Mass Spectrometry

• Liquid chromatography-mass spectrometry (LC-MS) separates and identifies proteins based on mass-to-charge ratios.
• Tandem mass spectrometry (MS/MS) fragments peptides for sequencing and identification.

Two-Dimensional Gel Electrophoresis

• It separates proteins based on isoelectric point and molecular weight for analysis.

Protein Identification

• Database search matches experimental mass spectra to known protein sequences for identification.
• De novo sequencing identifies protein sequences directly from mass spectra without a reference database.

Protein Structure Analysis

• X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) are used to determine protein structures at atomic resolution.

Bioinformatics Analysis

• Database search tools analyze and interpret proteomic data for functional insights and pathway analysis.

Metabolomics

• Metabolomics is the study of an organism's metabolome, which includes identifying all metabolites and their functions.
• It identifies metabolites associated with specific diseases and environmental conditions.
• It explores metabolic processes and pathways in biological systems.

Mass Spectrometry in Metabolomics

• Gas chromatography-mass spectrometry (GC-MS) analyzes volatile and thermally stable metabolites.
• Liquid chromatography-mass spectrometry (LC-MS) separates and identifies metabolites based on their mass-to-charge ratio.
• Tandem mass spectrometry (MS/MS) fragments metabolites for structural elucidation.

Prokaryotes and Eukaryotes

• Prokaryotes are bacteria and archaea.
• Eukaryotes are all other living organisms, including animal protists like amoebas and paramecia, algae, fungi, plants, and animals.
• Prokaryotes lack a true nucleus, unlike eukaryotes, where the genetic material (DNA) is contained within a nuclear membrane.
• Eukaryotes have nuclear and mitochondrial genomes; photosynthetic eukaryotes also have chloroplast genomes.
• The genomes of mitochondria and chloroplasts resemble those of bacteria and archaea.

Watson and Crick Model

• The Watson and Crick model remains largely accepted with minor refinements.
• DNA is a double-stranded helix held together by hydrogen bonds.
• Base pairing follows Chargaff's rule: A pairs with T, and C pairs with G.
• The DNA double helix is right-handed, except for Z-DNA, which is left-handed.
• The helix is anti-parallel; the 5' end of one strand pairs with the 3' end of the other strand.
• Phosphate groups link nucleotides by binding the 3′ end of one sugar to the 5′ end of the next sugar.
• The nitrogen-containing bases are exposed for potential hydrogen bonding with other molecules, including proteins involved in DNA replication and expression.

Conformations of DNA

• The DNA double helix can exist in three conformations: A-DNA, B-DNA, and Z-DNA.
• B-DNA is the most common in living cells and is the one proposed by Watson and Crick.
• A-DNA is shorter and wider, found in dehydrated DNA samples and rarely under normal physiological conditions.
• Z-DNA is a transient left-handed conformation that exists under specific biological conditions.
• Some proteins bind strongly to Z-DNA suggesting a role in viral defense.