Draft:Original research/Genomics



Genomics is a branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes.

The H (heavy, outer circle) and L (light, inner circle) strands are given with their corresponding genes. There are 22 transfer RNA (TRN) genes for the following amino acids: F, V, L1 (codon UUA/G), I, Q, M, W, A, N, C, Y, S1 (UCN), D, K, G, R, H, S2 (AGC/U), L2 (CUN), E, T and P (white boxes). There are 2 ribosomal RNA (RRN) genes: S (small subunit, or 12S) and L (large subunit, or 16S) (blue boxes). There are 13 protein-coding genes: 7 for NADH dehydrogenase subunits (ND, yellow boxes), 3 for cytochrome c oxidase subunits (COX, orange boxes), 2 for ATPase subunits (ATP, red boxes), and one for cytochrome b (CYTB, coral box). Two gene overlaps are indicated (ATP8-ATP6, and ND4L-ND4, black boxes).

The control region (CR) is the longest non-coding sequence (grey box). Its three hyper-variable regions are indicated (HV, green boxes).

Genomes
The genome is the entirety of an organism's hereditary information. In humans, it is encoded in DNA. The genome includes both the genes and the non-coding sequences of the DNA.

Def. the "complete genetic information ... of an organism" is called a genome.

Genetic information is encoded as a sequence of nucleobases: adenine (A), cytosine (C), guanine (G), and thymine (T).

There are "3.2 billion base pairs in the human genome."

Associated with genomes are epigenomes.

Theoretical genomics
Def. the "study of the complete genome of an organism" is called genomics.

Sequencing
Genomics involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.

Epistasis
Def. the "modification of the expression of a gene by another unrelated one" is called epistasis.

Heterosis
Def. the "tendency of cross-breeding to produce an animal or plant with a greater hardiness than its parents; hybrid vigour" is called heterosis.

Pleiotropy
Def. the "influence of a single gene on multiple phenotypic traits; pleiotropism" is called pleiotropy.

Genomic diseases
"Genomics includes the scientific study of complex diseases such as heart disease, asthma, diabetes, and cancer because these diseases are typically caused more by a combination of genetic and environmental factors than by individual genes."

Mitachondrial diseases
Genomic "mutations that cause mitochondrial disease [in T-cell mitochondria such as those imaged on the right] may also compromise affected people's immune response."

Structural genomics
Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome.

This raises new challenges in structural bioinformatics, i.e. determining protein function from its 3D structure.

Epigenomics
Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. Epigenetic modifications are reversible modifications on a cell’s DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p. 475). Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

Metagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use "shotgun" chain termination methods (Sanger sequencing) or massively parallel (pyrosequencing) to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its power to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.

As diagrammed in the image on the right, Environmental Shotgun Sequencing (ESS) is a key technique in metagenomics: (A) Sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds.

Hypotheses

 * 1) The human genome has less than 40,000 isoforms.