Genomics and Epigenetics

genome

the complete set of sequences in the genetic material of an organism

nuclear genome

the genetic material that is located in the nucleus of the cell

mitochondrial genome

the genetic material that is located in the mitochondria of cell

transcriptome

set of expressed genes (everything that gets transcribed)

proteome

complete set of proteins expressed

epigenome

consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it

exons

found in mature RNA; coding portions of the DNA

introns

intervening sequences that are spliced out of the primary transcript; usually non-coding

open reading frame (ORF)

includes the promoter, coding region, and terminator region

linkage mapping

describes how mutations are distanced in terms of recombination frequencies; close mutations recombine more frequently and are therefore linked

restriction mapping

cutting the DNA with restriction enzymes and looking for changes in sizing of the fragments identifies areas where mutations may have occured

sequence mapping

comparisons of DNA sequence as a whole between samples

genomes are…

• not static but rather variable

• they change and evolve

gene family

a set of genes whose exons are related

intergenic

DNA found between genes

intragenic

DNA found within gene but is not coding

introns

account for 50% if the genome in humans

exons

account for only 1% if the genome in humans

non repetitive sequences

haploid genome contains only one copy of the sequence

moderately repetitive sequences

found in multiple copies, may be identical or related, includes transposons

highly repetitive sequences

very short and present in large numbers of copies, often tandem repeats

redundancy

the concept that two or more genes may fulfill the same function so that no single one of them is essential

polymorphism

the coexistence of multiple alleles at a locus is called genetic polymorphism

single nucleotide polymorphisms (SNP)

caused by a change in a single nucleotide, responsible for most of the genetic variation between individuals-changes how well a specific enzyme functions

non-coding DNA

DNA that does not code for a protein

chromosome

a discrete unit of the genome carrying many genes

gene

segment of the DNA specifying production of polypeptide chain

allele

one of several alternative forms of a gene occupying a given locus on a chromosome

locus

the position on a chromosome at which the gene for a particular trait resides

loss of function mutation

results in the lost or reduced activity of a gene

gain of function mutation

results in a mutation that causes an increase to the normal gene activity

cis acting sites

sites are configured such that two sites are on the same DNA molecule; the sites affects the activity only of sequences on its own molecule of DNA- usually does not code for protein-mutations in control sites are cis-acting

trans acting

two sites are configured such that they are present on different molecules of DNA - mutations in protein encoding regions generate mutant proteins which are trans acting

superfamily

set of genes all related by presumed descent from a common ancestor, but now showing considerable variation

haplotype

the particular combination of alleles in a defined region of some chromosome

genome mapping

a map that can include a variety of types of maps that describe the set up and resulting organization of the genome

indel

mutations defined by either the insertion or deletion of nucleotides in the genome

whole genome duplication

rare mutational event in which the chromosome number is doubled or fails to be reduced during cell division

pseudogenes

nonfunctional genes in the genome that are no longer expressed in any member of the species

sub-genomic duplication

duplication of part of the genome but not of the entire genome, more common than whole genome duplication

gene cluster

a group of adjacent genes that are identical or related

copy number variants

variations found in the populations genome that represent multiple copies of the same gene

positive transcription factors

increase level of transcription

negative transcription factors

decrease level of transcription

histone acetyl transferases

enzymes that transfer acetyl groups from molecule to histones

histone deacetylases

enzymes that remove acetyl groups from histones

silenced

a genes whose expression is turned off, commonly by negative transcription factors or epigenetic modifications such as methylation or histone deacetylation

DNA methyltransferase

enzyme that transfers a methyl group from donor molecule to DNA

CpG islands

regions within the genome that are rich is C and G nucleotides which are sensitive to methylation

hypomethylation

lower than normal levels of DNA methylation

hypermelthylation

higher than normal levels of DNA methylation

acetylation

addition of an acetyl group to histones

methylation

addition of a methyl group to certain DNA nucleotides

phosphorylation

addition of phosphate groups to enzymes or proteins

ubiquitylation

addition of a ubiquitin to proteins

non-coding RNA-associated gene silencing

silencing from small pieces of RNA that have been transcribed and exist as RNA but are never translated into protein but they decrease the level of expression

DNA microarray chips

prepared experimental chips that contain complementary RNA to the mRNA of a variety of genes for which scientist wishes to screen expression levels