genes, genomes, and transposable elements

genome

entirety of an organism’s hereditary information (usually DNA)

difference in genome size between species

mostly due to differences in amounts of non-coding DNA and transposable elements

gene

entire nucleic acid sequence that is necessary for the synthesis of a functional product

exon of a gene

contains the coding region or open reading frame (ORF)

control regions

promoter and cis-regulatory factors that recruit RNA polymerase

introns of genes

separate exons and are spliced out during mRNA processing

transcription unit

region in DNA bounded by an initiation site and termination site that is transcribed into a single primary transcript

alternative splicing

many eukaryotic genes are alternatively transcribed and processed, generating multiple different transcripts from the same gene

isoforms

multiple forms of a protein produced by alternative splicing

solitary genes

protein-coding genes that are represented once in the genome

duplicate or multiple copy genes

protein-coding genes that occur twice or more in the genome

gene family

set of genes formed by duplication of an original single-copy (solitary) gene

gene duplication

important process in evolution, new copies of genes can either evolve a new function or degenerate over time

pseudogene

new copy of a gene that degenerates over time, losing its function

orthologs

same protein in different species

paralogs

closely related proteins in the same species

non-coding DNA

• intragenic DNA

• introns

• untranslated regions (UTRs)

minisatellite DNA

• repeats are ~ 14-100 bp in length

• 20-50 tandem repeat units

• arrays of 1-5 kbp in length

• often in centromeres or telomeres

microsatellite DNA

• repeats are ~ 1-4 bp in length

• arrays of up to 600 bp and composed of tandem repeat units

• sometimes found in transcription units

• expansions underlie several neurodegenerative diseases (myotonic dystrophy, spinocerebellar ataxia)

expansions of DNA repeats

caused by DNA polymerase slipping backwards on template strand

Huntington’s disease

caused by expansion of CAG repeats, leading to the production of proteins that form toxic aggregates in neuronal cells

simple sequence repeats (SSRs)

• minisatellite DNA

• microsatellite DNA

• hypervariable between individuals

types of transposable elements (TEs)

• transposons

• retrotransposons

transposable elements

can move to within genomes, can cause mutations leading to disease

DNA transposons

• are inserted through a cut-and-paste mechanism

• ligating blunt-ended transposon sequences in the staggered-ended recipient sequence results in short duplication of DNA

transposase

enzyme that catalyzes the insertion of transposons

mechanism for increasing copy number of DNA transposons

transposon moves from a region that has been replicated to one that has not, copy number will increase by one in one of the daughter chromosomes

long terminal repeat (LTR) retrotransposons

• contain long repeated units on both ends of the retrotransposon

• similar to retroviruses but lack envelope proteins

• protein coding region encodes reverse transcriptase and integrase

copy-paste mechanism of LTR retrotransposons

• LTRs are transcribed into an RNA copy of their sequence (excluding parts at the ends)

• retrotranscriptase converts the RNA molecule into DNA in the cytoplasm

• a molecule of tRNA is used as a primer

• DNA is imported into the nucleus with integrase and is inserted into the genome

long interspersed element (LINE)

• about 21% of total genome

• contain ORFs encoding an RNA binding protein (ORF1) and reverse transcriptase and a nuclease (ORF2) to mediate insertion into the genome

short interspersed element (SINE)

• do not contain ORFs

• about 13% of total genome

DNA insertion of LINEs

• RNA is produced and exported from the nucleus

• ORF1 and ORF2 are translated and bind LINE RNA

• RNA-protein complex is imported into the nucleus

• nuclease cuts DNA at AT-rich sequences and uses DNA ends as primers

• no transposase or integrase used

genome changes caused by TE movement

recombination between repeated elements can shuffle exons and produce new genes with new combination of exons