Repetitive DNA-STRs, Gene structure and expression Flashcards
the human genome
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what is repetitive DNA
tandem repeats
interspersed repeats
tandem repeats
- – Satellites
- – Minisatellites
- – Microsatellites aka STRs (short tandem repeats), SSRs (simple sequence repeats)
interspersed repeats
- – LINES
- – SINES
- – LTRs
- – Transposons
Interspersed repetitive DNA
- nearly half the genome derives from what
transposable elements (TEs)
They abundant in gene sequences and are also present in a significant portion of mature mRNAs, mostly in their untranslated regions.
transposable elements (TEs)
- fundamental components of most eukaryotic genomes, with important contributions to their size, structure and variation.
- ## They occur as families with a variable copy number and they are (or were) able to transpose from one locus to another.
what is the most abundant among different TEs
the primate-specific Alu sequences (SINEs) are the most abundant and their 1.1 million copies account for more than 10% of the human genome!
Class I elements (interspersed repetitive)
- also called retroelements, can be divided into LTR retrotransposons
- which are flanked by long terminal repeats (LTRs) sharing an over-all organization similar to retroviruses and non-LTR retrotransposons
- which terminate at one end with a poly(A) tract and have structural features of long and short interspersed nuclear elements (LINEs and SINEs, respectively).
LTR retrotransposons have been further classified as either
- gypsy/Ty3-like or copia/Ty1-like elements based on the order of their encoded proteins, that include a reverse transcriptase (RT) and integrase (IN)
class II elements ((DNA) transposons)
- characterized by terminal inverted repeats (TIRs)
have been grouped into superfamilies on the basis of the target site duplication, the presence or not of the DDE triad (acidic amino acid motif), the sequence similarities at the DNA and protein levels (e.g. Tc1/mariner, hAT, Mutator-like, CACTA).
how are most DNA transposons organized
in families of autonomous and non autonomous elements, characterized by their ability to respond to the same transposase.
satellite DNA
α (alphoid) 171bp, centromeres
β (Sau3A) 68bp, certain centromeres
Sat 1 25-48bp most centromeres
Sat 2 & 3 5bp all chromosomes
minisatellite DNA
Telomeric >6bp all telomeres
Hypervariable 9-64 many near telomeres
microsatellite DNA
• Microsatellite DNA = SSR = STR
SSRs <10bp (or <6bp), dispersed
what did alec jeffereys discover
the so called hypervariable minisatellites which are repetitive sequences within the DNA.
• Composition and length of hypervariable minisatellites
varies between individuals, even within the same species.
what may be present within these minisatelite regions
• There may be interspersed polymorphic restriction sites within these minisatellite regions.
treating the DNA in hypervariable minisatellites with endonucleases does what
cleaves the DNA into fragments to create a pattern that is unique to each individual. Using the Southern blotting technique, the patterns of restriction fragments can be viewed.
• This results in a barcode-like pattern which is unique to the individual. This became known as DNA fingerprinting.
advances to DNA fingerprinting
- There have been several advances to this approach which provides a simple pattern with high discriminatory power.
- However, requires a large amount of sample material for the analyses, which is a disadvantage in criminal applications. In addition, inter-laboratory standardisation has been difficult to achieve and its relatively slow and expensive and difficult.
- PCR of STR loci has overcome these difficulties and has greatly enhanced the role of DNA profiling in forensic science.
STRs are dispersed where
short tandem repeats are dispersed throughout the whole genome and can be found in large numbers, even in the gene introns
whats the most common STR
Dinucleotide polymorphisms are the most common STRs (ignoring mononucleotide) but they are strongly affected by strand slippage during amplification, producing artefactual stutter bands.
what is less prone to slippage
- Tetra- and pentanucleotide repeats are less prone to slippage and are therefore more suitable for forensic analyses.
STR methods can be..
can be easily standardised and are suitable for multiplexing. Amplicon (PCR product) length measurement is automated; its cheap, quick, accurate and easy.
- Short tandem repeats (STRs), simple sequence repeats (SSRs) or microsatellites are defined as
tandemly repeated tracts of DNA composed of 1–6 base pair long motifs.
