Repetitive DNA

Larger genomes are not generated by increasing the number of copies of the same sequences present in smaller genomes.

It is due to the presence of

more repetitive DNA

Six major types of noncoding human DNA

have been described

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I. Noncoding DNA within genes-Protein-encoding exons are embedded within much larger noncoding introns

II. Structural DNA-Called constitutive heterochromatin-Localized to centromeres and telomeres

III. Simple sequence repeats (SSRs)-One- to six-nucleotide sequences repeated thousands of times

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IV. Segmental duplications-Consist of 10,000 to 300,000 bp that have duplicated and moved

V. Pseudogenes -Inactive genes

Transposable elements (transposons)-Mobile genetic elements-Four types:

-Long interspersed elements (LINEs)-Short interspersed elements (SINEs)-Long terminal repeats (LTRs)-Dead transposons

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Introns--Untranslated intervening sequences in mRNA

Exons– Translated sequences

Process-RNA splicing

Heterogeneous nuclear RNA (hnRNA)-Transcript before splicing is complete

Introns contain invariant 5’-GU and 3’-AG sequences at their borders (GU-AG Rule)

Recognized by small nuclear ribonucleoprotein particles (snRNPs) that catalyze the cutting and splicing reactions.

Internal intron sequences are highly variable even between closely related homologous genes.

Distribution of Uninterrupted and Interrupted Genes in Various Eukaryotes

While majority of the genes in yeast are uninterrupted, most of genes in flies are interrupted by one or two introns and most genes in mammals are interrupted by many introns

Sizes of Exons and Introns

Exons coding for proteins usually are short, but introns usually range from very short to very long

Exons Introns

II. Structural DNA

Prokaryotic Prokaryotic genes that

are turned on and off together are often clustered into operons which are transcribed into one mRNA molecule and translated together

Eukaryotic Eukaryotic genes

coding for enzymes of a metabolic pathway are often scattered over different chromosomes and are individually transcribed

There is an increasing complexity of regulatory sequences from a simple bacterial gene controlled by a repressor to a human gene controlled by multiple activators and repressors.

Major types of regulatory DNA elements in eukaryotes

S – silencer P – promoter I – insulator E – enhancer

TF – transcrition factor

heterochromatin

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o Promoters – recognition sequences for binding of RNA polymeraseo Enhancers – increase transcription of a related geneo Silencers – decrease transcription of a related geneo Insulators or boundary elements – block undesirable influences on genes:

1. enhancer blockers – prevent ‘communication’ between enhancers and unrelated promoters

2. barrier sequences – prevent spread of heterochromatin3. combined

o LCR – locus control regions – activate some gene clusters

Each cell in our bodies has about 6 feet of DNA stuffed into it -However, less than one inch is devoted to genes!

Complex genomes have roughly 10x to 30x more DNA than is required to encode all the RNAs or proteins in the organism or have any apparent regulatory function

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Non-Protein Coding Genes

Encode functional

RNAs

• There are non-protein genes in the genome that encode functional RNAs.

• These RNAs are important in regulating the expression of genes

• Assigned Reading: The functional genomics of noncoding RNA. Mattick et al. (2005), Science 309: 1527-1528.

By fluorescence in situ hybridization (FISH),the simple-sequence DNAs are localized near the centromers and telomeres of mouse chromosome

Types of repited dna

Two typesTandemly repetitive

Interspersed repetitive

1- Satellite DNAs

When eukaryotic DNA is centrifuged, fragmented and centrifuged to equilibrium in a Cesium chloride (CsCl) density gradient (CsCl gradient), two components are observed:

Main band: most of the genomic DNA

Satellite band: one or multiple miner bands; they could be heavier or lighter than the main band

The main band DNA has density of 1.701 g/cm with a G-C content of 42%, and minor band DNA has the buoyant density of 1.690 g/cm with a G-C content of 30%

Satellite DNAs

Satellite DNA highly repetitive DNA consisting of short unusual nucleotide sequences that are tandemly repeated 1000’s of times

It is found at the tips of chromosomes and the centromere

Its function is not known, perhaps it plays a structural role during chromosome replication and separation.

• Highly repetitive DNA (simple sequence DNA): Satellite DNA is characterized by rapid rate of hybridization, consists of very short sequences repeated many times in tandem in large clusters.

• In addition, multi-cellular eukaryotes have complex satellites with longer repeat units mainly in heterochromatic region (Centromeric heterchromatin---necessary for separation of chromosome to daughter cells

Satellite DNA Simple-sequence DNA (6% of the

human genome), size 14 to 500 bp

Microsatellite, (also called as transposable elements) 1-13 bp. Interspersed repetitive DNA dispersed throughout the genome

Telomere is a series of short tandem repeats at the ends of eukaryotic chromosomes; prevents chromosomes from shortening with each replication cycle

Species Repeat Sequence

Arabidopsis TTTAGGG

Human TTAGGG

Oxytricha TTTTGGGG

Slime Mold TAGGG

Tetrahymena TTGGGG

Trypanosome TAGGG

Until recently, little was known about molecular structure of telomeres. However, during the last few years, telomeres have been isolated and characterized from several sp.

Eukaryotic chromosomes are linear, not circular like prokaryotic chromosomes. Most eukaryotic chromosomes have short, species-specific sequences tandemly repeated at their telomeres

Blackburn and Greider have shown that chromosome lengths are maintained by telomerase, which adds telomere repeats without using the cell’s regular replication machinery.

The ends of eukaryotic chromosomes are formed by an enzyme called telomerase .Telomerase an enzyme adds repeats of 3´ ends of eukaryotic chromosomes

In the ciliate Tetrahymena, the telomere repeat sequence is 5` TTGGGG-3`

The telomeres of this organism end in the sequence 5'-TTGGGG-3'.

The telomerase adds a series of 5'-TTGGGG-3' repeats to the ends of the lagging strand.

A hairpin occurs when unusual base pairs between guanine residues in the repeat form.

Finally, the hairpin is removed at the 5'-TTGGGG-3' repeat. Thus the end of the chromosome is faithfully replicated.

TetrahymenaTetrahymena - - protozoa organism.protozoa organism.

RNA Primer  -  Short stretches of ribonucleotides (RNA substrates) found on the lagging strand during DNA replication. Helps initiate lagging strand replication

Interspersed repetitive

~1/2 of the human genome consists of interspersed repetitive sequences.

5- Transposable elements (transposons)

Transposons jump and interrupt the normal functioning may increase or decrease production of one or more proteins

can carry a gene that can be activated when inserted downstream from an active promoter and vice versa

Retrotransposons transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA to insert it must be converted back to DNA by reverse transcriptase

5- Transposable elements (transposons)-Mobile genetic elements-Four types:

-Long interspersed elements (LINEs)

-Short interspersed elements (SINEs)

-Long terminal repeats (LTRs)-Dead transposons

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Current definitions:

LINEs = Active or degenerate descendants of transposable elements.

SINEs = Non-autonomous transposable elements (lacking the ability to mediate their own transposition) and their degenerate descendents.

LINEs & SINEs

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interspersed repeats

Original definitions:

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The reverse transcriptase The reverse transcriptase

has has LINELINE specificity specificity, i.e., a reverse , i.e., a reverse transcriptase from one transcriptase from one LINELINE will only will only recognize the 3’ end of that recognize the 3’ end of that LINELINE, and will be , and will be less efficient at recognizing and reverse less efficient at recognizing and reverse transcribing other transcribing other LINELINEs. s.

Ex: LINE in Human

• 6 Kb in length• Has a poly A tail• Flanked by short repeats • 5% of genome• 95% of the sequence are truncated at the 5’ end• Contains two reading frames• - OPR I ( 375 codons)• - OPR II ( 1,300 codons)• Does not posses long terminal

repeats

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SINESINEs are s are retrosequencesretrosequences that that range in length from 75 to 500 bp. range in length from 75 to 500 bp.

SINESINEs do not possess any s do not possess any reading reading frameframe. .

Thus, their retroposition Thus, their retroposition mustmust be be aided by aided by other genetic elementsother genetic elements. .

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SINESINE

7SL-RNA derived tRNA-derived

Primate Alu+

Rodent B1

All others

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Length = ~300 bp Repetitive: > 1,000,000 times in the human

genome Constitute >10% of the human genome Found mostly in intergenic regions and introns Propagate in the genome through

retroposition (RNA intermediates).

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Alu elements are found only in primates.

All the millions of Alu elements have accumulated in a mere ~65 million years.

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Alu elements can be sorted into distinct families according to shared patterns of variation. At any given point in time, only one or several Alu “master copies” are capable of transposing.

Early in primate evolution, Early in primate evolution, AluAlu transposition transposition rate was approximately rate was approximately one new jump in every one new jump in every live birthlive birth. .

Today, it is about Today, it is about one new jump in every 200 one new jump in every 200 live birthslive births. .

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Evolution of Alu elements & Rodent BI DNA

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GENETIC AND EVOLUTIONARY EFFECTS OF TRANSPOSITION1. Duplicative transposition increases genome size.

Lily Edible frog Sunflower

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2. Bacterial transposons often carry genes that confer antibiotic or other forms of resistance.

Plasmids can carry such transposons from cell to cell, so that resistance can spread throughout a population or an ecosystem.

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3. Gene expression may be altered by the presence of a transposable element.

a.a. An insertion may eliminate the reading frame (phenotypic effects).

b.b. A transposable element may contain regulatory elements (effects on transcription of nearby genes).

c.c. Transposable elements may contain splice sites (effects on RNA processing even if the element is in an intron).

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Caused by the insertion of a transposable element.

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4. Transposable elements promote gross genomic rearrangements

a.a. directly (moving a DNA sequence from one genomic location to another).

b.b. indirectly (as a result of transposition, two sequences become similar to one another so that unequal crossing-over between them is possible).

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That is the end