Genomics – The Language of DNA

1. Genomics – The Language of DNA Honors Genetics 2006

2. The structure and meaning of the human genome • Genes span about 25% of the human chromosomes • Coding sequences amount to about 1%( the exons) • The intragenic regions or introns amount to the remaining 24% • Intergenic sequences are non coding and are between genes

3. Genes • About 20-30%of the genes are clustered in CpG islands. • There are gene deserts that comprise about 20% of the genome. • There are also sequences that are made of heterochromatin ( centromeres and telomeres)

4. Repetitive DNA • Highly repetitive:  About 10-15% of mammalian DNA reassociates very rapidly.  This class includes tandem repeats. • Moderately repetitive:  Roughly 25-40% of mammalian DNA reassociates at an intermediate rate.  This class includes interspersed repeats. • Single copy (or very low copy number):  This class accounts for 50-60% of mammalian DNA.

5. Satellite DNA • Satellites • The size of a satellite DNA ranges from 100 kb to over 1 Mb.  In humans, a well known example is the alphoid DNA located at the centromere of all chromosomes.  • Its repeat unit is 171 bp and the repetitive region accounts for 3-5% of the DNA in each chromosome.  Other satellites have a shorter repeat unit.  • Most satellites in humans or in other organisms are located at the centromere.

6. Minisatellites • The size of a minisatellite ranges from 1 kb to 20 kb.  One type of minisatellites is called variable number of tandem repeats (VNTR).  Its repeat unit ranges from  9 bp to 80 bp.  They are located in non-coding regions.  The number of repeats for a given minisatellite may differ between individuals.  This feature is the basis of DNA fingerprinting.

7. VNTR- individual differences • Variable Number of Tandem Repeat (VNTR) Polymorphism  • VNTR may result from unequal crossover. It is the molecular basis of DNA fingerprinting which has many practical applications

8. Telomeres • Another type of minisatellites is the telomere.  In a human germ cell, the size of a telomere is about 15 kb.  In an aging somatic cell, the telomere is shorter.  The telomere contains tandemly repeated sequence GGGTTA.

9. Microsatellites • Microsatellites are also known as short tandem repeats (STR), because a repeat unit consists of only 1 to 6 bp and the whole repetitive region spans less than 150 bp.  • Similar to minisatellites, the number of repeats for a given microsatellite may differ between individuals.  Therefore, microsatellites can also be used for DNA fingerprinting

10. Miniature Inverted-repeat Transposable Elements (MITES) • almost identical sequences of about 400 base pairs flanked by • characteristic inverted repeats of about 15 base pairs such as 5' GGCCAGTCACAATGG..~400 nt..CCATTGTGACTGGCC 3'3' CCGGTCAGTGTTACC..~400 nt..GGTAACACTGACCGG 5'

11. Transposons • Transposons are segments of DNA that can move around to different positions in the genome of a single cell. In the process, they may • cause mutations • increase (or decrease) the amount of DNA in the genome. • These mobile segments of DNA are sometimes called "jumping genes".

12. Transposons • Class II Transposons consisting only of DNA that moves directly from place to place. • Class III Transposons; also known as Miniature Inverted-repeats Transposable Elements or MITEs. • Retrotransposons (Class I) that • first transcribe the DNA into RNA and then • use reverse transcriptase to make a DNA copy of the RNA to insert in a new location.

13. Transposase actions • Both ends of the transposon, which consist of inverted repeats; that is, identical sequences reading in opposite directions. • A sequence of DNA that makes up the target site. Some transposases require a specific sequence as their target site; other can insert the transposon anywhere in the genome.

15. LINES • The human genome contains some 850,000 LINEs (representing some 21% of the genome). • Most of these belong to a family called LINE-1 (L1). • These L1 elements are DNA sequences that range in length from a few hundred to as many as 9,000 base pairs. • Only about 50 L1 elements are functional "genes"; that is, can be transcribed and translated.

16. L1 elements • The functional L1 elements are about 6,500 bp in length and encode three proteins, including • An endonuclease that cuts DNA • A reverse transcriptase that makes a DNA copy of an

17. L1 activity • L1 activity proceeds as follows: • RNA polymerase II transcribes the L1 DNA into RNA. • The RNA is translated by ribosomes in the cytoplasm into the proteins. • The proteins and RNA join together and reenter the nucleus. • The endonuclease cuts a strand of "target" DNA, often in the intron of a gene. • The reverse transcriptase copies the L1 RNA into L1 DNA which is inserted into the target DNA forming a new L1 element there.

18. SINEs (Short interspersed elements) • SINEs are short DNA sequences (100–400 base pairs) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III; that is, molecules of tRNA, 5S rRNA, and some other small nuclear RNAs. The most abundant SINEs are the Alu elements. There are over one million copies in the human genome (representing about 11% of the total DNA).

19. Alus • Alu elements consist of a sequence of 300 base pairs containing a site that is recognized by the restriction enzyme AluI. They appear to be reverse transcripts of 7S RNA, part of the signal recognition particle. • Most SINEs do not encode any functional molecules and depend on the machinery of active L1 elements to be transposed; that is, copied and pasted in new locations.