Unit II MSc 2nd Sem.

Satellite DNA Most simple-sequence are concentrated in specific chromosomal locations. In eukaryotic chromosomes, duplicated protein-coding genes and tandemly repeated genes are present. Besides this, eukaryotic cells also contain multiple copies of other DNA sequences, and these sequences generally referred to as repetitious DNA. Two types of repetitious DNA are present and the one which are less prevalent is called as simple-sequence DNA, or DNA.

Satellite DNAs consist of short sequences (about five to a few hundred base pairs in length) that form very large linear arrays, each containing up to several million base pairs of DNA. In many species, the base composition of these DNA segments is sufficiently different from the bulk of the DNA that fragments containing the sequence can be separated into a distinct “satellite” band during density gradient centrifugation (hence the name satellite DNA). Satellite DNAs tend to evolve very rapidly, causing the sequences of these genomic elements to vary even between closely related species. This type of DNA constitutes about 6 percent of the human genome.

Centromere and DNA

Th DNA contained within and and the proteins attached to this DNA have special features related to the particular functions of these structures.

Centromere

Each chromosome contains a site where the outer surfaces are markedly depressed. This site of the constriction on chromosome are called centromere.

In humans the centromere contains a tandemly repeated, 171‐base‐pair DNA sequence (called α ‐satellite DNA) that extends for at least 500 kilobases. This stretch of DNA associates with specific proteins that distinguish it from other parts of the chromosome. For instance, centromeric chromatin contains a unique H3 histone variant, called CENP‐A in mammals, which replaces conventional H3 in a certain fraction of the centromeric nucleosomes and gives these nucleosomes unique properties. During the formation of mitotic chromosomes, the CENP‐A‐containing nucleosomes become situated on the outer surface of the centromere where they serve as the platform for the assembly of the . The kinetochore, in turn,

serves as the attachment site for the microtubules that separate the chromosomes during cell division. Chromosomes lacking CENP‐A fail to assemble a kinetochore and are lost during cell division.

DNA sequences responsible for essential cellular functions tend to be conserved. It came as a surprise, therefore, to discover that centromeric DNA exhibited marked differences in nucleotide sequence, even among closely related species. This finding suggests that the DNA sequence itself is not an important determinant of centromere structure and function, a conclusion that is strongly supported by the following studies on humans. Approximately one in every 2000 humans is born with cells that have an excess piece of chromosomal DNA that forms an additional diminutive chromosome, called a marker chromosome. In some cases, marker chromosomes are devoid of α ‐satellite DNA, yet they still contain a primary constriction and a fully functional centromere that allows the duplicated marker chromosomes to be separated normally into daughter cells at each division. The centromere appears at the same site on a marker chromosome in all of the person’s cells, indicating that the property is transmitted to the daughter chromosomes during cell division. In one study, marker chromosomes were found to be transmitted stably through three generations of family members.

Telomere

The tips of each DNA molecule are composed of an unusual stretch of repeated sequences that, together with a group of specialized proteins, form a cap at each end of the chromosome called a telomere. Sequencing of telomeres from multiple organisms, including humans, has shown that most are repetitive oligomers with a high G content located in the strand with its 3′ end at the end of the chromosome. Human telomeres contain the sequence TTAGGG repeated from about 500 to 5000 times. These simple sequences are repeated at the very termini of chromosomes for a total of a few hundred base pairs in yeasts and protozoans and a few thousand base pairs in vertebrates. The 3′ end of the G-rich strand extends 12–16 nucleotides beyond the 5′ end of the complementary C-rich strand. This region is bound by specific proteins that protect the ends of linear chromosomes from attack by exonucleases.

The need for a specialized region at the ends of eukaryotic chromosomes is apparent when we consider that all known DNA polymerases elongate DNA chains at the 3′ end, and all require an RNA or DNA primer. As the replication fork approaches the end of a linear chromosome, synthesis of the leading strand continues to the end of the DNA template strand, completing

one daughter DNA double helix. However, because the lagging-strand template is copied in a discontinuous fashion, it cannot be replicated in its entirety. When the final RNA primer is removed, there is no upstream strand onto which DNA polymerase can build to fill the resulting gap. Without some special mechanism, the daughter DNA strand resulting from lagging-strand synthesis would be shortened at each cell division. The problem of telomere shortening is solved by an enzyme that adds telomeric repeat sequences to the ends of each chromosome. The enzyme is a protein–RNA complex called telomere terminal transferase, or telomerase. Because the sequence of the telomerase-associated RNA, as we will see, serves as the template for addition of deoxyribonucleotides to the ends of telomeres, the source of the enzyme, and not the source of the telomeric DNA primer, determines the sequence added. This was proved by transforming Tetrahymena with a mutated form of the gene encoding the telomerase- associated RNA. The resulting telomerase added a DNA sequence complementary to the mutated RNA sequence to the ends of telomeric primers. Thus, telomerase is a specialized form of a reverse transcriptase that carries its own internal RNA template to direct DNA synthesis. While telomerase prevents telomere shortening in most , some organisms use alternative strategies. Drosophila species maintain telomere lengths by the regulated insertion of non-LTR into telomeres. This is one of the few instances in which a mobile element has a specific function in its host organism.