Eukaryotic Genomes

1. Eukaryotic Genomes CHAPTER 19

2. Structural Levels of DNA • a single linear DNA double helix averages about 4 cm in length • DNA associates with proteins that condense it so it will fit in the nucleus • DNA-protein complex = chromatin • chromatin looks like “beads on a string” when unfolded • “beads” = nucleosomes made up of histones (proteins) “string” = DNA • http://www.youtube.com/watch?v=9kQpYdCnU14&feature=relmfu • http://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=relmfu

3. chromatin fiber (30 nm) • created by interactions between adjacent nucleosomes and the linker DNA • chromatin fiber (300 nm) • created when the 30 nm chromatin fiber forms loops called looped domains attached to a protein scaffold made of nonhistones • chromosome • forms when the 300 nm chromatin fiber folds on itself

4. Regulation of Chromatin Structure • compactness of chromatin helps regulate gene expression • heterochromatin – highly compact so it is inaccessible to transcription enzymes • euchromatin – less compact allowing transcription enzymes access to DNA • chemical modifications that can alter chromatin compactness: • histoneacetylation (-COCH3) neutralizes the histones so they no longer bind to neighboring nucleosomes causing chromatin to have a looser structure

5. DNA Methylation • addition of methyl groups to DNA bases (usually cytosine) inactivate DNA • methylation patterns can be passed on • after DNA replication, methylation enzymes correctly methylate the daughter strand • accounts for genomic imprinting in mammals – expression of either the maternal or paternal allele of certain genes during development • (NOTE: inheritance of chromatin modifications that do not involve a change in the DNA sequence is called epigenetic inheritance) • http://www.youtube.com/watch?NR=1&v=dfdnf1Wpg0E&feature=endscreen

6. Cell Differentiation • process of cell specialization (form & function) during the development of an organism • differences in cell types results from differential gene expression • several control points at which gene expression can be regulated (turned on/off, accelerated, slowed down) • most commonly regulated at transcription in response to an extracellular signal

7. Regulation of Transcription Initiation • general transcription factors – proteins that form a transcription initiation complex on the promoter sequence (ex: TATA box) allowing RNA polymerase to begin transcription • control elements – segments of noncoding DNA that help regulate transcription by binding certain proteins • proximal control elements • distal control elements (enhancers) - interact with specific transcription factors: • activators –stimulate transcription by binding to enhancers • repressors - inhibit transcription by binding directly to enhancers or by blocking activator binding to enhancers or other transcription machinery

8. activators bind to enhancer with 3-binding sites • a DNA-bending protein brings the bound activators closer to the promoter • activators bind to general transcription factors & mediator proteins, helping them to form a functional transcription initiation complex • activators can also promote histone acetylation & repressors can promote histone deacetylation

9. Cell Type-Specific Transcription • the # of different genes far exceeds the # of different control elements; therefore, the particular combination of control elements is what is important in controlling transcription along with the available activators in the cell

10. Co-expressed Genes • most co-expressed genes are found scattered over different chromosomes • to coordinate their gene expression, each gene is regulated by the same control elements & these control elements are activated by the same chemical signals

11. Post-Transcriptional Regulation • alternative RNA-splicing: regulatory proteins specific to a cell type control intron-exon choices, thereby producing different mRNA molecules from the same primary transcript

12. methods of mRNA degradation: • enzymatic shortening of the poly-A tail triggers the removal of the 5′ cap which is followed by the digestion of the mRNA by nucleases • nucleotide sequences in the untranslated region at the 3′ end regulate the length of time an mRNA remains intact • microRNAs (miRNAs) – small RNA molecules that bind to complementary sequences on mRNA causing degradation by associated proteins; miRNAs may also block translation • RNA interference (RNAi) pathway – involve small interfering RNAs (siRNAs) that function in the same way as miRNAs

13. initiation of translation: • can be blocked by regulatory proteins that bind to specific sequences or structures within the untranslated region at the 5’ end of the mRNA & prevent the attachment of ribosomes • translation will not begin if the poly-A tails are not long enough • “global” control – activation or inactivation of one or more of the protein factors required to initiate translation • protein processing & degradation: • regulation of the modification or transporting of a protein • ubiquitin-tagged proteins are degraded by proteasomes

14. Genes Associated With Cancer • proto-oncogenes = normal cellular genes that code for proteins that stimulate normal cell growth & division • can be converted to oncogenes (cancer-causing genes) by: • translocation – proto-oncogene ends up near an active promoter or vice versa • amplification – increases # of proto-oncogenes in cell • point mutations in a promoter, enhancer, or the coding region itself • tumor-suppressor genes = encode proteins that help prevent uncontrolled cell growth • mutations that decrease the normal activity of these genes may contribute to the onset of cancer

15. Example: ras gene & p53 gene • ras gene is a proto-oncogene • it encodes a G protein that, in response to growth factors, triggers a cell signaling pathway that synthesizes a cell cycle stimulating protein • mutations in this gene can lead to the production of a hyperactive G protein that continuously triggers this pathway even when growth factors are absent • p53 gene is a tumor-suppressor gene • it promotes the synthesis of cell cycle inhibiting proteins • a mutation that knocks out this gene can lead to excessive cell growth & cancer

16. Model of Cancer Development • changes that must occur at the DNA level for a cell to become fully cancerous: • appearance of at least one oncogene • mutation or loss of several tumor-suppressor genes • in most cases mutations must knock out both alleles to block tumor suppression

17. Tumor Viruses • can transform cells into cancer cells through the integration of viral nucleic acid into host cell DNA • retroviruses may donate an oncogene to the cell • integrated viral DNA may disrupt a tumor-suppressor gene or convert a proto-oncogene to an oncogene • produce proteins that inactivate p53 and other tumor-suppressor proteins

18. Predisposition to Cancer • an individual inheriting an oncogene or a mutant allele of a tumor-suppressor gene is one step closer to accumulating the necessary mutations for cancer to develop • (ex) breast cancer genes: BRCA1 or BRCA2 • a woman who inherits one mutant BRCA1 allele has a 60% chance of developing breast cancer before the age of 50

19. Eukaryotic vs. Prokaryotic Genomes Eukaryotes Prokaryotes • larger genome but fewer genes in a given length of DNA • more noncoding DNA (10,000 times as much as prokaryotes ) • most of the DNA does not encode protein or RNA • genes contain introns so they are much longer than prokaryotic genes • smaller genome but more genes in a given length of DNA • less noncoding DNA • most of the DNA codes for protein, tRNA, or rRNA • genes are not interrupted by introns

20. Human Genome • 98.5% does not code for proteins, rRNAs, or tRNAs • 24% is gene-related regulatory sequences and introns • 44% is repetitive DNA made up of transposable elements & related sequences

21. Transposable Elements • two types: • transposons – move within a genome by means of a DNA intermediate • can move by “cut-and-paste” or “copy-and-paste” • retrotransposons – move within a genome by means of an RNA intermediate • always leave a copy at the original site because they are initially transcribed into an RNA intermediate • to be inserted at another site, the RNA intermediate must be converted back to DNA by reverse transcriptase

22. Other Types of Repetitive DNA • probably arose by mistakes that occurred during DNA replication or recombination • accounts for about 15% of the human genome • about 1/3 of this consists of large-segment duplications (10,000-300,000 base-pairs) • long stretches of DNA that have been copied from one chromosomal location to another • remaining 2/3 is simple sequence DNA – copies of tandemly repeated short sequences like GTTAC • most is located at chromosomal telomeres and centromeres indicating it has a structural role

23. Gene-Related DNA • consists of coding & noncoding DNA • constitutes about 25% of the human genome • about ½ of the total coding DNA consists of solitary genes • remaining ½ occurs in multigene families = collections of identical or similar genes • (ex) identical gene family = rRNA • allows for quick production of millions of ribosomes • (ex) non-identical families = α-globin and β-globin

24. Evolution of Genomes • extra sets of chromosomes can arise from: • errors during meiosis • polyploidy – extra sets of genes • mutations can accumulate in the extra sets of genes • unequal crossing-over • can result in one chromosome with a deletion and another with a duplication • errors during DNA replication • slippage • occurs when DNA template shifts with respect to the new complementary strand resulting in a region of the DNA not be copied or being copied twice

25. rearrangement of existing DNA sequences by: • exon duplication • exon shuffling • mixing & matching of different exons either within a gene or between two nonallelic genes owing to errors in meiotic recombination • transposable elements: • can promote recombination • disrupt cellular genes or control elements • carry entire genes or individual exons to new locations

26. Evolution of Globin Genes • all the α-globin and β-globin genes likely evolved from one common ancestral globin gene • the ancestral globin gene duplicated and diverged into α-globin and β-globin ancestral genes • the ancestral α-globin and β-globin genes later duplicated several times and their copies diverged into the current family genes • the divergences undoubtedly arose from accumulated mutations • some of the gene duplications and subsequent divergences are also suspected to have produced new genes with novel, yet related functions