1. Concepts of Genetics PCB 3063 Kim Hughes, Yingxue Ren, Denise Everhart Chapter 12 DNA Organization in Chromosomes

2. 12.1Viral and Bacterial Chromosomes Are Relatively Simple DNA Molecules Bacterial and viral chromosomes are usually: a single nucleic acid molecule largely devoid of associated proteins much smaller than eukaryotic chromosomes

3. Chromosomes of viruses consist of single- or double-stranded DNA or RNA. Can be linear or circular. Section 12.1 Phage Double-stranded DNA DNA is linear before infection, circular after DNA molecule = 7  m. Phage head <0.1  m DNA is inert when packaged in the phage head

4. Chromosomes of viruses consist of single- or double-stranded DNA or RNA. Can be linear or circular, depending on the virus. Section 12.1 Phage T2 Double-stranded DNA Linear molecule = 52  m Phage head = 0.1mm

5. Section 12.1 Bacterial chromosomes are double-stranded DNA and are compacted into a nucleoid DNA binding proteins HU and H1 (positively charged) E. coli Circular DNA molecule = 1200  m. Bacteria = 2  m Unlike viruses, DNA is active even though it is highly compacted within the cell

6. 12.2Supercoiling Facilitates Compaction of the DNA of Viral and Bacterial Chromosomes Supercoiling compacts DNA. Most closed circular DNA molecules in bacteria are slightly underwound and supercoiled.

7. Figure 12.4

8. Eukaryotic Chromosomes Larger More complex (chromatin) More compacted Some specialized eukaryotic chromosomes were invaluable for early insights into structure: Polytene and Lampbrush Chromsomes

9. Polytene chromosomes and lampbrush chromosomes are very large and can be visualized by light microscopy. Polytene: Salivary glands and guts of some flies, protozoans, and plants (somatic cells) Lampbrush: vertebrate oocytes (germ cells--meiotic) Unusual eukaryotic chromosomes

10. Polytene chromosomes: have distinctive banding patterns represent paired homologs are composed of many DNA strands Section 12.3

11. Figure 12.5

12. The DNA of the paired homologs of polytene chromosomes undergoes many rounds of replication without strand separation or cytoplasmic division. Section 12.3

13. Polytene chromosomes have puff regions where the DNA has uncoiled and are visible manifestations of a high level of gene activity. Section 12.3

14. Figure 12.6 Puffs where active RNA transcription is occurring

15. Lampbrush chromosomes are large and have extensive DNA looping. They are found in oocytes in the diplotene stage of meiosis. Thought to be extended, uncoiled versions of normal meiotic chromosomes Section 12.3

16. Figure 12.7a Loops where active RNA transcription is occurring

17. Coiled and uncoiled DNA “Uncoiling” seems to be associated with gene activity But DNA in cells is usually highly coiled and compact.

18. 12.4Eukaryotes: DNA Is Organized into Chromatin Nucleosomes are condensed several times to form the intact chromatids The DNA in a human cell would be ~2 meters long if it were “unwound”. The nucleus is 5-10 mm (5 x 10-6 m) in diameter Eukaryotic chromosomes are complexed into a nucleoprotein structure called chromatin. Chromatin is bound up in nucleosomes with histones H2A, H2B, H3, and H4

19. Figure 12.9 Interphase Mitosis/Meiosis Metaphase

20. The nucleosome core particle derived from X-ray crystal analysis at 2.8 Å resolution. The double- helical DNA surrounds four pairs of histones. Histone tail

21. Table 12.2

22. Chromatin remodeling must occur to allow the DNA to be accessed by DNA binding proteins. Section 12.4 Histone tails are important for histone modifications such as acetylation, methylation, and phosphorylation. Histone Methylation usually turns a gene off. Histone Acetylation usually turns a gene on. Histone Phosphorylation -- we're not sure what that does.

23. Inactive chromosomal regions Inactivated X in eutherian mammals The H4 histones are under-acetylated

24. Euchromatin is uncoiled and active Heterochromatin remains condensed and is inactive. Heterochromatic Regions Centromeres Telomeres Mammalian Y chromosome Inactive Mammalian X (Barr Body) Unique to eukaryotic DNA C-banding

25. Chromosome Banding Mitotic chromosomes have a characteristic banding pattern. In C-banding, only the centromeres are stained. G-banding is due to differential staining along the length of each chromosome.

26. Differential staining in G banding reflects the heterogeneity & complexity of the chromosome. Section 12.5 Used to identify inversions and translocations

27. Eukaryotic Chromosomes have non- repetitive and repetitive DNA Repetitive DNA sequences are repeated many times within eukaryotic chromosomes. There are a number of categories of repetitive DNA

28. Multi-copy genes: Some coding genes occur in multiple copies (e.g., genes encoding ribosomal DNA). However, most repetitive DNA is non-coding There are several different kinds of repetitive DNA Repetitive DNA sequences are repeated many times within eukaryotic chromosomes.

29. Satellite DNA: highly repetitive, consists of short repeated sequences. Repetitive DNA Centromeres are the primary constrictions along eukaryotic chromosomes mediate chromosomal migration during mitosis and meiosis D. melanogaster centromeres characterized by AATAACATAG, repeated many times

30. Satellite DNA: highly repetitive, consists of short repeated sequences. Section 12.6 Telomeres DNA sequences consist of short tandem repeats that contribute to the stability and integrity of the chromosome. In vertebrates 5’-TTAGGGG-3’ is repeated many times Up to 1000 telomeric repeats in some organisms

31. Moderately repetitive DNA includes: Minisatellites (variable number tandem repeats or VNTRs): DNA sequences 15-100 bp, repeated hundreds of times. Microsatellites: Sequences 2-4 bp, repeated 5 to 100 times. VNTRs and microsatellites are used in DNA fingerprinting and other forms of genetic identity and kinship analysis because number of repeats highly variable among individuals Section 12.6

32. Short interspersed elements (SINES) and long interspersed elements (LINES) are dispersed throughout the genome rather than tandemly repeated, and constitute over 1/3 of the human genome. SINEs are ~ 500 bp, and may occur >500,000 times in the human genome LINEs are ~6000 bp, and may occur up to 850,000 times in the human genome. LINEs are retrotransposons because they encode RNAs that are reverse-transcribed back to DNA, which integrates back into genome in a new place. SELFISH GENES Section 12.6

33. Only a small portion of the eukaryotic genome (2%– 10%) constitute protein-coding genes. In addition to repetitive DNA, there are also a large number of single-copy noncoding regions, some of which are pseudogenes. Pseudogenes are evolutionary vestiges of functional genes that are no longer functional. Pseudogenes are previously functional genes that have acquired “stop codons” and other mutations that make them non-functional. Section 12.7 The Vast Majority of a Eukaryotic Genome Does Not Encode Protein-coding Genes