1. To talk about number of genes maybe we should revisit What is a gene?? (p270 and p290 and this chapter) How about “a locus or place on a chromosome” Problem? (perhaps a little vague) How about ….”a nucleotide sequence from here to here” Problem? (Do you include promoter and introns?)

2. How about a slight variation on the previous…a sequence that makes something-a polypeptide-or protein Problems? Does not really solve your promoter and intron problem are these then not part of the gene?? (Promoter not transcribed but needs to be present) Plus…

3. 1. Many proteins are made of several polypeptide chains (hemoglobin has two chains made by two “different” genes) 2. Plus there is alternative RNA splicing where …. different polypeptide chains are made by the same gene Fig 15.12

4. Figure 15.12 DNA Primary RNA transcript mRNA or Exons Troponin T gene RNA splicing 1 2 3 4 5 1 2 3 5 1 2 4 5 1 2 3 4 5 Alternative RNA splicing

5. Then …..DNA makes a number of RNAs (tRNA and rRNA) but they do not code for a polypeptide…final product is the RNA. Your text has this definition.. A gene is a region of DNA that produces a final functional product that is either a polypeptide or an RNA molecule

6. Traditional genome sequencing and then also metagenomics (what is that?) Genomes by the numbers…

7. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898077/#!po=96.8750 Estimates of number of genes in human genome

8. Where do we fit? 2010 paper entitled “Between a chicken and grape….”

9. Table 18.1 3 DOMAINS! Where would Tetrahymena fit? Mb per million base pairs

10. Exploring the Landscape of the Genome! CODING and Noncoding regions 1.5% codes for proteins or is transcribed into rRNAs and tRNAs 5% Gene regulatory regions (think promotors) 20% Introns We used to think of noncoding stuff as junk DNA but now rethinking this…why? Much of it is “highly conserved” over long periods of time-What does that mean?

11. EXAMPLE Within mammals …… Humans, rats and mice have 500 non-coding regions that are IDENTICAL..so suggests to us that it is doing something important-variation within these regions must have been selected against. In fact more mutations or changes have accumulated in many protein coding regions.

12. So what kinds of non-coding sequences are there? 1. Pseudogenes?? What are these? 2. “Repetitive DNA” (A big category but transposable elements are most common)

13. Transposable elements Move -”jumping genes” but don’t actually jump (enzymes and proteins bend DNA and then chunks excised) Some have lost their ability to move… Some may make proteins but ……..those proteins don’t seem to do much so still remain in “non- coding” categories.. There are two kinds in Eukaryotes (transposons and retrotransposons) –no need to know mechanism In mammals 25-50% of genome

14. The very large sizes of some genomes in plants and amphibians are due to transposable elements Make up 85% of corn genome

15. Figure 18.6 Barbara McClintock discovered them! (1940s and 50s) Confirmed much later

16. 2. “Repetitive DNA” In addition to transposons there are Alu elements Related to transposable elements Smaller than functioning transposable elements… 10% of human genome Another difference from transposable elements is that they may be transcribed into RNA-don’t know what it does…

17. “OTHER” Repetitive DNA There are some other forms of repetitive DNA your text goes over.

18. What are gene families or multigene families? Collections of sometimes identical but more typically just very similar genes. About half of all genes are part of a family. EX of an identical gene family makes rRNA which is part of ribosome (these happen to be clustered near each other). Why have lots of an identical gene?? when need lots of whatever it is you are making!

19. EX of non-identical gene family “globin” family One bunch on chromosome 16 makes various forms of alpha globin Another bunch on chromosome 11 encodes beta globin

20. Why do we mammals have so many sets????? Affinity for oxygen differs…(how much it really wants oxygen) from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140315/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140315/ “Under conditions of high-altitude hypoxia, adult alpacas and yaks are known to upregulate a fetal β- like globin gene, which results in the synthesis of a relatively high affinity fetal Hb (Reynafarje et al., 1975; Sarkar et al., 1999)” 19751999

21. More on globin genes We can recreate their evolutionary history There were a series of duplication events Compare sequences to infer the order in which they evolved

22. Figure 18.13 Ancestral globin gene Further duplications and mutations Transposition to different chromosomes Mutation in both copies Duplication of ancestral gene Evolutionary time  -Globin gene family on chromosome 16  -Globin gene family on chromosome 11       2   1  2  1   G  A               450-500mya

23. Figure 18.13 Ancestral globin gene Further duplications and mutations Transposition to different chromosomes Mutation in both copies Duplication of ancestral gene Evolutionary time  -Globin gene family on chromosome 16  -Globin gene family on chromosome 11       2   1  2  1   G  A               450-500mya

24. Figure 18.13 Ancestral globin gene Further duplications and mutations Transposition to different chromosomes Mutation in both copies Duplication of ancestral gene Evolutionary time  -Globin gene family on chromosome 16  -Globin gene family on chromosome 11       2   1  2  1   G  A               450-500mya

25. Figure 18.13 Ancestral globin gene Further duplications and mutations Transposition to different chromosomes Mutation in both copies Duplication of ancestral gene Evolutionary time  -Globin gene family on chromosome 16  -Globin gene family on chromosome 11       2   1  2  1   G  A               450-500mya Green ones are pseudogenes

26. Figure 18.13 Ancestral globin gene Further duplications and mutations Transposition to different chromosomes Mutation in both copies Duplication of ancestral gene Evolutionary time       2   1  2  1   G  A               450-500mya Embryo only… Fetus and Adult Fetus Adult

27. Once you have duplication events……Mutations accumulate in different globin genes some had no effect on protein structure-neutral mutation (may persist) some made the protein not work-this would be bad (selected against) some made the protein not work (and they persisted as psuedogenes) some may have altered protein structure in a positive way (selected for)

28. Sometimes after duplication events, genes gain a completely new function p355 EX. Mammals and Birds both have lysozyme gene- breaks down bacterial cell walls Mammals have a protein (alpha lactabumin) that plays a role in milk production that is very similar in structure. Must have been duplicated in mammal lineage and evolved

29. Not only can genes be duplicated but exons can be duplicated..

30. Proteins have different functional parts or “domains” EX. Transcription factors (a kind of protein) have a part or domain that binds to DNA, “A DNA binding domain” EX. Enzymes (another kind of protein) might have An active site A part that binds to cellular membranes

31. Often each domain or part is encoded by a different exon. These exons can get duplicated within a gene, so rather than just having one part or domain you can have multiple copies of that domain which in turn evolve. “exon families” –although we don’t call them that!

32. EX is collagen it has lots of copies of one exon Exon shuffling is when a duplicated exon is swapped with other genes (know concept p 357 but not Fig 18.14)

33. “The presence of introns, and thus exons, in effect made genes modular. In an uninterrupted gene, mutations that add or remove sections usually change the way the rest of the gene is read, producing gibberish. Exons, by contrast, can be moved around without disrupting the rest of the gene. Genes could now evolve by shuffling exons within and between them.” New Scientist “A brief history of the human genome”

34. Back to Transposable Elements and their effects (p357) 1. Encourage crossing over, recombination-Why? 2. May plunk themselves into a regulatory sequence-What might happen? Ex. McClintock’s corn and its pigment synthesizing enzyme 3. As they move they may accidently move chunks of genetic material around to a new position. Ex. Entire globin genes moved around to different chromosomes Or Exons can also be moved around!

35. What else do we know about big picture evolution of pieces of genome in humans?

36. Figure 18.10 12 Centromere-like sequences Telomere-like sequences Centromere sequences Telomere sequences Human chromosome 2 Chimpanzee chromosomes 13

37. Figure 18.11 Human chromosome 16 Mouse chromosomes 7 8 16 17

38. Homeotic genes are “genes that affect development” Homeobox region is the place on the genome where these genes reside In Animals these are called Hox genes Protein that is made by this region binds to DNA and acts as a transcriptional regulator-What does that mean? (180 nucleotides long so how many amino acids??)

39. Here is that protein with introns and 7 Exons… RRRKRTA-YTRYQLLE-LEKEFLF-NRYLTRRRRIELAHSL- NLTERHIKIWFQN-RRMK-WKKEN=60!

40. It controls the body plan of the embryo (head to tail). Determines the type of segment structures (e.g. legs, antennae, and wings in fruit flies or the different vertebrate ribs in humans) that will form on a given segment. As "executive" level genes they regulate genes that in turn regulate large networks of other genes. Ultimately they are themselves regulated by maternally- supplied mRNA. A transcription factor cascade!

41. Different lineages have different numbers of copies of these Hox genes due to a series of duplication events-are a gene family! Highly conserved. Fly can function perfectly well with a chicken Hox protein in place of its own (these lineages diverged 670mya).

43. RRRKRTA- YTRYQLLE-LEKEFLF-NRYLTRRRRIELAHSL- NLTERHIKIWFQN –RRMK-WKKEN

44. Figure 18.17 Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse chromosomes Mouse embryo (12 days) Adult mouse

45. Figure 18.18 Genital segments Thorax Abdomen Thorax Abdomen