Introduction to Genetics and Genomics

1. Introduction to Genetics and Genomics 51:123 Terry Braun M.S. (EE), Ph.D. (Genetics)

2. Announcements • Textbook • Survey • Portal • NoMachine • Genetics

3. Today • Basic Mendelian Genetics • Mendel’s laws • Rule independent assortment • Rule of segregation • mitosis and meiosis

4. Mendelian Genetics • Humans have 22 pairs (diploid) of chromosomes • Haploid would be 1 of each chromosome • plus XX or XY • genes on X/Y have sex-linked consequences • male pattern baldness is on X (and recessive) •  why are men twice as likely to get MPB (assuming only 1 carrier)? P(X) = ½ P(XX) = ¼ -- more on this later

5. Definitions chromosome – molecule of DNA (linear in eukaryotes) gene – all portions of a genome that affects the expression of a molecule (typically protein), but may include RNA and other molecules (ligands) allele – a specific variation (or instantiation) of a gene DNA – deoxyribonucleic acid RNA – ribonucleic acid EST – Expressed Sequence Tag (a portion of an mRNA) nucleotide – subunits of DNA (A,G,T,C), aka bases gamete – egg or sperm cell pharmacogenomics: is the study of how an individual's genetic inheritance affects the body's response to drugs. The term comes from the words pharmacology and genomics and is thus the intersection of pharmaceuticals and genetics. It combines traditional pharmaceutical sciences such as biochemistry with annotated knowledge of genes, proteins, and single nucleotide polymorphisms.

6. Genome Lexicon Overview (3 Bb haploid) Adenine Thymine Guanine Cytosine ATGC purines AG pyrimidines CT Size Centromeres Telomeres Euchromatin Heterochromatin Cytogenetics www.ensembl.org

7. Some sequence >sequence ATGCCGTATGCTAGCCCCTGAAATGAAATGATTCCTTTACCTTTCCCGCTGAGGGTAAaatgcatgcccctgaaa (FASTA format)

8. Nucleus Graphics used from www.roche.com

9. Sizes • # 0.1 nm (nanometer) diameter of a hydrogen atom • # 0.8 nm Amino Acid • # 2 nm Diameter of a DNA Alpha helix • # 4 nm Globular Protein • # 6 nm microfilaments • # 10 nm thickness cell membranes • # 11 nm Ribosome • # 25 nm Microtubule • # 50 nm Nuclear pore • # 100 nm Large Virus • # 200 nm Centriole • # 200 nm (200 to 500 nm) Lysosomes • # 200 nm (200 to 500 nm) Peroxisomes • # 1 um (micrometer) • # (1 - 10 um) the general sizes for Prokaryotes • # 1 um Diameter of human nerve cell process • # 2 um E.coli - a bacterium • # 3 um Mitochondrion • # 5 um length of chloroplast • # 6 um (3 - 10 micrometers) the Nucleus • # 9 um Human red blood cell • # 10 um • # (10 - 30 um) Most Eukaryotic animal cells • http://www.cbc.umn.edu/~mwd/cell_www/cell_intro.html

10. Mendelian Genetics • Rule of Segregation • offspring receive ONE allele (genetic material, gene) from the pair of alleles possessed by BOTH parents (offspring receives 2 out of 4 possible) • a gamete receives only one allele from the pair of alleles possessed by an organism • fertilization (union of 2 gametes) reestablishes the double number • easy to forget that there is very meticulous accounting of gene number in reproduction • estimated that 2/3 of fertilized eggs spontaneously abort • if the gene number goes awry, usually detrimental consequences for organisms (trisomy – 3 copies of chr 21 == Down's syndrome) • almost never see extra copies of larger chromosomes

11. Mendelian Genetics • Rule of Independent Assortment • alleles of one gene can segregate independently of alleles of other genes • (Linkage Analysis relies on the violation of Independent Assortment Rule) • (in general, 1 cM approx. 1 MB, but not always)

12. Dense Packaging

13. Nucleotides

14. Complementarity between bases C – G G – C T – A T – A A – T G – C A – T T – A G,A = purines T, C = pyrimidines (U in RNA)

15. Complementarity http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/dnast.htm

17. Directionality (5' -> 3'), Reverse Complement Seq G C A A T C T A Rev A T C T A A C G Com T A G A T T G C DNA is "directional" -- made 5' to 3' prime

18. Wikipedia: Directionality • Directionality, in molecular biology, refers to the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 3' end and a 5' end. The relative positions of structures along a strand of nucleic acid, including genes, transcription factors, and polymerases are usually noted as being either upstream (towards the 5' end) or downstream (towards the 3' end). • The importance of having this type of naming convention is easily demonstrated by the fact that nucleic acids can only be synthesized in vivo in a 5' to 3' direction, as the polymerase used to construct new strands must attach a new nucleotide to the 3' hydroxyl (-OH) group via a phosphodiester bond. Traditionally DNA and RNA sequences are written going from 5' to 3'.

19. adenine

20. DNA is double stranded • directional • reverse and reverse complement 5’ 3’ ATGCCCTTTGACG ||||||||||||| TACGGGAAACTGC 3’ 5’

22. A genomic code for nucleosome positioning. 1: Nature. 2006 Aug 17;442(7104):772-8. Epub 2006 Jul 19.Click here to read Links * Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore I, Wang JP, Widom J. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel. eran.segal@weizmann.ac.il Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approximately 50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

23. Motivation for mitosis/meiosis • terminology of bioinformatics • DNA, genes, ESTs, proteins, mRNA, transcripts, contigs, haplotype, etc. • omit technical details • however, provide a biological context for these terms

24. mitosis • cell duplication (duplicate genetic material) • DNA synthesis (broad bean) • S phase (40%), Gap2 (25%), Mitosis (10%), Gap1 (25%) • DNA duplicates in S phase (engineering marvel) • Error rate ~ 1/10 billion * VS 1 bit error occurs in 256MB of ram every month ** => 39 / 10 billion bytes *Radman, Miroslav and Robert Wagner. "The High Fidelity of DNA Duplication". Scientific American. pp40-46. **EE Times, 1998

25. mitosis • mitosis • prophase • metaphase • anaphase • telophase

26. Start of mitosis

27. Prophase • prophase • -chromosomes coalesce (shorten, thicken – analogous to “packaging”) • -each “chromosome” is now a pair of sister “chromatids”

28. Prophase -other structural activities (formation of spindle – microtubules that is structural mechanism for separating homologous chromosomes --centrosome divides [individual centriole]) --nuclear membrane breaks down

29. Metaphase -microtubules attached to centromeres -homologous pairs are lined up

30. Anaphase • -physical separation of chromosomes • -microtubule consumed

31. Telophase • -sister chromatids are separated (end of anaphase) and pulled to opposite poles of cell

32. Telophase • -nuclear membranes reform • -cell constricts and separates

33. Telophase • -chromosomes uncoil and protein synthesis resumes

34. 2 Cells – complete copy of genome, assuming no mistakes

35. meiosis • gamete formation (halving of genetic material, diploid to haploid) • but also duplicating (cell divides in 2 phases, meiosis I, and meiosis II) • prophase I • see Holliday structure for “homologous recombination” • origins for "independent assortment" and "segregation"

36. meiosis I • prophase I • metaphase I • anaphase I • telophase I • meiosis I separates maternal and paternal chromosome pairs • meiosis II separates sister ("identical") chromatids (or chromsome "pairs")

37. meiosis II • metaphase II • anaphase II • telophase II

38. meiosis I

39. prophase I • -chromosomes more spread out (relative to mitosis)

40. prophase I • -identical pairs matched

41. prophase I • -homologous pairs match up (called a bivalent) • -crossing over can now occur • -note the difference from meiosis (daughter cells are unlikely to get identical genetic material)

42. prophase I -as chromatids shorten, and thicken, they are called “tetrads” -“chiasmata” – regions where crossover occurs -virtually all tetrads form at least one “chiasma” -thought to stabilize the tetrad

43. metaphase I • -tetrads line up • -microtubules attach to sister chromosomes

44. Metaphase I maternal centromeres migrate together (but independent of other chromosome pairs) nuclear membrane breaks down paternal chromosomes migrate together tetrad aster crossing over

45. Anaphase I maternal centromeres migrate together (but independent of other chromosome pairs) paternal chromosomes migrate together remember independent assortment * * * ** ** aster In mitosis, identical chromosomes are pulled apart, maintaining haploid number. Here, they stay together, but are shuffled independently.

46. Telophase I If I remove the recombinants….

47. meiosis I reductional reduces number of chromosomes to haploid number Total number of unique chromosomes in BOTH cells is 4, each cell now only has 2

48. anaphase I • sister chromatids are pulled to the same pole (in mitosis, sister chromatids were pulled apart)

49. Telophase I • cell divides

50. metaphase II • sister pairs line up • (what’s wrong in this figure?)