Chromosome and genome

1. Chromosome and genome 11-16-2015

2. Genome: whole set of DNA to store all genetic information Circular versus linear chromsome

4. Human Genome • How many chromosomes does each human cell have? • 22 pairs of autosomal chromosome and 1 pair of sex chromosomes • What is the size of the human genome? • The human genome is made up of 3 billion base pairs • How many genes does the Human Genome code for? • Define the meaning of gene first!

5. Chromosomes p Centromere q Chromosome 5

6. Chromosomes as seen at metaphase during cell division TelomereDNA and protein capEnsures replication to tipTether to nuclear membrane Light bandsReplicate early in S phaseLess condensed chromatinTranscriptionally activeGene and GC rich Short armp (petit) CentromereJoins sister chromatids Essential for chromosome segregation at cell division100s of kilobases of repetitive DNA: some non-specific, some chromosome specific Long arm q Dark (G) bandsReplicate lateContain condensed chromatinAT rich Telomere

7. Total Genes On Chromosome 17: 723 373 genes in region marked red, 20 are shown FZD2 AKAP10 ITGB4 KRTHA8 Genes are arranged in linear order on chromosomes WD1 SOST MPP3 MLLT6 STAT3 BRCA1 breast cancer 1, early onset GFAP NRXN4 NSF NGFR CACNB1 HOXB9 HTLVR ABCA5 CDC6 ITGB3 Chromosome 17source: Human Genome Project

8. Genome Comparison

9. Human Genome • What is a gene? • A gene is segment of a genome that encodes a single specific end product (a protein or RNA) or a functional unit or information • How much of the genome are “genes”? • ~1.5% of the genome for protein coding • What accounts for the rest of the DNA in the genome?

10. Human Genome • Other items in genome • Introns • Repeated sequences (telomeres, centromeres) • Non-coding RNAs • tRNA, rRNA, snRNA. • miRNA • Long non-coding RNA • Functional or noise???? • Transposons (SINES and LINES) • Psuedogenes (genes that no longer produce functional products)

11. Transposons: Mobile DNA • Class II transposons: DNA (transposons) that moves directly from place to place. • Class I transposons: retrotransposons • That first transcribe the DNA into RNA and then • use reverse transcriptase to make a DNA copy of the RNA to insert in a new location

12. Discovery of transposons Barbara McClintock (1902-1992) Nobel prize in Physiology and Medicine 1983 Mobile genetic elements in maize 1940-1950

13. Discovery of TE • study of chromosomal breakage • increased frequency in certain site (= marker „dissociation“ Ds) • location of Ds (dissociator) was unstable after crossing with some lines with Ac (activator) (= line carrying „activator“ Ac)

14. Discovery of TE • in one location – Ds insertion was connected with loss of purple pigment of endosperm • - after crossing with activator line pigment synthesis was recovered in some cells

15. Three of the many types of mobile genetic elements found in bacteria Transposase gene: encoding enzymes for DNA breakage and joining Red segments: DNA sequences as recognition sites for enzymes Yellow segments: antibiotic genes

16. Transposition: Cut and Paste (command/control-X and command/control-V in your computer) DNA-only

17. What is wrong about class I element? How to handle such problem?

18. The transposable element content of the human genome

19. What we should know about Alu element! • All Alus are approximately 300 bp in length. • A single recognition site for the restriction enzyme AluI located near the middle of the Alu element. • Alu elements are found only in primates. • Human chromosomes contain about 1,000,000 Alu copies (10% of the total genome). • Alu is a "jumping gene" – a transposable DNA sequence that "reproduces" by copying itself and inserting into new chromosome locations.

20. What we should know about Alu element! • No evidence that it is ever excised or lost from a chromosome locus. Each Alu insertion is the "fossil" of a unique transposition event that occurred only once in primate evolution. • Each Alu element has an internal promoter for RNA polymerase III. • However, Alu lacks the enzyme functions to produce a DNA copy of itself and to integrate into a new chromosome position

21. Alu transposition via an RNA intermediate:L1 provides RT for reverse transcription and a nick on the host chromosome!Alu is a parasite of L1, which, in turn, is a relic of a retrovirus ancestor.

22. What we should know about Alu element! • The rate of Alu transposition is about one in every 200 newborns today. • The vast majority of Alu insertions occur in non-coding regions and are thought to be neutral. • An Alu insertion in the NF-1 gene is responsible for neurofibromatosis I. • Alu insertions in introns of genes for tissue plasminogen activator (TPA) and angiotensin converter enzyme (ACE) are associated with heart disease.

23. PV92, a human-specific Alu insertion on chromosome 16

24. How Alu jump! http://labcenter.dnalc.org/labs/dnafingerprintalu/dnafingerprintalu_d.html

25. DNA Nucleosome

27. 細胞所有的遺傳資訊都完全登錄在DNA上的ATGC序列嗎？細胞所有的遺傳資訊都完全登錄在DNA上的ATGC序列嗎？ Epigenetics: the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence (Riggs et al. 1996)

28. Epigenetic chromatin regulation A. Modification at the DNA level 1. cytosine methylation B. Histone modification - the histone code 1. Histone acetylation 2. Histone methylation 3. Histone phosphorylation 4. Histone ubiquitilation 5. Different types of histones

29. The five nucleotides that make up the DNA

30. Maintenance of methylation

31. Genomic imprinting Some genes are expressed only from the maternal genome and some only from the paternal genome It is estimated that about 40 genes are imprinted and they can be found on several different chromosomes

32. Imprinting is maintained by DNA methylation

33. Why gene imprinting? Parent Offspring Conflict Hypothesis (Haig hypothesis) Conflict between male and female over allocation of maternal resources to offspring Paternally expressed genes would promote growth, maternally expressed genes should slow it down. For example: IGF2 (growth factor) / IGF2 receptor (make IGF2 inactive) IGF2 gene is paternal or maternal imprinted? How about IFG2 receptor?

34. Epigenetic chromatin regulation A. Modification at the DNA level 1. cytosine methylation B. Histone modification - the histone code 1. Histone acetylation 2. Histone methylation 3. Histone phosphorylation 4. Histone ubiquitilation 5. Different types of histones

35. Features of Histone Modifications SUMO Methyl Acetyl Phospho Ubiquitin Cell, 111:285-91, Nov. 1, 2002 • Covalently attached groups (usually to histone tails) • Reversible and Dynamic • Enzymes that add/remove modification • Signals • Have diverse biological functions

36. Features of Histone Modifications • Small vs. Large groups • One or up to three groups per residue Ub = ~8.5 kDa H4 = 14 kDa Jason L J M et al. J. Biol. Chem. 2005

38. Types of Histone Modifications Bhaumik, Smith, and Shilatifard, 2007.

39. Histone Modifications and Modifers • Writers: enzymes that add a mark • Readers: proteins that bind to and “interpret” the mark • Erasers: enzymes that remove a mark Tarakhovsky, A., Nature Immunology, 2010.

40. Dynamic of chromosome structure

41. Copy Number Variation (CNV) in human genome • Total 1,447 CNV were identified across the 270 samples • Established average length of CNV regions per genome was over 20 million base pairs

42. Nature 444:445 (2006)

43. Copy number variation of amylase gene among different people with different diet!

44. EXPANDING THE GENE CONCEPT BEYOND THE PROTEIN ENCODING SEQUENCESES of DNA:TRANSCRIPTION OF SOME GENES PRODUCES NONCODING RNAs

45. Non-Coding RNA: Formerly known as “JUNK” A Key to Eukaryotic Complexity?

46. Types of RNA CODING In translation (mRNA) NON-CODING In translation (tRNAs and rRNAs) In RNA processing: ribozymes Regulatory RNAs: Riboswitch; microRNA and lincRNA

47. Capping by Branching: A New Ribozyme Makes Tiny Lariats Science 309: 1350-1; 2005

48. A decade of riboswitch Cell 152: 17-24; 2013