1. The Structure of Human Gene and Genome
Nattiya Hirankarn, MD, PhD
Dept of Microbiology
Faculty of Medicine
Chulalongkorn University

2. Further Reading
หนังสือ “เวชศาสตร์โมเลกุล”
book lists
Molecular Cell Biology
Genome

3. Genome

7. Chromosome change structure dramatically during cell cycle
Cell cycle consists of a nuclear division and the interphase
Mitosis is a marvelous copying process, prophase, prometaphase, metaphase, anaphase, and telophase : chromosome is highly organized and condensed
During Interphase the chromosomes are diffuse and the nuclear envelop is intact

8. Key Concepts
* Metaphase chromosomes have a protein scaffold to which the loops of supercoiled DNA are attached
* DNA of interphase chromatin is a tangled mass occupying a large part of the nuclear volume

9. * A nucleosome contains ~ 200 bp of DNA, 2 copies of each core histone (H2A, H2B, H3, H4) and 1 copy of H1
* DNA is wrapped around the outside surface of the protein octamer

10. Figure 9-30. Structure of the nucleosome
Figure Structure of the nucleosome. (a) Ribbon diagram of the nucleosome shown face-on (left) and from the side (right). One DNA strand is shown in green and the other in brown. H2A is yellow; H2B, red; H3, blue; H4, green. (b) Space-filling model shown from the side. DNA is shown in white; histones are colored as in (a). H2A, H2A, H2B, H2B, H3, and H4 indicate the positions of the respective histone N-terminal tails visible in this view. The H2A N-terminal tail interacts with the upper loop of DNA, while the H2A N-terminal tail (only partially seen in this view) interacts with the bottom loop of DNA. The N-terminal tail of one H4 extends from the bottom of the nucleosome and interacts with the neighboring histone octamer in the crystal lattice (not shown). The N-terminal tails of histones H2B, H2B, H3, and H3 pass between the two loops of DNA. The N-terminal tails of H2A, H4, H3, and H2B include an additional 3, 15, 19, and 23 residues, respectively, that are not visualized in the crystal structure because they are not highly structured. They extend further from the surface of the nucleosome where they may participate in nucleosome-nucleosome interactions in the 30 nm fiber or interact with other chromatin-associated proteins. [From K. Luger et al., 1997, Nature 389:251; courtesy of T. J. Richmond.]

11. Chromatin Individual chromosomes can be seen only during mitosis
Chromatin is the DNA-protein complex in chromosome
During interphase, the general mass of chromatin is in the form of euchromatin, which is less tightly packed than mitotic chromosomes
Regions of heterochromatin remain densely packed throughout interphase

12. Bandind Pattern (The human karyogram)
Certain staining techniques cause the chromosomes to have the appearance of a series of striations called G-bands
The bands are lower in G-C content than the interbands
Genes are concentrated in the G-C rich interbands

13. Gene

15. Figure 9-1. Comparison of bacterial operons and simple eukaryotic transcription units. (a) The trp operon in the E. coli genome contains five genes (A E) encoding enzymes required for synthesis of tryptophan. A control region located near the start site regulates transcription of the entire operon, which yields an 7-kb polycistronic mRNA. A mutation within the transcription-control region (a) can prevent expression of all the proteins encoded by the trp operon. In contrast, a mutation within any one gene of an operon (e.g., b in the trpA gene) generally affects only the protein encoded by that gene (TrpA protein). (b) A simple eukaryotic transcription unit includes a region that encodes one protein, extending from the 5 cap site to the 3 poly(A) site, and associated control regions. Intron sequences, which lie between exons, are removed during processing of the primary transcripts and thus do not occur in the functional monocistronic mRNA. Dashed lines indicate spliced-out introns. Mutations in a transcription- control region (a, b) may reduce or prevent transcription, thus reducing or eliminating synthesis of the encoded protein. A mutation within an exon (c) may result in an abnormal protein with diminished activity. A mutation within an intron (d) that introduces a new splice site results in an abnormally spliced mRNA encoding a nonfunctional protein.

16. Figure 9-2. Two examples of complex eukaryotic transcription units and the effect of mutations on expression of the encoded proteins. The RNA transcribed from a complex transcription unit (blue) can be processed in alternative ways to yield two or more functional monocistronic mRNAs. Dashed lines indicate spliced- out introns. (a) A complex transcription unit whose primary transcript has two poly(A) sites produces two mRNAs with alternative 3 exons. (b) A complex transcription unit whose primary transcript undergoes exon skipping during processing produces alternative mRNAs with the same 5 and 3 exons. In this example, some cell types would express the mRNA including exon 3, whereas in other cell types, exon 2 is spliced to exon 4, producing an mRNA lacking exon 3 and the protein sequence it encodes. In (a) and (b), mutations (designated a) within exons shared by the alternative mRNAs (solid red) affect the proteins encoded by both alternatively processed mRNAs. In contrast, mutations (designated b and c) within exons unique to one of the alternatively processed mRNAs (red with diagonal lines) affect only the protein encoded by that mRNA.

17. How can the number of genes in the genome be identified?
By defining open reading frame
By defining the number of genes directly in terms of transcriptome (by directly identifying all the mRNAs) or proteome (by directly identifying all the proteins)
Note: The number of genes is less than the number of potential proteins because of alternative splicing

20. Read more in“Locating the Genes in the Genome Sequence” in Genomes 2nd edition

21. The Genetic Code (รหัสพันธุกรรม)

24. Nucleic Acid

26. DNA and RNA

28. DNA composition within the Genome

30. Extragenic DNA

31. Interspersed Repeated DNA

32. Satellite Repetitive DNA

34. Mitochondria Genome

35. Figure Human mitochondrial DNA (mtDNA), which has been sequenced in its entirety. Proteins and RNAs encoded by each of the two strands are shown separately. Transcription of the outer (H) strand occurs in the clockwise direction and of the inner (L) strand in the counterclockwise direction. The abbreviations for amino acids denote the corresponding tRNA genes. ND1, ND2, etc., denote genes encoding subunits of the NADH- CoQ reductase complex. The 207-bp gene encoding F0 ATPase subunit 8 overlaps, out of frame, with the N-terminal portion of the segment encoding F0 ATPase subunit 6. No mammalian mtDNA genes contain introns, although intervening DNA lies between some genes. [See D. A. Clayton, 1991, Ann. Rev. Cell Biol. 7:453.]

37. Gene Function and Control

44. The Inheritance of Gene

45. Molecular Genetic Analysis

46. Mutation

48. Genetic Variation & Polymorphism

50. Gene Mapping

53. Principles and Strategies in Identify Disease Genes

57. Human Genome Project