1. By Dr. Chandrama P. Upadhyaya
Chapter 4
Chromatin and chromosomes By
Dr. Chandrama P. Upadhyaya

2. Chromosomes vs. Chromatin
Unwound DNA
Active throughout Interphase
DNA is being used for macromolecule synthesis
Chromosomes
Tightly packaged DNA
Very active during cell division
DNA is not being used for macromolecule synthesis

3. Chromosomes & Genomes Chromosomes Genome
complexes of DNA and proteins – chromatin
Viral – linear, circular; DNA or RNA
Bacteria – single, circular
Eukaryotes – multiple, linear
Genome
The genetic material that an organism possesses
Nuclear genome
Mitochondrial & chloroplasts genome

4. Chromosome in viruses
Genome is Infectious particles containing nucleic acid surrounded by a protein capsid.
Rely on host cell for replication, transcription, translation
Exhibit a limited host range
Genomes vary from a few thousand to a hundred thousand nucleotides

5. Some Virus Structures
Phage
Capsid protein
TMV

7. Bacterial Chromosomes
In a region called the nucleoid
DNA in direct contact with cytoplasm

8. Bacterial Chromosomes
Chromosomal DNA is compacted ~ 1000 fold to fit within cell

9. Bacterial Chromosomes
Size
Escherichia coli ~ 4.6 million bp
Haemophilus influenzae ~ 1.8 million bp
Composition
E coli ~6000 genes
Genes encoding proteins for related functions arranged in operons
Intergenic regions nontranscribed DNA
Single origin of replication (Ori)

10. Prokaryotic Gene (Operon) Structure
Stop Codon TAA, TAG, TGA
Regulatory Elements
Cistron 1
Coding Sequence= ORF +1
ATG
Cistron 2
Promoter & Operator
DNA
Terminator sequence
Regulatory and Coding Sequence Unit = Operon
Protein A
Protein B
Structural or Coding Sequences
Regulatory Sequences

11. Eukaryotic Chromosomes
Eukaryotic species contain one or more sets of chromosomes (ploidy level)
Each set is composed of several linear chromosomes
DNA amount in eukaryotic species is greater than that in bacteria
Chromosomes in eukaryotes are located in the nucleus
To fit in there, they must be highly compacted
This is accomplished by the binding of many proteins
The DNA-protein complex is termed chromatin
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12. Eukaryotic genomes vary substantially in size
variation not related to complexity of the species
i.e - a two fold difference in genome size between two salamander species
Size difference due to accumulation of repetitive DNA sequences

13. Variations in DNA Content
Figure 10.10

14. Eukaryotic Chromosome Organization
Eukaryotic chromosomes are long, linear DNA molecule
Three types of DNA sequences are required for chromosome replication and segregation
Origins of replication (multiple)
Centromeres (1)
Telomeres (2)

15. Centromere
Kinetochore proteins
Origin of replication
Telomere
Genes
Repetitive sequences

16. Chromosome Organization
Genes located between centromere & telomeres
hundreds to thousands of genes
lower eukaryotes (i.e. yeast)
Genes are relatively small
Very few introns
higher eukaryotes (i.e. mammals)
Genes are long
Have many introns
Non-gene sequences
Repetitive DNA
Telomere
Centromere
Satellite

17. Eukaryotic Gene Structure
Start Codon ATG
Stop Codon TAA, TAG, TGA
Cis-Regulatory Elements
Exon1
Exon2
Exon3
Promoter/ Enhancer

18. Repetitive Sequences
Sequence complexity refers to the number of times a particular base sequence appears in the genome
2 main types of sequences
Moderately repetitive
Highly repetitive (low complexity)

19. Repetitive Sequences Unique or non-repetitive sequences
Found once or a few times in the genome
Includes structural genes as well as intergenic areas
Moderately repetitive
Found a few hundred to a few thousand times
Includes
Genes for rRNA and histones
Origins of replication
Transposable elements
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20. Repetitive Sequences Highly repetitive
Found tens of thousands to millions of times
Each copy is relatively short (a few nucleotides to several hundred in length)
Some sequences are interspersed throughout the genome
Example: Alu family in humans
Other sequences are clustered together in tandem arrays
Example: centromeric satellite & telomeric regions

21. Eukaryotic Chromatin Compaction
Stretched end to end, a single set of human chromosomes will be over 1 meter long
nucleus is only 2 to 4 mm in diameter
The compaction of linear DNA in eukaryotic chromosomes involves interactions between DNA and various proteins
Proteins bound to DNA are subject to change during the life of the cell
These changes affect the degree of chromatin compaction

22. Nucleosomes
Histone proteins basic (+ charged lysine & arginine) amino acids that bind DNA backbone
Four core histones in nucleosome
Two of each of H2A, H2B, H3 & H4
Fifth histone, H1 is the linker histone
Figure 10.14

23. Nucleosomes
Figure 10.14

24. Beads on a String Shortens DNA length ~ seven-fold
Overall structure of connected nucleosomes resembles “beads on a string”
Shortens DNA length ~ seven-fold

25. Nucleosomes Join to Form 30 nm Fiber
Nucleosomes associate to form more compact structure - the 30 nm fiber
Histone H1 plays a role in this compaction
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26. Further Compaction of the Chromosome
The two events we have discussed so far have shortened the DNA about 50-fold
A third level of compaction involves interaction between the 30 nm fiber and the nuclear matrix
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27. Nuclear Matrix Association
Nuclear matrix composed of two parts
Nuclear lamina
Internal matrix proteins
10 nm fiber and associated proteins
Figure 10.18

28. DNA Loops on Nuclear Matrix
The third mechanism of DNA compaction involves the formation of radial loop domains
Figure 10.18
Matrix-attachment regions
Scaffold-attachment regions (SARs) or
MARs are anchored to the nuclear matrix, thus creating radial loops
25,000 to 200,000 bp

29. Further Compaction of the Chromosome
The attachment of radial loops to the nuclear matrix is important in two ways
1. It plays a role in gene regulation
Discussed in Chapter 15
2. It serves to organize the chromosomes within the nucleus
Each chromosome in the nucleus is located in a discrete and nonoverlapping chromosome territory
Refer to Figure 10.19
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30. Heterochromatin vs Euchromatin
Compaction level of interphase chromosomes is not uniform
Euchromatin
Less condensed regions of chromosomes
Transcriptionally active
Regions where 30 nm fiber forms radial loop domains
Heterochromatin
Tightly compacted regions of chromosomes
Transcriptionally inactive (in general)
Radial loop domains compacted even further

31. Types of Heterochromatin
Figure 10.20
Constitutive heterochromatin
Always heterochromatic
Permanently inactive with regard to transcription
Facultative heterochromatin
Regions that can interconvert between euchromatin and heterochromatin
Example: Barr body

32. Figure 10.21

33. 10-64 Figure 10.21 Compaction level in euchromatin
During interphase most chromosomal regions are euchromatic
Compaction level in heterochromatin
Figure 10.21
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34. Metaphase Chromosomes
Condensed chromosomes are referred to as metaphase chromosomes
During prophase, the compaction level increases
By the end of prophase, sister chromatids are entirely heterochromatic
These highly condensed metaphase chromosomes undergo little gene transcription
In metaphase chromosomes, the radial loops are compacted and anchored to the nuclear matrix scaffold

35. Chromosome Condensation
The number of loops has not changed
However, the diameter of each loop is smaller
During interphase, condensin is in the cytoplasm
Condensin binds to chromosomes and compacts the radial loops
Condensin travels into the nucleus
The condensation of a metaphase chromosome by condensin
Figure 10.23

36. Chromosomes During Mitosis
Cohesins along chromosome arms are released
Cohesin at centromer is degraded
Cohesin remains at centromere
The alignment of sister chromatids via cohesin

37. Chromosome condensation is caused by condensins
SMC proteins are ATPases that include the condensins and the cohesins.
A heterodimer of SMC proteins associates with other subunits.
Cohesins are responsible for holding sister chromatids together.
Condensins cause chromatin to be more tightly coiled by introducing positive supercoils into DNA.

38. Condensins could compact DNA.
Condensins are responsible for condensing chromosomes at mitosis.
Chromosome-specific condensins are responsible for condensing inactive X chromosomes in C. elegans.
Condensins could compact DNA.