Chromosome Structure and Org

Junk DNA
During
the late 1960s papers began to appear that showed eukaryotic DNA contained large amounts of repetitive DNA that did not appear to code for proteins (ie, Britten and Kohne, 1968). By the early 1970s, the term Junk DNA had been coined to refer to this noncoding DNA (ie. Ohno, 1972).
Chromosome Structure
and
DNA Sequence Organization
An Overview
Eukaryotes Have Large Complex Geneomes
human genome is ≈ 3 x 109 bp 3 x 109 bp x 0.34 nm/bp x 1 m/109 nm ≈ 1m Because humans are diploid, each nucleus contains 6 x 109 bp or ≈ 2 m of DNA That is a lot to pack into a little nucleus! Eukaryotic DNA is highly packaged

Types of Junk DNA Nine different types of DNA were listed as junk DNA by Nowak (1994) These nine types can be grouped into three larger groups:
1Repetitive DNA sequences 2Untranslated parts of RNA transcripts (pre-mRNA) 3Other non-coding sequences
What is Junk DNA?
“Junk DNA” is DNA that does not code for proteins, this is the definition that we will use. The meaning of “junk DNA” has become restricted significantly in recent years as the functionality of much of what was once considered junk has become obvious. Most modern genetics texts avoid the term. Even when junk DNA is mentioned, it may be given significantly different definitions. For example, Lodish et al. (1995) called it “Extra DNA for which no function has been found.”
30 nm
Tight helical fiber
Looped 200 nm Domains
Protein scaffold
Hale Waihona Puke Packaging DNA
Nucleosomes
11 nm
30 nm
Tight helical fiber
Metaphase Chromosome 700 nm 200 nm Looped Domains
Evidence
Conservation
of protein (and DNA) sequences is commonly interpreted to indicate functionality Significant variation in non-coding DNA is evident between relatively closely related species and even within species (ie Zeyl and Green, 1992). Mutation of some non-coding DNA does not produce significant changes in phenotype (Nei, 1987).
11 nm Histone octomer
Histone proteins Nucleosome B DNA Helix 2 nm
Packaging DNA
Histone H1
Packaging DNA
Histone H1
Packaging DNA
“Beads on a string” 11 nm
Four
proteins: H2A, H2B, H3, and H4 H3 and H4 are arginine rich and highly conserved H2A and H2B are slightly enriched in lysine Both arginine and lysine are basic amino acids making the histone proteins both basic and positively charged The octomer is made of two copies of each protein
Nucleosomes
Nucleosome
- Nucle - kernel, some -
body The lowest DNA packaging level Can be thought of as like a length of thread wound around a spool, the thread representing DNA and the spool being histone proteins
2 nm
B DNA Helix
Protein scaffold
Highly Packaged DNA Cannot be Expressed
The most highly packaged form of DNA is “heterochromatin” Heterochromatin cannot be transcribed, therefore expression of genes is prevented Constitutive heterochromatin - Permanently unexpressed DNA e.g. satellite DNA Facultative heterochromatin - DNA that could be expressed if it was not packaged
Repeated sequences seem too short to code for proteins and are not known to be transcribed. Five major classes of repetitive DNA:

Repetitive DNA
1 Satellites - Up to 105 tandem repeated short DNA sequences, concentrated in heterochromatin at the ends (Telomeres) and centers (centromeres) of chromosomes. 2 Minisatellites - Similar to satellites, but found in clusters of fewer repeats, scattered throughout the genome 3 Microsatellites - Shorter still than minisatellites. 1 4 and 5 Short (300 bp) and Long (up to 7,000 bp) Interspersed Elements (SINEs and LINEs) - Units of DNA found distributed throughout the genome
The Histone Octomer
The Histone Octomer
A
fifth protein, H1, is part of the nucleosome, but seems to be outside the octomer H1 varies between tissue and organisms and seems to stick to the 19 bases attached to the end of the core sequence Ausio (2000) discusses data showing that, at least in fungi, survival is possible without H1 Lack of H1 does not impact cell viability but shortens the lifespan of the organism This raises the question of how H1 evolved in single celled organisms
The Fifth Histone, H1
Packaging DNA
Histone octomer Histone proteins B DNA Helix 2 nm
Packaging DNA
Histone octomer Histone proteins B DNA Helix 2 nm