Eukaryotic Genomes

Organization & Regulation

http://www.ncbi.nlm.nih.gov/books/NBK21128/

What is a gene ?

Definitions
1. Classical definition: Portion of a DNA that determines a
single character (phenotype)
2. One gene one enzyme (Beadle & Tatum 1940): Every
gene encodes the information for one enzyme
3. One gene one protein: One gene contains information
for one protein (structural proteins included) one gene
one polypeptide
4. Current definition: A piece of DNA (or in some cases RNA)
that contains the primary sequence to produce a
functional biological gene product (RNA, protein).

Gene classification
intergenic
region
coding genes

non-coding
genes

Chromosome
(simplified)

Messenger RNA

Structural RNA

Proteins
transfer
RNA
Structural proteins

Enzymes

ribosomal
RNA

other
RNA

Cellular Genomes
Viruses Procaryotes

Eucaryotes
Nucleus

Capsid

Plasmids

Viral genome

Bacterial
chromosome

Chromosomes
(Nuclear genome)

Mitochondrial
genome

Chloroplast
genome
Genome: all of an organisms genes plus intergenic DNA
Intergenic DNA = DNA between genes

Prokaryote genomes

Example: E. coli
89% coding
4,285 genes
122 structural RNA genes

Haploid circular genomes

Polycistronic transcription units
Usually asexual reproduction, great variety of
recombination mechanisms
Transcription and translation take place in the same
compartment

Eukaryotic genome

Chromosomes
genes
Coding region

en.wikipedia.org

The Structure of Chromatin

Prokaryotic and eukaryotic cells
Gene expression in eukaryotes has two main differences from
the same process in prokaryotes.
First, the typical multicellular eukaryotic genome is much
larger than that of a bacterium.
Second, cell specialization limits the expression of many
genes to specific cells.
The estimated 35,000 genes in the human genome includes
an enormous amount of DNA that does not program the
synthesis of RNA or protein.

The Structure of Chromatin

Eukaryotic chromosomes contain an enormous amount of DNA
relative to their condensed length.
Each human chromosome averages about 2 x 108
nucleotide pairs.
If extended, each DNA molecule would be about 6 cm
long, thousands of times longer than the cell diameter.
This chromosome and 45 other human chromosomes fit
into the nucleus.
This occurs through an elaborate, multilevel system of
DNA packing.

The Structure of Chromatin

Histone proteins are responsible for the first level of DNA

packaging.
Their positively charged amino acids bind tightly to
negatively charged DNA.
The five types of histones are very similar from one
eukaryote to another and are even present in bacteria.
Unfolded chromatin has the appearance of beads on a
string, a nucleosome, in which DNA winds around a core
of histone proteins.

The Structure of Chromatin

Histones leave the DNA only transiently during

DNA replication.
They stay with the DNA during transcription.
By changing shape and position, nucleosomes
allow RNA-synthesizing polymerases to move
along the DNA.
The beaded string coils to form the 30-nm
chromatin fiber.
This fiber forms looped domains attached to a
scaffold of nonhistone proteins.

Levels of chromatin
packing.
Diagram and transmission
electron micrographs

In a mitotic
chromosome,
the looped domains
coil and fold to
produce the
characteristic
metaphase
chromosome.
These packing steps
are highly specific and
precise with particular
genes
located in the same
places.

 Interphase chromatin is generally much less

condensed than the chromatin of mitosis.
The chromatin of each chromosome occupies a
restricted area within the interphase nucleus.
Interphase chromosomes have areas that
remain highly condensed, heterochromatin,
and less compacted areas, euchromatin.

Eukaryotic genes

Most have introns

Produce monocistronic mRNA: only one encoded protein
Introns: intervening sequences within a gene that are not translated
into a protein sequence. Collagen has 50 introns.
Exons: sequences within a gene that encode protein sequences
Splicing: Removal of introns from the mRNA molecule.

Eukaryotic genome
Example: C. Elegans
Transparent nematode (roundworm), about
1 mm in length, which lives in temperate soil
environments. Research into
the molecular and developmental
biology of C. elegans was begun in 1974
by Sydney Brenner and it has since been
used extensively as a model organism

10 chromosomes
19,099 genes
Coding region 27%
Average of 5 introns/gene
Both long and short duplications

en.wikipedia.org

Eukaryotic genome organization

Multiple genomes: nuclear, plastid genomes: mitochondria,

chloroplasts

More about the nuclear genome:

Multiple linear chromosomes, total size 5-10000 MB, 5000 to 50000

genes
Monocistronic transcription units
Discontinuous coding regions (introns and exons)
Large amounts of non-coding DNA
Transcription and translation take place in different compartments
Variety of RNA genes: rRNA, tRNA, snRNA (small nuclear), sno (small
nucleolar), microRNAs, etc.
Often diploid genomes and obligatory sexual reproduction
Standard mechanism of recombination: meiosis

Human Genome Organization

by Dr Finbarr Hayes

HUMAN GENOME

Nuclear genome
3200 Mbp
65-80000 genes

30%
Genes and generelated sequences

Mitochondrial genome
16.6 kb
37 genes

70%
Extragenic
DNA

Two rRNA
genes

Unique or moderately repetitive

10%
90%
Coding
DNA

Pseudogenes

Noncoding
DNA

Gene
fragments

Introns,
untranslated
sequences, etc.

22 tRNA
genes

13 polypeptideencoding genes

80%

20%

Unique or
low copy
number

Moderate to
highly
repetitive

Tandemly
repeated
or clustered
repeats

Interspersed
repeats

Eukaryotic genome
Moderately repetitive
Functional (protein coding, tRNA coding)
Unknown function
SINEs (short interspersed elements)
200-300 bp
100,000 copies

LINEs (long interspersed elements)

1-5 kb
10-10,000 copies

Eukaryotic genome
Highly repetitive
Minisatellites
Repeats of 14-500 bp
1-5 kb long
Scattered throughout genome

Microsatellites
Repeats up to 13 bp
100s of kb long, 106 copies
Around centromere

Telomeres
Short repeats (6 bp)
250-1,000 at ends of chromosomes

Genome Organization at the DNA level

Chromosome organization
Eucaryotic chromosome
Centromere

Telomere
p-arm

Telomere
q-arm

Centromere:
DNA sequence that serve as an attachment for protein during mitosis.
In yeast these sequences (~ 130 nts) are very A+T rich.
In higher eucaryotes centromers are much longer and contain
satellite DNA
Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA.
Satellite DNA is the main component of functional centromeres, and form the main
structural constituent of heterochromatin
Telomeres:
At the end of chromosomes; help stabilize the chromosome
In yeast telomeres are ~ 100 bp long (imperfect repeats)
Repeats are added by a specific telomerase

Types of DNA repeats

Perfect repeats vs degenerate repeats

Tandem repeats (e.g. satellite DNA)

5-CATGTGCTGAAGGCTATGTGCTGCGACG- 3
3-GTACACGACTTCCGATACACGACGCTGC- 5
Inverted repeats (e.g. in transposons)
5-CATGTGCTGAAGGCTCAGCACATCGACG- 3
3-GTACACGACTTCCGAGTCGTGTAGCTGC- 5
Form stem-loop structures
Palindroms = adjacent inverted repeats
(e.g. restriction sites)
Form hairpin structures

Loop
Stem

Hairpin

Types of DNA sequences in the human genome .

The vast majority of the human genome does not code for human
proteins or RNAs and much of it is repetitive DNA.

Stages in gene expression that can be

regulated in eukaryotic cells.
Colored boxes indicate the processes
most often regulated

A simple model of histone tails and

the effect of histone acetylation .
Histones can also undergo other types of
modifications that help determine
the chromatin configuration.

A eukaryotic gene and its transcript.

Each gene has a promoter, a DNA sequence where RNA polymerase binds ,
a number of control elements, a ploy-A tail and the 5 cap.

A model for the action of enhancers and transcription activators.

Bending of the DNA by a protein enables enhancers to influence
a promoter hundreds or even thousands of nucleotides away.

Cell type-specific transcription.

Both liver cells and lens cells have the genes for
making the proteins albumin and crystallin, but
only liver cells make albumin (a blood protein),
and only lens cells make crystallin (the main
component of the lens of the eye).

Alternative RNA splicing.

The primary transcripts of some genes can be
spliced in more than one way, generating
differente mRNA molecules.

Regulation of gene expression by microRNAs.

Movement of eukaryotic transposable elements.

Transposons are segments of
DNA that can move around to
different positions in the
genome of a single cell.
In the process, they may
cause mutations increase (or
decrease) the amount of DNA
in the genome of the cell, and if
the cell is the precursor of a
gamete, in the genomes of any
descendants.
These mobile segments of
DNA are sometimes
called "jumping genes".
There are two distinct types:
Class II transposons. These
consist of DNA that moves
directly from place to place.
Class I transposons. These
are 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.

Degradation of a protein by a proteosome.

A proteosome, an enormous protein complex chops up unneeded proteins in the cell.