Genome Organization from Nucleotides to

Chromatin

Mohammed Qaisiya
 Genome
• Genome is the whole genetic material of an organism.
(the complete set of DNA within a single cell of an organism).

• It consists of DNA (or RNA in RNA viruses).

• The genome includes: The coding regions(genes), The
noncoding DNA, and the genomes of the mitochondria
and chloroplasts.

• Genomics the branch of molecular biology concerned

with the structure, function, evolution, and mapping of
genomes.
Human Genome
The diversity of mechanisms for packaging very long molecules of DNA into very
small cellular spaces is truly remarkable.

Cellular DNA content of various species.

Diversity of DNA-based genome organization.

 General features
• Human nuclear genome about 30.000 genes (2% of nuclear genome)
• 27.000 protein-coding genes and about 3000 RNA-coding genes
• 2% coding DNA and 98% non-coding DNA

• C. elegans roundworm (19.100 protein coding gene)

• There is no correspondence between biological

complexity and number of genes
 Human Genome sequence

Ref seq: is considered to be

the “wild type” sequence,
the major allele present in
the human population, and
the allele used in the latest
genome build
Organization of the Human Genome in chromosomes
Information Content of the Human Genome
 Amplification of information content

1. Many genes are capable of generating

multiple different products, not just one
(Alternative splicing) and the subsequent
biochemical modification of the encoded
protein

These 30,000 human genes can encode many

hundreds of thousands of different proteins,
collectively referred to as the proteome
 Amplification of information content
2. Individual proteins do not function by themselves.
They form elaborate in networks and respond in a
coordinated and integrated fashion to many different
genetic, developmental, or environmental signals
Genes location on chromosomes
 Gene families
❑ Share closely related DNA sequences and encode polypeptides with closely related
amino acid sequences

❑ Arisen by duplication of a primitive precursor gene

Gene superfamily ??
 Genes organization in families

1. Single cluster: all on single chromosomes

2. Dispersed: at different chromosome locations

3. Multiple cluster: gene clustered on different chromosome

Example…
Gene structure
Exons: (expression sequences)

Introns: (intervening sequences)

Pseudogenes
❑ Sequences that are related to the functional globin and OR genes but that do not
produce any functional RNA or protein product.
Non-coding DNA
 NON-coding DNA
• Satellite DNA: Composed of very large-sized blocks (100 kb →
several Mb) of tandemly repeated sequence.

• Minisatellite DNA: Composed of moderately-sized blocks (0.1

kb →20 kb) of tandemly repeated sequence (telomer region
TTAGGG)

• Microsatellite DNA: Composed of small-sized blocks (<100 bp)

of tandemly repeated sequence.
• Transposons: (Transposable Elements; “Jumping Genes”).
Composed of interspersed repetitive sequence, which that make
up an incredible 45% of the human nuclear genome.

• Short interspersed nuclear elements (SINEs). The Alu repeat (280

bp) is the most abundant sequence in the human genome.
Located within genes, they are confined to introns and other
untranslated regions.

• Long interspersed nuclear elements (LINEs). LINE-1 (~ 6.1 kb) is

the most important human transposon in that it is still actively
jumping and occasionally causes disease by disrupting important
functioning genes.
 Allele
Expression
 Monoallelic Expression
X Chromosome Inactivation
- Example of random monoallelic expression in the genome
- Mechanism of dosage compensation
- Epigenetic silencing of most genes on one of the two X chromosomes
in females.
 Eukaryotic genome
• Eukaryotic cells must fit approximately up to 2 m of unpacked
DNA into the spherical nucleus, which is a less than 10
micron diameter space. (HOW)!

• DNA molecules is packed into several chromosomes.

• Chromosome is a thread-like structure of nucleic acids and

protein found in the nucleus of most living cells, carrying
genetic information in the form of genes.

• Each chromosome have two complete sets of genes one from

each parent (Diploid).
DNA Packaging
 DNA Packaging
The DNA is first coiled around a histone complex
called a Nucleosome.

• Runs of nucleosomes are formed into a

zig-zagging string of chromatin which is then
folded into loop domains, and finally the
metaphase chromosome.
 Histone
• Histones are a family of small, positively charged
proteins.

• Nuclear DNA is highly condensed and wrapped around

histones in order to fit inside of the nucleus and take
part in the formation of chromosomes.

• Histones are basic proteins, and their positive charges

allow them to associate with DNA, which is negatively
charged.

• Histones H2A, H2B, H3 and H4 are known as the core

histones, and they come together to form one
nucleosome.
 Nucleosome Components
• Two molecules of each of the histones H2A, H2B, H3, and H4
come together to form a histone octamer (protein core), which
binds and wraps about 146 base pairs.
Post-Translation modifications for gene expression regulation
 Nucleosome Components
• Complete Nucleosomes is a nucleosome core, DNA linker and
non-histone associated protein.
• This structure is stabilized by the binding of one molecule of
histone H1.
 Chromatin Fibers
• Chromatin is made by series of beads called
(Nucleosomes) and joined by threads of DNA
called linker.
 Chromatin Fibers
• In vivo, Nucleosomes interact with
one another to condense the 11
nanometer nucleosome into 30
nanometer chromatin fibers which
are the basic structural unit of the
metaphase chromosomes.
 Third Level of Condensation
• Metaphase chromosomes are not dependent on the histones.

• Electron micrographs of isolated metaphase chromosomes

from which the histones have been removed reveal a Scaffold.

• Scaffold is made by non-histone proteins that support the

structure.

• Metaphase chromosomes are highly condensed in order to

organize the giant DNA molecules of different chromosomes
into structure that will facilitate their segregation to daughter
nuclei without being broken during the anaphase separation.
Third Level of Condensation
heterochromatin is such part of the chromosomes, which is a firmly packed
form and are genetically inactive, while euchromatin is an uncoiled (loosely)
packed form of chromatin and are genetically active
 Prokaryotic Cell
• Without a nucleus; no nuclear membrane (genetic
material dispersed throughout cytoplasm).

• No membrane-bound organelles.
• Cell contains only one circular DNA molecule
contained in the cytoplasm.

• DNA is naked (no histone).

• Simple internal structure.
 Bacterial genome
• The genome of Escherichia coli:

– is 4700 kb in size and exists as one

double-stranded circular DNA molecule. No free
5ʹ or 3ʹ ends.
– The chromosomal DNA is organized into a
condensed ovoid structure called a nucleoid.

– A considerable number of nonessential proteins,

called histone-like proteins or nucleoid-associated
proteins
 Plasmids
• Plasmids are small, double-stranded circular or
linear DNA molecules carried by bacteria, some
fungi, and some higher plants.
• They are extrachromosomal (separate from the
host cell chromosome), independent, and
self-replicating.
• At least one copy of a plasmid is passed on to
each daughter cell during cell division.

• They range in size from 2 to 100 kb

- Plasmids are important for our study for two main reasons:
-
1- They are carriers of resistance to antibiotics

2- They provide convenient vehicles for recombinant DNA

technology (formed by laboratory methods , joining together
DNA molecules from two different species that are inserted into
a host organism to produce new genetic combinations that are
of value to science, medicine, agriculture, and industry).
 Bacteriophages and mammalian DNA viruses

- Is a virus that infects and replicates within Bacteria and

Archaea

- The motivation for most of the early studies on viruses

centered on their pathogenicity, but they have also proved
extremely useful systems for analysis of fundamental
principles of molecular biology.

- Bacteriophages and mammalian DNA viruses have DNA

genomes that occur in a countless of forms, ranging from
double-stranded to single stranded DNA and linear to
circular forms
 Bacteriophages
- The chromosome of bacterial viruses usually consists of a single
DNA molecule, largely devoid of associated proteins.

- For example, bacteriophage lambda (λ) has a double-stranded

linear genome.

- Upon infection of a host bacterium, the DNA closes to form a

circle. This phage is used widely as a tool for molecular biology
research

- All bacteriophages have the ability to package an exceedingly

(very) long DNA molecule into a relatively small volume
 Mammalian DNA viruses
- Mammalian DNA viruses infect mammalian cells and
make use of the host cell machinery for their
replication.

- Their genomes come in a diversity of forms. For

example, human papilloma virus (HPV), a causative
agent of cervical and other cancers.

- Likewise, simian virus 40 (SV40) from rhesus monkey,

also has a double-stranded circular genome.

- In contrast, adenovirus, a vector used for human gene

therapy, has a double-stranded linear genome.
 Organelle genomes
• Organelle genomes are inherited independently of
the nuclear genome and they exhibit a uniparental
mode of inheritance, with traits being passed to
offspring only from their mother.

• The organelles are only contributed from the

maternal gamete (e.g. egg cell), and NOT from the
paternal gamete (e.g. sperm cell or pollen grain).
 Mitochondrial DNA (mtDNA)
• The mtDNA encodes essential enzymes
involved in ATP production

• mtDNA is usually a circular, double-stranded

DNA molecule that is NOT packaged with
histones.

• mtDNA differs greatly in size among organisms.

In animals, it is typically 16–18 kb, while in plants
it ranges in size from 100 kb to 2.5 Mb.
Mitochondrial DNA (mtDNA)
mtDNA
Typical human cell — including the egg cell — contains only one nucleus but hundreds of mitochondria.

A single cell can contain both mutant mitochondria and normal mitochondria, and the balance between the
two will determine the cell’s health.

This helps explain why the symptoms of mitochondrial disease can vary so much from person to person, even
within the same family.

Also, the woman may or may not have symptoms of mitochondrial disease herself.
These diseases also can arise in a sporadic fashion, meaning they may occur with no family history.
https://www.youtube.com/watch?v=IgX6p3n5xtw
Leber’s hereditary optic neuropathy,
LHON
Kearns–Sayre syndrome
RNA-based Genomes
 Retroviruses
• Retroviruses are also called “RNA tumor viruses” because many
members play a role in cancer

• Retroviruses have single-stranded RNA genomes that replicate through

a DNA intermediate by reverse transcription.

• Upon infecting an animal cell, the retrovirus converts the single-stranded

RNA (ssRNA) into a double-stranded DNA copy (enzyme: reverse
transcriptase).

• The retrovirus DNA is then inserted into the host cell DNA. This process is
done by another enzyme carried in the virus called integrase. Once
integrated, the retrovirus DNA remains permanently inserted in the host
genome.

• Some Retroviruses vectors are important vectors for gene therapy

 Retroviral Vectors
• Retroviral vectors are created by removal of
the retroviral gag, pol, and env genes.

• These are replaced by the therapeutic gene.

-Group-specific antigen (gag) codes for core and structural proteins of the virus

- polymerase (pol) codes for reverse transcriptase, protease, integrase,

-envelope (env) codes for the retroviral coat proteins