Page 1
Gene Regulation in Eukaryotes – Part 1
Structure of DNA and Epigenetics:
- The Central Dogma states that gene expression consists
of transcription of DNA to RNA, and translation of RNA
into protein
- Protein and RNA content differ in different eukaryotic cell
types
- DNA content is stable across all cell types in an organism
- Multicellular eukaryotes are composed of different cell
types that have variable differentiation states
- Since DNA content is stable, these differentiation states
must be attributed to differences in the RNA or protein
content in the different cell types
- Cell differentiation is regulated by variable gene expression patterns because genes that are
expressed will determine which mRNAs are present, and thus which proteins will be produced
- Gene expression patterns are therefore controlled at the transcriptional level
- Transcription requires an activator, which can be an extracellular protein that triggers an
intracellular signalling cascade
- This promotes expression of specific genes ➞ protein production
➢ Transcriptional activation alone is not sufficient for adequate gene regulation
- e.g. when oviduct cells and liver cells are both exposed to oestrogen, it stimulates transcription
of different genes
- The process of transcription is therefore tightly regulated at different levels
, Page 2
Eukaryotic Gene Regulation:
- Transcriptional regulation:
- Genome organisation ➞ exposed region
of chromatin will be transcribed
- Chromatin remodelling ➞ rearrange-
ment of chromatin from a condensed to a
transcriptionally accessible state
- Epigenetic modifications to DNA and
histones ➞ changes in gene expression
through addition or removal of functional
groups
- Post-transcriptional regulation:
- mRNA processing and nuclear export
- mRNA stability and localisation
Eukaryotic Gene Structure:
- Eukaryotic genes are composed of a promoter containing upstream regulatory elements and
the transcribed region
- Upstream regulatory elements / transcription factor binding sites are not transcribed, BUT
they are important in regulating how a gene is expressed
- Regulatory elements can include binding sites for repressors, enhancers or silencers
- Transcribed region contains 5′ and 3′ untranslated regions (UTRs)
- Exons and introns are transcribed to form pre-mRNA, which is later spliced to form preliminary
mature mRNA
- Mature mRNA is formed after processing to remove introns has occurred, and a 5′ cap and
PolyA tail at the 3′ end have been added
, Page 3
Eukaryotic Genome Packaging:
- Double-stranded DNA is wrapped around a histone octamer to form the nucleosome
- Nucleosomes are further coiled to form 30 nm chromatin fibres
- These form 300 nm loops which are further compressed to form the chromatid and
chromosome that is 1400 nm in width
➢ Chromatin is most firmly compacted during metaphase
- During the cell cycle, chromatin is more loosely packed to allow for gene expression
- Chromatin can be heterochromatic or euchromatic
- Heterochromatic regions of DNA are highly repressed due to very tight coiling
- When DNA is very compacted / coiled, the DNA cannot be expressed to form mRNA or
protein as transcription machinery cannot access that region of the DNA
- Euchromatic regions are slightly less coiled and less compacted
- Genes occupy distinct positions on chromosomes
- Chromatin compaction inhibits transcription
, Page 4
- Chromosomes occupy distinct positions in the nucleus ➞ chromosome territories
- Positions of territories are called compartments, and vary between cells within a population
or during different stages of the cell cycle
- Chromosomal DNA can cluster into Topology Associated Domains (TADs) that have
stochastic / variable positions
- TADs contain chromatin with varying degrees of compaction
Chromosome Territories and Chromatin Domains:
The Nucleosome:
- Nucleosome = histone octamer comprised of two molecules of each of the four core histones
H2A, H2B, H3 and H4, consisting of 146 bp of DNA
- Chromatosome includes histone H1 – winds an additional 20 bp of DNA to form two full turns
of DNA around the octamer
- H2A-H2B and H3-H4 form heterodimers via the histone fold
- DNA around chromatosome plus linker DNA between nucleosomes = 200 bp
MOLECULAR
HISTONE TYPE MOLAR RATIO
WEIGHT
H1 Lysine-rich 23,000 1
H2A Slightly lysine-rich 13,960 2
H2B Slightly lysine-rich 13,744 2
H3 Arginine-rich 15,342 2
H4 Arginine-rich 11,282 2
Gene Regulation in Eukaryotes – Part 1
Structure of DNA and Epigenetics:
- The Central Dogma states that gene expression consists
of transcription of DNA to RNA, and translation of RNA
into protein
- Protein and RNA content differ in different eukaryotic cell
types
- DNA content is stable across all cell types in an organism
- Multicellular eukaryotes are composed of different cell
types that have variable differentiation states
- Since DNA content is stable, these differentiation states
must be attributed to differences in the RNA or protein
content in the different cell types
- Cell differentiation is regulated by variable gene expression patterns because genes that are
expressed will determine which mRNAs are present, and thus which proteins will be produced
- Gene expression patterns are therefore controlled at the transcriptional level
- Transcription requires an activator, which can be an extracellular protein that triggers an
intracellular signalling cascade
- This promotes expression of specific genes ➞ protein production
➢ Transcriptional activation alone is not sufficient for adequate gene regulation
- e.g. when oviduct cells and liver cells are both exposed to oestrogen, it stimulates transcription
of different genes
- The process of transcription is therefore tightly regulated at different levels
, Page 2
Eukaryotic Gene Regulation:
- Transcriptional regulation:
- Genome organisation ➞ exposed region
of chromatin will be transcribed
- Chromatin remodelling ➞ rearrange-
ment of chromatin from a condensed to a
transcriptionally accessible state
- Epigenetic modifications to DNA and
histones ➞ changes in gene expression
through addition or removal of functional
groups
- Post-transcriptional regulation:
- mRNA processing and nuclear export
- mRNA stability and localisation
Eukaryotic Gene Structure:
- Eukaryotic genes are composed of a promoter containing upstream regulatory elements and
the transcribed region
- Upstream regulatory elements / transcription factor binding sites are not transcribed, BUT
they are important in regulating how a gene is expressed
- Regulatory elements can include binding sites for repressors, enhancers or silencers
- Transcribed region contains 5′ and 3′ untranslated regions (UTRs)
- Exons and introns are transcribed to form pre-mRNA, which is later spliced to form preliminary
mature mRNA
- Mature mRNA is formed after processing to remove introns has occurred, and a 5′ cap and
PolyA tail at the 3′ end have been added
, Page 3
Eukaryotic Genome Packaging:
- Double-stranded DNA is wrapped around a histone octamer to form the nucleosome
- Nucleosomes are further coiled to form 30 nm chromatin fibres
- These form 300 nm loops which are further compressed to form the chromatid and
chromosome that is 1400 nm in width
➢ Chromatin is most firmly compacted during metaphase
- During the cell cycle, chromatin is more loosely packed to allow for gene expression
- Chromatin can be heterochromatic or euchromatic
- Heterochromatic regions of DNA are highly repressed due to very tight coiling
- When DNA is very compacted / coiled, the DNA cannot be expressed to form mRNA or
protein as transcription machinery cannot access that region of the DNA
- Euchromatic regions are slightly less coiled and less compacted
- Genes occupy distinct positions on chromosomes
- Chromatin compaction inhibits transcription
, Page 4
- Chromosomes occupy distinct positions in the nucleus ➞ chromosome territories
- Positions of territories are called compartments, and vary between cells within a population
or during different stages of the cell cycle
- Chromosomal DNA can cluster into Topology Associated Domains (TADs) that have
stochastic / variable positions
- TADs contain chromatin with varying degrees of compaction
Chromosome Territories and Chromatin Domains:
The Nucleosome:
- Nucleosome = histone octamer comprised of two molecules of each of the four core histones
H2A, H2B, H3 and H4, consisting of 146 bp of DNA
- Chromatosome includes histone H1 – winds an additional 20 bp of DNA to form two full turns
of DNA around the octamer
- H2A-H2B and H3-H4 form heterodimers via the histone fold
- DNA around chromatosome plus linker DNA between nucleosomes = 200 bp
MOLECULAR
HISTONE TYPE MOLAR RATIO
WEIGHT
H1 Lysine-rich 23,000 1
H2A Slightly lysine-rich 13,960 2
H2B Slightly lysine-rich 13,744 2
H3 Arginine-rich 15,342 2
H4 Arginine-rich 11,282 2
