Genetic elements in
gene regulation
Objectives
At the end of this
lecture, students will be able to –
• Describe the role of following elements in gene expression
– Nucleosomes
– Histones
– Histone acetylation
– Histone deacetylases
– DNA binding protein families
Content
Genetic elements controlling gene expression
– Nucleosomes
– Histones
– Histone acetylation
– Histone deacetylases
– DNA binding protein families
Genetic
elements that control gene expression
Nucleosomes
• Basic units of DNA packaging in eukaryotes
• Segment of DNA wound in sequence around 8 histone protein
cores
• Fundamental repeating units of eukaryotic DNA
• Packs large eukaryotic genome into nucleus – ensure
appropriate access to it
• Made up of less than 2 turns of DNA wrapped around a set
of 8 proteins called histones
• Each nucleosome has 2 copies of histone protein – H2A,
H2B, H3 and H4
• Linker histone such as H1 and its isoform – involved in
chromatin compaction
• Nucleosome appearance – beads on a string
Histones
• Major protein components of chromatin
• Most of the protein in eukaryotic chromatin consists of
histones
• Five families, or classes of histones-H2A, H2B, H3 and H4:
core histones
• Core histones are small proteins, with masses between 10
and 20 kDa
• H1: little larger at around 23 kda
• All histone proteins have a large positive charge
• 20 – 30% of their sequences consist of the basic amino
acids, lysine and arginine
• Histones will bind very strongly to the negatively charged
DNA in forming chromatin
Nucleosome
and associated structures
Histone
acetylation
• Occurs in a cell, neutralises the + ve charge on histone
• Changes amine to amides
• Decreases the ability of histone to bind to DNA
• Decreases binding and allow chromatin expansion
• Histone deacetylase remove acetyl group, increases +ve
charge
• Encourages high affinity binding between histone and DNA
backbone
• Increased binding condenses DNA structure, prevent
transcription
• Histones are acetylated on lysine residue in N-terminal
tail
• Catalysed by histone acetyltransferase (HAT)
• Source of acetyl group – Acetyl – Coenzyme A
• Acetylation is associated with activation of
transcriptional activity, with condensation of Chromatin
Histone
deacetylases
• Class of enzymes that removes acetyl groups from acetyl
lysine aminoacid on a histone
• Allow the histone to wrap DNA tightly
• Acetyl group is transferred to coenzyme A
• DNA is wrapped around histone
• DNA expression regulated by acetylation and de-acetylation
• Action opposite to histone acetyl transferase
HAT vs.
HDAC
DNA binding
protein
• Abundant protein -HU, a small basic (positively charged)
protein
• Binds DNA nonspecifically by the wrapping of the DNA
around the protein
• H-NS (protein H1)- a monomeric neutral protein
• binds DNA nonspecifically in terms of sequence
• Also known as histone-like proteins
• Compacting the DNA – essential for the packaging of the
DNA into the nucleoid
• Stabilizes and constrain the supercoiling of the
chromosome
• Half of this is constrained as permanent wrapping of DNA
around proteins such as HU
• About half the supercoiling is unconstrained
• RNA polymerase
and mRNA molecules,
site-specific DNA- binding
proteins such as integration host factor (IHF), a homolog of HU, which binds to
specific DNA sequences and bends DNA through 140°
Non-specific
DNA protein interaction
• Structural protein that bind to DNA
• Structural proteins + DNA structure – Chromatin
• Non-specific interactions are formed through basic
residues
• Forms ionic bonds to acidic sugar phosphate backbone of
DNA
• Chemical modifications include – methylation,
phosphorylation and acetylation
DNA-binding
proteins specifically binding to single-stranded DNA
• Distinct group of DNA binding protein
• Replication protein A – involved where double helix is
separated
• DNA replication, recombination and DNA repair
• Stabilises single stranded DNA
• Protects from forming stem-loops or nuclease degradation
Proteins
binding to particular DNA sequence
Transcription factor
• Binds to specific DNA sequence
• Control flow of genetic information from DNA to mRNA
• Function alone or in a complex
Xeroderma pigmentosum
group 0f DNA protein
• Encoded by XPA gene
ORC or Origin
recognition complex
• Multi-subunit DNA binding complex
• Binds to ORC in an ATP dependent manner
• Encoded by ORC1, ORC2, ORC3, ORC4, ORC5, ORC6
• Central component of ORC gene replication
Replication protein A
• 70 kDa DNA-binding protein
• Encoded by RPA1 gene
Replication factor C
• 5 subunit protein complex
• Required for DNA replication
• Binds to 3’ end of DNA
• Uses ATP, opens PCNA encircles DNA
Prokaryotic protein
factors for –
• Inversion stimulation protein
• Leucine responsive regulatory protein
• Integration host factor
Other ungrouped proteins
• Butyrate response factor 1
• Centromere protein b
• Erythroid specific DNA binding factor
• Interferon regulatory protein
• Nuclear receptor factors
• Mismatch-binding proteins
Summary
• Genetic elements that control gene expression include –
histone, nucleosomes, histone acetylation, histone deacetylase and DNA binding
protein families
• Nucleosomes are segment of DNA wound in sequence around 8
histone protein cores
• Histone acetylation occurs with the help of acetly transferase
• Histone deacetylases are class of enzymes remove acetyl
group from the lysine residue and allow histone to wrap DNA tightly
• Different families of DNA binding proteins helps in
wrapping DNA tightly to proteins