Genetic elements in gene regulation

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