Eukaryotic genome

structure of eukaryotic chromatin

it is a nucleoprotein complex made up of DNA and proteins (histone and non-histone)

nucleoprotein complex

1. DNA

   • each eukaryotic chromosome contains a DNA double helix

   • each eukaryotic DNA molecule is precisely combined with a large amount of protein

2. Histone proteins

   • H2A, H2B, H3, H4 (within chromosome) and there is two of each molecule in histone octomer

   • H1 (helps organise nucleosome into solenoid)

   • primary structure of histone proteins composed of mainly positively charged amino acids e.g lysine to form ionic bonds with negatively charged DNA (-ve due to phosphate groups of nucleotides in DNA)

3. Non-histone proteins

   • proteins involved in transcription (e.g RNA polymerase, transcription factors etc.), replication (DNA polymerase, helicase etc.), gene regulation and scaffolding

types of interphase chromatin

1. heterochromatin

   • highly compacted

   • transcriptionally inactive due to it being inaccessible to transcription enzymes

   • appears small and darkly stained

2. euchromatin

   • more diffused regions (less compact)

   • transcriptionally active

   • lightly stained

   • may be depleted of nucleosomes to allow for binding of transcriptional factors and other protein for genes present in euchromatin to be transcribed

Successive levels of DNA packing

“Describe how DNA is packaged in eukaryotic cells undergoing nuclear division”

1. nucleosome + linker DNA

2. solenoid (30nm chromatin fibre)

3. radial loops

4. formation of metaphase chromosome

1st level: nucleosome + linker DNA

• DNA is wound around a histone octomer to form a nucleosome which is joined to adjacent nucleosome with linker DNA, giving rise to 10nm chromatin fibre with “beads-on-string” appearance

• non-histone proteins bind to linker DNA

• ionic bonds are formed between positively charged amino acid residues of histones and negatively charged DNA

c

interactions between positively charged histone tails of neighbouring nucleosomes, negatively charged linker DNA and H1 histone proteins cause 10nm chromatin fibre to coil or fold, resulting in formation of 30nm chromatin fibre known as solenoid

3rd level: formation of radial loops

solenoid attaches to non-histone central protein scaffold to form radial loops

• during interphase, radial loops are present on nuclear lamina to help organize regions of active transcription for sythesis of mRNA which is translated into proteins. It also prevents the chromatin of each chromosome from becoming entangled

• during prophase, the radial loops are present on central protein scaffold, forming 300nm chromatin fibre

4th level: formation of metaphase chromosome

radial loops coil and fold further to condense to form metaphase chromosome

non-coding DNA

1. repetitive sequences

   • centromere — involved in chromatid adhesion and formation and binding of protein complex called kinetochore

   • telomeres — disposable buffer and forms protective nucleoprotein cap

2. control elements (regulatory DNA sequence)

   • promoter — required for initiation of basal rate of transcription

   • enhancer — increases rate of transcription

   • silencer — decreases rate or represses transcription

   • terminator

3. introns

   • allows for RNA splicing

   • regulates gene expression

control elements

• defined as specific DNA sequences that interact with regulatory proteins to determine the rate and timing of gene expression

• they can up-regulate or down-regulate gene expression

• control elements and the proteins that bind to them are critical to precise regulation of gene expression

promoter

structure:

• contains TATA box and is located 25-30 base pairs upstream of transcription initiation site (for eukaryotes)

functions:

• is the attachment site of general transcription factors

• the attachment facilitates binding of RNA polymerase II to promoter

• this results in assembly of transcription initiation complex to initiate a basal rate of transcription of RNA transcripts

structure of enhancer

• contains several different control elements within it

• can be found distant from promoter, near promoter or within genes

• can be found either upstream or downstream of a gene it regulated or even occasionally within genes

function of enhancer

• serves as a recognition and attachment site for activator proteins which can bind to other transcription factors

• this facilitates efficient positioning of RNA polymerase II binding to promoter

• greatly increases the stability of RNA polymerase II binding to promoter

• increases rate of transcription for full level of transcription

• involved in time and tissue-specific gene expression

structure of silencer

• found in regions surrounding the promoter or even within enhancer regions

function of silencer

• recognition and attachment site for repressor proteins

• the repressor proteins block binding of activators to enhancers

• decreases rate or repress transcription

structure of introns

• non-coding DNA sequence found within a gene

function of introns

• contains splice sites which allows mRNA splicing to occur. this allows all introns to be excised and exons to be ligated for continuous sequence for translation

• involved in process of alternative splicing which allows the cell to synthesis different mRNA from the same gene thus allowing same gene to code for different proteins

• may contain silencers or other regulatory sequences hence plays regulatory roles in gene expression