Regulatory regions and introns

Promoters 1

Are regulatory regions of DNA upstream of a gene, which provide a control point for regulated gene transcription. That also determine when and where a genes is expressed

Promoter elements

Core promoter

• the minimal portion of the promoter required to properly initiate transcription, located around position -34

Proximal promoter

• the proximal sequence upstream of the gene that contains primary regulatory elements, located around position -250

Distal promoter

• very ill-defined area which can range from beyond the 5’ end of the gene up to an even into the next gene

Control elements of promoter

Enhancers, silencers and insulators

Eukaryote promoter

Enhancers

Short region of 50-1500 bp of DNA that can bind activator proteins to trigger the transcription of a gene

• important role in evolution of species

• Developmental biology- development, differentiation and growth of cells/tissues

• Invertebrate segmentation

• Vertebrate patterning- body axis antero-posterior and left-right

• Developmental robustness

• Developmental mechanisms- limb development

Promoter silencers

DNA sequences that bind repressor proteins that inhibit expression and act in the opposite way of enhancers

They can reduce or totally inhibit expression

Sequence can be anywhere in the promoter

Binding of repressor proteins may inhibits RNApol complex formation

Can be caused by bending the DNA

Silencer example

NRSF

Neuronal-restrictive silencer factor- produced by rest gene

Repress the transcription of neuronal genes in non-neural cells

When represses REST, NRSF is also inhibited- allowing for the transcription of neuronal genes

Huntingtons disease

Promoter insulators

Genetic boundary elements that block the action of enhancers

• sequence that binds proteins can be anywhere

• Determine set of genes and enhancer can influence

• Stop enhancer working on adjacent genes

• Present at boundary of topological association domains (TADs) which divide the chromosomes in- chromosome neighbourhoods

• Act by forming loops

• Prevent spread of heterochromatin from a silenced gene to an actively transcribed gene

Transposing

Jumping genes

• dna sequence that can change position with in the genome

• Create mutations and alter size of genome

• Transportation often results in a duplication of the transposon

• 90% maize genome, 50% human genome made up of TEs

Transposon class 1

Reyrotransposons

Copy and paste- from DNA to RNA then, RNA to reverse transcribed DNA

Long terminal repeats

Line 1- transcribed by RNA pol II

SINEs- transcribed by RNA pol III

Transposon class 2

DNA transposon- cut and paste.

Does not involve RNA intermediate

Transpositions are catalysed by several transpositions enzymes

TE- mutagens

Can damage the genome and produce diseases like haemophilia A and B

Severe combined immunodeficiency, porphyria, predispostistion to cancer and Duchenne muscular dystrophy

Epigenetic mechanisms - 1

Variations that are caused by external or environmental factors

Do not later DNA sequence

Alter gene expression levels

Covalent modification

Epigenetic mechanism

DNA methylation and hydroxymethylation

Protein acetylation, methylation, phosphorylation, ubiquitination and sumoylation

MicroRNAs

Epigenetic mechanisms

Non-coding RNAs of 17-25 nt long

MRNA methylation

Epigenetic mechanism

MRNA plays a critical role in human energy homeostatsis

SRNAs

50-250 nucleotides

Virulence gene pathogens

Prions

Epigenetic mechanism

Infectious forms of proteins

Structural inheritance

Epigenetic mechanism

Seems existing structures act as templates for new structure

Nucleosome positioning

Epigenetic mechanism

Nucleosome position is not random, and determine the accessibility of DNA to regulate proteins. This determines differences in gene expression and cell differentiation

Introns

Non-coding sequences in the gene that do not appear in their mature mRNA and they interrupt the coding sequence

Intron group 1

Found in nuclear, mitochondrial and chloroplast genes coding for rRNAs, mRNAs an tRNAs

Introns group 2

Found in primary transcripts of mitochondrial chloroplast mRNA in fungi, algae and plants

A lariat is formed before splicing occurs

Introns group 3

Largest class of introns

Found in nuclear mRNA primary transcripts

Lariat is or med and a RNA protein complex of nuclea ribonucleoproteins is required

RNA is called small nuclear RNA

Introns group 5

Found in certain tRNAs

Splicing endonucleoases cleaves the phosphodiester bond at both ends of the intron

2 exons are joined by a similar mechanism to DNA ligament reaction

Intron structure

Sequence of the intron always starts with GU and ends with GU

Sequences next to GU/AG and also another in the middle are all similar in each intron

Branch point is a iced distance from 3’ end

Splicing of introns

Spliceosome cuts the intro and rejoins the exon of the mRNA

Consists of several proteins

Intron splicing group III

Small nuclear RNAs bind to donor sequence, forming spliceosome complex

2 transesterfication reactions exercise the intron- forming a loop structure (lariat)

The exons are then lighted to form mature mRNA

Intron splicing extra

The spliceosome cuts 5’ boundary

The 5’ end of the intro is joined to the branch point

The spliceosome cuts the 3’ boundary

The exons are joined and the lariat is released

The snRNAs are released

Lariats

Introns exercised into a loop, by 2 transesterification reactions

Why do genes have introns

To regulate gene expression

• control elements such as enhancers found with in introns

• Introns allow for differential splicing

Evolutionary relics

Alternative splicing

Process that allows the DNA to code for more than one protein by varying the exons present in a mRNA

• 40% of humans

• Can encode many related proteins with 1 gene

• Exactly which intron boundaries are spliced is decided by protein factors that bind to the intron boundries and either help or hinder cutting by the spliceosome

• Some genes can be spliced in different ways

Intron retention fate

Impact of alternate RNA splicing

5’UTR- altered translation, Change ion protein expression

Protein coding sequence- Altered protein structure and function, change in protein is oformratios

3’UTR- mRNA instability, change in protein expression levels

Alternative splicing 3

The same pre-mRNA can make many different mRA transcripts and may different proteins

Exon order is always preserved

Introns are always discarded

Protein domains

Regions within proteins that fold up in a semi-independent wat and have independent function

Unfolded protein → partially folded protein → fully folded protein

Evolution of introns

Archaebacteria (introns uncommon)

• eubacteria (introns very rare)

• Eukaryotes (almost every gene has introns)

Intron early theory

Supports idea that introns and RNA splicing were relics of the RNA world

Both eukaryotes and prokaryotes had introns in the beginning

Prokaryotes eliminated them to be more efficient, while eukaryotes kept them to have more genetic plasticity

Introns late theory

Supports that prokaryotic genes are similar to the ancestral genes and introns were inserted later in the gene of eukaryotes

Exon shuffling

Molecular mechanisms to form new genes

2 or more exons from different genes can be brought together ectopically, or the same exon can be duplicated, to create a new exon-intron structure

Exon shuffling mechanism

Transposon mediated exon shuffling.

Crossover during sexual recombination of parental genomes.

Illegitimate recombination.

Question

1- what are promoter elements

2-what are enhancers, silencers and insulator transposon

3- describe the Epigenetic mechanisms

4- what is the intron structure

5-