Gene Expression and Regulation

• Modifications of gene expression, not nucleotide sequence, cause differences between cells with the same DNA.

Basics of Gene Expression

• Some proteins are universal, while others are specific to cell types.
• Approximately 30-60% of the 25,000 genes in a human cell are expressed.
• Alternative splicing produces varied proteins from a single gene.
• External signals change cell expression of genes.
• Gene Expression is regulated throughout the DNA to protein pathway.

Stages of Gene Expression

• Controlling transcription initiation.
• Regulating RNA transcript splicing and processing.
• Selecting mRNA for export from nucleus.
• mRNA selection for translation by ribosomes.
• mRNA destabilization.
• Activating/inactivating protein molecules.

Genetic Regulation in Eukaryotes

• Processes include: DNA to chromatin, transcription, maturation, transport, stabilisation
• Regulation can occur at transcriptional, post-transcriptional, and translational control points.

Prokaryotic vs. Eukaryotic Regulation

• Prokaryotes have genetic regulation via operons and regulons.
• Eukaryotes genetic regulation occurs including transcriptional, epigenetic, and post-transcriptional control.

Prokaryotic Gene Regulation: Operons

• Regulatory units of genes transcribed from the same promoter form a single mRNA translated into multiple proteins.
• Structure of the unit: structural genes, regulatory genes for proteins, and control elements in DNA.
• Gene expression is controlled through positive and negative regulation.

Negative control in Bacteria

• Gene expression is regulated by available nutrients.
• Example: the tryptophan repressor in E. coli.
• Active DNA-binding proteins turn genes off.
• Transcriptional repressors or gene repressor proteins mediate this negative control.

Positive Control in Bacteria

• Transcriptional activators or gene activator proteins enable positive control genes
• Activators can boost transcription up to 1000-fold.

CAP Examples for Activators

• Aid polymerase binding, provide extra surface contact.
• Help polymerase transition to transcribing form, stabilizes the state of enzyme.
• CAP activates genes for alternative resources when glucose is low.

Regulation of Lactose Operon

• Lactose operon regulated in Escherichia Colion and bacteria.
• Enzymes include 360 aa repressor, 1021 aa B-Galactosidase, and -275 aa Permease Transacetylase
• These enzymes are necessary to cleave and utilise lactose as a nutritive substrate

Lactose Operon Regulation: Absence of Lactose

• Transcription of Lac1 gene leads to repressor synthesis.
• Lac Z, LacY, and Lac A are not synthesized.

Positive Control with Lactose

• Fixation of lactose in repressor will cause RNA polymerase to transcribe structural genes

Lactose Operon: Glucose Presence

• CAP site (activator) on the lactose operon's promoter is activated when a CAP protein binds and associates with cAMP.
• Low glucose leads to low cAMP, meaning CAP doesn't bind, inhibiting transcription of the operon.

Molecular Regulation in Prokaryotes

• Ligand binding removes regulatory protein.
• Ligand addition switches gene on by removing repressor protein.

Glucose and Intracellular Cycle AMP

• Glucose levels cause cyclic intercellular Molecule AMP levels

The Lac Operon

• Lac Operon proteins transport and break down lactose.
• Lac repressor protein, CAP controls it

Conditions the Lac Operon needs

• The operon gets used if BOTH conditions are met;
• Must be present, Glucose must be absent

Bacterial DNA Looping

• Stabilises protein-DNA interactions.
• Allows remote contact.
• Average sequence is on a 200 nps curve.
• Restriction is based on the proteins.

Regulons

• Functional sets of genes (operons).
• Located at sites regulated by transcript repressors.

Ribo-Regulators

• Regulate expression of ribo-regulator due to its activity depending on its target molecule

RNA Polymerase Subunits

• It is interchangeable
• Regulates transcription.
• Core polymerase interacts with subunits for promoter direction.

Regulation of RNA Polymerase Strategies

• Regimes of gene activation/deactivation through subunit replacement.
• Viruses steal the host polymerase.

Genetic Regulation

• Prokaryotes One enzyme and factor, regulation for one operon.
• Eukaryotes Various enzymes and factors and subunits, regulation for individual genes

Transcriptional Control: Key Definitions

• Gene = segment of DNA transcribed to RNA.
• Gene Control Region = DNA sequences that control that area's regulation and transcribing.
• Eukaryotic Gene’s Control = promoter + regulatory DNA.
• Promoter = region for transcription factor/polymerase assembling

Transciption Regulation

• Regulatory proteins attach to regulate processes.
• "Spacer" provides flexibility for efficient DNA loops.

Regulation Proteins (humans)

• Allows genes to repress or activate individually, binding on genes.
• Human Regulatory contains a high amount of abundance and its regulator is based on the site.

1. 1 Chromatin Domain at the DNA Level

• Heterochromatin: transcriptionally inactive, facultative.
• Euchromatin: sensitive to DNase, associated regions.
• LCR (Locus Control Regions) isolates control.

Locas Control Region (human)

• Globin genes transcribed in stages are an example.
• Regulatory protein activates proteins.
• Regulatory regions control transcription of genes within the cluster.

Insulator sequences

• Genome segmented into distinct regions
• Isolators block proteins genes from regulating.
• Barrier sequence is blocked by heterochromatin.

Genetic Regulation at the DNA Level

• Epigenetics control the expression of genes.
• The regulation occurs without DNA change.
• The control consists of 3 key elements;
• Methylation histone, modification /non-coding RNA ,and chromatin.

Histone code

• Modifying Histone tail enzymes (HATs)
• Phosphate (Ks) is promoted to then transcribe open genes.
• Histone tail, and modifying genes inhibit these enzymes.

Histone Modification (with Enzymes)

• enzymes (Histone acetyltransferase)
• HDAC: (Histone deactylase complex)
• HMT: (Histone methyltransferase)
• kinase: (Histone kinase)
• all assist in Histone acetlytransferace

Modulation of Local Chromatic Structure (gene activator)

• By locally activating genes
• Can occur through modifications of histones
• Can occur through Nucleosome replacement/removal

Chromatin Structure Modulation and Translation

• DNA becomes easier to access
• Facilitates machinery and RNA polymerase on the promoter
• Duration can vary (expression profile)
• Provide a favorable state

Genetic Regulatory (Histone) Processes

• Activator causes it and is bound and leads to changes

Some specific meanings of the histone code

• DNA Transcription is mostly code regulated
• Is regulated mostly by post translational

Covalent Modification

• Key role in gene and expression

Gene Regulator (Histone) Process

Gene

• Is a DNA Segment from RNA
• Control binding
• In a gene, this modifies the general factors.
• Leads to the beginning of the transcription

Transcription Factor

• Regulatory proteins work through protein Mediator and RNA polymerase factors

DNA Regulation can be done by

• Structure not being able transcriptional
• Methylation occurs with cytosines
• Methyl groups will conservative
• The CG in the islands regulates by recognitions
• Enzymes are methylated
• Transferase can be used to help methyl groups at the same time

Parental Imprinting from Genes

• Reduced description can occur if you have cancer
• Gene allele for disease
• Requires stimulation

Methylation effect

• Leads to the activation
• Causes description gene to not transcript Methylation
• Contributes to description and innovation

Transcriptional Regulator (regulation of transcription)

• Transcription of controlled gene are near the site
• Switches have fundamental components
• Binding for DNA
• Regulatory genes proteins can read sequences
• Proteins have special features

Key Regulatory factors

• Cis Regulatory (has promoter motif)
• Trans Regulatory (protein families with motifs or repressors)

Gene Activation occurs via

• Enhancer= site where transcription initiates.
• Activate the gene

Design of Genes

• Is a DNA binding protein/structural motif
• Activating domain
• Function =modify/attract/position the genes

Interaction through Proteins

• This is how certain components of the cell accelerate

Genes Regulatory (with Proteins)

• Often will have different motifs

Proteins bind to genes using specific motifs

• Helix, loops etc

Transcription of DNA

• Regulation done by regulator, proteins binding to affects confirmation