Gene Regulation and Expression

• Bioinformatics Lecture is on the topics of Gene Regulation and Expression
• Author of the lecture is Adeena Tahir

What is a Gene?

• A gene is the basic physical and functional heredity unit.
• Every gene is located on a specific region of a chromosome, having a specific, ordered nucleotide sequence.
• Each human body cell contains about 25,000 to 35,000 genes.
• Genes carry genetic information determining traits passed from parents to offspring.

Genes and Regulatory Elements

• Gene expression regulation is critical for all organisms.
• Structural genes encode proteins.
• Regulatory genes encode products interacting with other sequences and affecting transcription and translation.
• Regulatory elements include DNA sequences not transcribed but regulating other nucleotide sequences.
• Constitutive expression is when genes are continuously expressed under normal cellular conditions.
• Positive control stimulates gene expression.
• Negative control inhibits gene expression.

Gene Expression

• Phenotypic manifestation of genes occurs through transcription and translation processes.
• Gene regulation happens at multiple points during transcription, translation, and involves epigenomic compounds.
• Gene expression is complex and highly regulated.

Proteins Involved In Gene Expression

• Messenger proteins transmit signals coordinating biological processes between cells, tissues, and organs.
• Hormones such as insulin and oxytocin are great examples of messenger proteins.
• Structural proteins provide structure and support for cells.
• Actin filaments and microtubules are examples of structural proteins.
• There are three types of structural proteins: fibrous, globular and membrane
• Fibrous proteins form hair, nails and skin.
• Enzymes catalyze chemical reactions in cells, such as muscle contraction.
• Enzymes assist with bodily functions like digestion and DNA replication.
• Transport proteins bind and carry atoms and small molecules.
• Hemoglobin is a transport protein for oxygen in red blood cells from the lungs to other tissues.

Gene Regulation

• Gene regulation is the on and off switching of genes.
• Gene expression is the flow of information process from genes to proteins.
• Controlled gene expression allows cells to produce specific proteins when and where they are needed.

Levels of Gene Regulation

• Gene regulation can occur through alteration of DNA or chromatin structure.
• Other levels of gene regulation include: transcription, mRNA processing, RNA stability,translation, and post translational modification.
• Gene regulation is important during development and in mediating variations, diseases, birth defects, and evolution.
• Gene regulation guides the development of organs, tissues, and cell types to digest and metabolize nutrients.
• Genes can be regulated at the levels of DNA, RNA, and protein.

Complex Assemblies of Proteins Control Eukaryotic Transcription

• Prokaryotes and Eukaryotes use regulatory proteins (activators and repressors).
• Regulatory proteins bind to DNA segments and either promote or block RNA polymerase binding, controlling transcription.
• Activator proteins appear to be more important than repressors in eukaryotes; therefore the default state for most genes is off.
• Most plant and animal cells only transcribe a small fraction of genes.
• Eukaryotic RNA polymerase needs assistance from transcription factors.
• Transcription factors include activator proteins, that bind to enhancers and start transcription, thus bending the DNA.
• Transcription factor proteins interact with activators bound by a complex at the gene's promoter.
• RNA polymerase attaches to the promoter for transcription to begin.
• Repressor proteins bind to DNA sequences (silencers) and inhibit transcription.
• Coordinated gene expression in eukaryotes depends on control element combinations with genes of a metabolic pathway.

Eukaryotic RNA Splicing

• Alternative RNA splicing produces different mRNAs from the same transcript.
• Alternative splicing results in production of more than one polypeptide from a gene and may be common in humans.

Gene Expression Regulation and mRNA

• Gene expression can still be regulated after mRNA is fully processed and transported to the cytoplasm.
• Can be regulated through processes such as breakdown of mRNA, translation initiation, protein activation, and protein brakedown.

Multiple Mechanisms Regulate Gene Expression in Eukaryotes

• Eukaryotes have multiple control points for gene expression that can be turned on, off, sped up, or slowed down.
• These controls are like valves in a series of water pipes.
• Control points include changes to chromosomes and DNA unpacking, transcription control, RNA processing (adding cap/tail, splicing), flow through the nuclear envelope,breakdown of mRNA, or in translation

Open Reading Frames (ORF)

• An ORF is a continuous DNA or RNA stretch that can be translated into a protein. -It starts with a start codon and ends with a stop codon without any interruptions.
• Open reading frames are essential for understanding gene structure, function, and expression.
• ORFfinder can locate open reading frames.

Gene Prediction in Eukaryotes

• Gene prediction identifies genes in a genome using computational and experimental approaches.
• Ab Initio(De Novo) methods: Use computational algorithms (GENSCAN, AUGUSTUS) to identify genes based on sequence patterns, i.e. codon bias, GC content, and splice site motifs.
• Evidence-Based (Homology) Methods: Use known genes from model organisms to use sequence similarity and predict genes using examples such as BLAST and GeneWise
• Hybrid Approaches: Combine ab initio and homology based methods to improve accuracy. For example the MAKER pipeline is a hybrid method.
• Experimental Methods: This includes RNA sequencing (RNA-Seq) which identifies expressed genes by sequencing mRNA. And includes EST (Expressed Sequence Tag) analysis, which uses short mRNA sequences to confirm predicted genes.

Signal Transduction

• Signal transduction pathways are molecular changes converting a cell surface signal into a response within the cell.
• Signal transduction pathways are crucial to cellular functions.

Gene Regulation in Eukaryotic Cells

• Gene regulation in eukaryotic cells takes place at multiple levels
• Chromatin remodeling complexes can bind directly to DNA sites and reposition nucleosomes.
• Histone Modification includes the addition of methyl or acetyl groups to the histone protein tails.
• Acetylation of histones controls flowering in Arabidopsis at the Flowering locus C (FLC) and D (FLD) gene.
• Transcriptional activators and repressors can bind to silencers.
• Enhancers are DNA sequences stimulating transcription away from a promoter.
• Insulators are DNA sequences blocking or insulating the effect of enhancers.
• Gene regulation can be achieved through RNA splicing, seen in alternative splicing in the T-antigen gene and in Drosophilia sexual development.

Epigenetic Effects

• Epigenetic effects include changes induced by maternal behavior, prenatal exposure effects, and effects in monozygotic twins.
• Molecular Mechanisms of Epigenetic Changes include DNA methylation maintained from generation to generation