Lecture 3.2: Regulation of Gene Expression PDF

Types of DNA Sequences Nuclear DNA Extragenic DNA o Interspersed repeats: Repeated sequences with certain length scattered in the genome (not clustered together). The length of these sequences varies from small (100-300 bp) up to large (6,000-8,000 bp) Interspersed repeats DNA o Tandem repeats - DNA...

Types of DNA Sequences Nuclear DNA Extragenic DNA o Interspersed repeats: Repeated sequences with certain length scattered in the genome (not clustered together). The length of these sequences varies from small (100-300 bp) up to large (6,000-8,000 bp) Interspersed repeats DNA o Tandem repeats - DNA elements that consist of a repeat unit (from 1 to 100 nucleotides) that runs in tandem and cluster together in the genome. - Shorter repeats are called Microsatellites (e.g., 1, 2, or 5 bp) - Microsatellites are used for forensic and paternity tests Tandem repeats ACT DNA Types of DNA Sequences Nuclear DNA Summary of the nuclear DNA DNA Gene Gene Gene Gene Genes Interspersed repeats Gene Regulatory elements Tandem repeats Regulation of Gene Expression Control Gene expression Not all genes are equally expressed Regulation factors Transcription Factors Regulatory elements Regulation of Gene Expression Control of Gene expression All cells in the body contain the same genetic material (DNA) but express a different set of genes (gene expression profile) Genes are expressed at different levels Genes that control cellular processes necessary for all cells, such as transcription and metabolism, are expressed in all cells and called housekeeping genes. Genes that control cell-type-specific functions, such as hemoglobin in red blood cells, are expressed only in these cells and called cell-type-specific genes. Stem Cell Red Blood Cell Muscle Cells Nerve Cell Regulation of Gene Expression Control Gene expression Genes are expressed at different levels Gene A Gene B DNA Transcription RNA Translation Protein Regulation of Gene Expression Control Gene expression Different cell types express different sets of genes Red Blood Cell Nerve Cell - Gene A Gene B - Gene C Gene D Expression Level Gene A is specific to nerve cells Gene B is specific to RBC Gene C is a house-keeping gene Gene D is expressed in different cells - Regulation of Gene Expression Control Gene expression Gene expression can be regulated at various steps degradation 2 RNA processing control 1 Transcriptional control DNA 3 mRNA transport and localization control Pre mRNA mRNA Degraded mRNA 4 mRNA degradation control 6 Protein degradation control Protein mRNA (A gene) 5 Translation control Nucleus Cytoplasm Inactive Protein 7 Protein activity control Active Protein Regulation of Gene Expression Control Gene expression Transcription control Transcription factors Regulatory elements Chromatin Structure Regulation of Gene Expression Transcription Factors (TF) Control Gene expression Transcription Factors (TF) A transcription factor is any protein required to initiate or regulate transcription (Except RNA polymerase). N DBD Functional domain C Activation domain or Repression domain Any transcription factor contains two domains: DNA Binding Domain (DBD) which is essential for all TF A functional domain ( activation domain for activators and repression domain for repressors) Regulation of Gene Expression Control Gene expression Regulatory elements Regulatory elements are specific DNA sequences (Ex. CACCA, TTCCCTG) that Transcription factors can recognize. They can promote gene expression (promoter and enhancer) or repress it (silencer). Locations: Promoters usually localize upstream of TSSs, while enhancers and silencers can be anywhere (upstream, downstream of a gene, within an intron, or far from the gene they regulate. 5’ Regulatory element 3’ promoter TSS A gene TTS DNA Regulation of Gene Expression Control Gene expression Regulatory elements A promoter is a DNA sequence that determines the site of transcription initiation of a gene by RNA polymerase. An enhancer is a DNA sequence recognized by a TF (activator) and promotes transcription. A silencer is a DNA sequence recognized by a TF (repressor) and inhibits transcription. Regulation of Gene Expression Control Gene expression Regulatory elements 2 3 1 TF TF: Activator RNA pol II TF promoter Enhancer 4 Transcription ON A gene When a TF binds to an enhancer, it recruits proteins necessary for transcription initiation. 2 Transcription OFF 1 3 TF: Repressor Silencer promoter A gene When a TF binds to a silencer, it prevents recruiting proteins necessary for transcription. Regulation of Gene Expression CLINICAL APPLICATIOM CLINICAL APPLICATION Wilms’ tumor (Nephroblastoma) a defect in a repressor Defects in a repressor can cause abnormal conditions. Wilms’ tumor gene is a gene for Wilm’s tumor (WT1) protein. This protein is a repressor that inhibits the expression of other genes essential for kidney development. A mutation in the WT1 gene leads to develop kidney tumors in young children Aniridia (absence of the iris of the eye) Some patients with aniridia (absence of the iris) have no mutation at the PAX6 gene but have a breakpoint 125kb downstream of the PAX6 gene, a gene essential for eye development, that results in a deletion of regulatory elements essential for PAX6 expression. Regulation of Gene Expression Control Gene expression Chromatin Structure Tight wrapping of DNA with histone proteins is required to fit the genetic material inside the nucleus, but this prevents accessibility to DNA. Transcription factors can’t bind to their regulatory elements and initiate transcription. Closed chromatin > Transcription OFF Open chromatin > Transcription ON Mechanisms that change the chromatin structure to regulate gene expression are known as Epigenetic mechanisms. Not accessible Transcription OFF Accessible Transcription ON Regulation of Gene Expression Expression Level - Gene A Transcription ON Activator Enhancer promoter Gene A Transcription Enhancer promoter Gene A Transcription Enhancer OFF promoter Gene A OFF Regulation of Gene Expression Expression Level - Gene A Transcription ON Activator Enhancer Activator Enhancer promoter Gene A Transcription Gene A Transcription Enhancer OFF Gene A OFF