Regulation of Gene Expression in Eukaryotes - Molecular Biology - Charmo University, 2024-2025 PDF

Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Regulation of Gene Expression In Eukaryotes Learning objectives explain regulation stages of Eukaryotic gene expression understand noncoding RNAs and c...

Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Regulation of Gene Expression In Eukaryotes Learning objectives explain regulation stages of Eukaryotic gene expression understand noncoding RNAs and controlling gene expression All cells in an organism contain all the DNA (the genetic information). The organisms must regulate or control which genes are turned on in which cells. Genes turned on determine cells’ function – for example, liver cells express genes for liver enzymes but not genes for stomach enzymes. A typical human cell might express about 20% of its protein-coding genes at any given time; Specialized cells (muscle, nerve cells) express an even smaller fraction; almost all cells contain an identical genome. However, the subset of genes expressed in each cell type is unique. Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome: 1 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Abnormalities in gene expression can lead to diseases including cancer Gene expression is regulated at many stages How do cells "decide" which genes to turn on? Different cell types express different sets of genes, as we saw above. However, two different cells of the same type may also have different gene expression patterns depending on their environment and internal state. A cell's gene expression pattern is determined by information from both inside and outside the cell.  Examples of information from inside the cell: the proteins it inherited from its mother cell, whether its DNA is damaged, and how much ATP it has.  Examples of information from outside the cell: chemical signals from other cells, mechanical signals from the extracellular matrix, and nutrient levels. Growth factors bind to their receptors on the cell surface and activate a signalling pathway in the cell. The signalling pathway activates transcription factors in the nucleus, which bind to DNA near division-promoting and growth-promoting genes and cause them to be transcribed into RNA. The RNA is processed and exported from the nucleus, then translated to make proteins that drive growth and division. 2 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Chromosomes – tightly coiled DNA around proteins during cell division Chromatin – loosely packed DNA around proteins Histones – protein which the DNA wraps around Nucleosomes – grouped histones together _Heterochromatin – tighter packed chromatin, so no transcription. _Euchromatin – looser packed chromatin so transcription occurring. 3 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Eukaryotic gene expression is regulated at many stages: Regulation of chromatin structure Regulation of transcription initiation Post-transcriptional regulation 4 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih 1) Regulation of chromatin structure Examples of chromatin modifications: A) Histone Modifications: chemical groups (i.e. acetyl groups, methyl groups) can be added to amino acids in the histone structure to alter chromatin folding: Histone acetylation – allows transcription factors to bind to DNA allowing transcription to occur. -Creates loosely packed DNA which is called euchromatin. B) DNA Methylation DNA Methylation occurs after DNA is synthesized. Enzymes add methyl groups (CH3) to certain bases in DNA (usually cytosine) typically inactivates these segments of DNA (they are not expressed). DNA methylation can cause long-term inactivation of genes in cellular differentiation. One X in females is highly methylated 5 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih C) Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells. The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance. 2) Regulation of transcription initiation Transcription involve RNA Polymerase II and transcription factors. RNA polymerase II attaches to the promoter (TATA box) sequence to begin transcription. Control elements are non-coding sequences of DNA where the transcription factors attach. Enhancer is control element far from a gene or intron. Activator bind to enhancers to turn on transcription of a gene. All of them together makes transcription initiation complex. Repressors – inhibit gene expression by blocking activators from binding to enhancers. 6  Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih. In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors Activation 7 domain DNA-binding domain Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih 3) Post-transcriptional regulation Transcription alone does not constitute gene expression. The expression of a protein-coding gene is ultimately measured by the amount of functional protein it makes! Much happens between the synthesis of mRNA and the activity of the protein in the cell: A) RNA Processing B) mRNA Degradation C) Initiation of Translation D) Protein Processing and Degradation A) RNA Processing and RNA stability We’ve already discussed: 5’ cap, 3’ poly-A tail, and removal of introns (exons remain) resulting in Alternative RNA splicing Another type of post-transcriptional control involves the stability of the mRNA in the cytoplasm. The longer an mRNA exists in the cytoplasm, the more time it has to be translated, and the more protein is made. Many factors contribute to mRNA stability, including the length of its poly-A tail. 8 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih B) mRNA Degradation In prokaryotes the RNA s have short life span and degraded in seconds and allows rapid response to environmental changes. In eukaryotes the mRNA survives from hours to weeks (i.e. mRNAs for hemoglobin polypeptides). C) Initiation of Translation There are regulatory proteins that can bind to specific sequences at the 5’ or 3’ end of mRNA and prevent the attachment of ribosomes. D) Protein Processing and Degradation Most polypeptides require some processing before they are functional. Proteasomes are giant protein complexes that bind protein molecules and degrade them. Chromati n Trans cripti RNA proces Ubi Protea mRN Tran A some Protein Prote processi ng and Protei Ubiqu Prot n to inated ein Protein entering frag 9 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Noncoding RNAs and controlling gene expression Genome sequencing has shown that protein- coding DNA only accounts for 1.5% of the human genome (and other eukaryotes). A small fraction of the non-protein coding DNA consists of genes for rRNAs and tRNAs.. Until recently, researchers assumed that most of the remaining DNA was un- transcribed” junk” DNA. However, new research suggests that a significant amount of the genome may be transcribed into non-protein-coding RNAs that are involved in regulation of gene expression! -microRNAs (miRNAs) -RNA interference (RNAi) -small interfering RNAs (siRNAs) miRNA’s – micro-RNA hat can degrade mRNA or block translation. Causes mRNA to fold on itself and base pair to create dsRNA which is then digested with an enzyme. 10 Chapter EIGHT Molecular Biology Charmo University 2024-2025 Dr Rebin M. Salih Short interfering RNA (siRNA) – all interfering RNAs (siRNAs), similar to miRNAs, can associate with the same proteins as miRNAs and block expression of a gene with the same sequence as the RNA. …End of Lecture Eight 11