L17 Regulation of Gene Expression - F2024 Exam Notes PDF

L17 Regulation of gene expression II Learning objectives: Understand the concepts of nucleosomes and chromatin structure Understand that chromatin remodeling complexes, histone modification enzymes, and DNA methylation can all regulate chromatin...

L17 Regulation of gene expression II Learning objectives: Understand the concepts of nucleosomes and chromatin structure Understand that chromatin remodeling complexes, histone modification enzymes, and DNA methylation can all regulate chromatin structure, thus affecting gene expression Understand the concept of a “master regulator” Understand that cell memory can Chromati be mediated by positive feedback, n DNA methylation or histone Readings: ECB6 Chapter 5 195-201 & modification remodeli ECB6 Chapter 8: 287-297 ng  Prelim 3: Next Monday, Nov 11th All exam are taken on CANVAS: CANVAS/EXAM/Exam Instruction Check your new seat assignment (by Friday night Nov 8th ): CANVAS/EXAM – either in Cal Auditorium or Klarman G70. Material: lectures 14-18 and sections 8-9; ***Note: we grade based on material taught in class Practice Prelim 3 CANVAS/EXAM TAs review sessions: Saturday/Sunday 1-4PM Biotech Racker Room (Instructions in CANVAS/EXAM) Instructor Office Hours: Mon 4-5pm Biotech 258 Wed 1:30-2:30pm on Zoom Full instructions on Canvas/Exams/Exam Instructions. It is your responsibility to read and follow the instructors. Not following the instructions can be considered cheating and may result in 0 in the Prelim and in further penalties.  Differential gene expression makes cells different and ensures spatial-temporal control of transcription Example of DNA regulatory sequence: enhan DNA looping and protein-protein interaction help RNA Polymerase initiate transcription DNA regulatory sequences Transcriptional regulators: -activators or repressors -DNA sequence specificity -act alone or together  Transcriptional regulators work together as a committee to ensure precise spatial-temporal transcriptional control ? ? ? DNA Looping Figure 8-13 ECB5  Today’s topics Mechanisms Generating of Maintaining specialized transcription cell identity cell types regulation Eukaryotic transcriptional machinery must deal with chromatin compaction Eukaryotic DNA is packaged into chromatin Regulatory sequence Interphase Transcription “ON Constitutive Constitutive Constitutive 30-100nm Facultative heterochromatin (w. genes) Mitosis Transcription “OFF Figure 5-23 & 5-26 ECB5  Eukaryotic DNA is packaged into chromatin restricting access of the transcriptional machinery to DNA Nucleosomes “transcriptional machinery”= “TM” = RNA Polymerase, general TFs, and regulatory can restrict access of transcriptional factors machinery (TM) to DNA Euchromatin is a relatively open form of chromatin fiber rich in genes Chromatin fiber can further restrict access of “TM” to DNA Telomeres and centromeres are devoid of genes and form ‘constitutive’ (always present) heterochromatin Facultative heterochromatin contains genes and varies in its chromosomal location in different cell types Heterochromatin strongly silences genes by restricting access of TM  Nucleosomes may restrict access of regulatory factors to their specific DNA sequence and hinder RNA polymerase Nucleosome core particle activity tructure as determined by X-ray crystallography Nucleosome core particle Histone H1 Linker DNA ~200bp RNA Pol II Essential Cell Biology, Fifth Edition Nucleosome Copyright © 2019 W. W. Norton & Company Tight packing of chromatin inhibits transcription Therefore, genes can be turned on and off by factors that influence chromatin regulatory sequence packing, such as: CHROMATIN REMODELING COMPLEXES HISTONE MODIFYING ENZYMES DNA METHYLATION  Chromatin remodeling complexes Chromatin remodeling DNA more complexes use the energy accessible to other of ATP to loosen the proteins which nucleosomal DNA and facilitates push it along the histone transcription octamer. Figure 5-26 ECB5, 5-26 ECB4 Tight packing of chromatin inhibits transcription Therefore, genes can be turned on and off by factors that influence chromatin regulatory sequence packing, such as: CHROMATIN REMODELING COMPLEXES HISTONE MODIFYING ENZYMES DNA METHYLATION  Histone modifying enzymes add/remove covalent modification on the core histone tails M: methylation Ac: acetylation P: phosphorylatio Figure 5-25 ECB5  Histone modifications can affect chromatin structure and influence transcription Histone modifications can affect chromatin structure by: 1. directly by altering the affinity of tails for adjacent nucleosome 2. indirectly by attracting general transcription regulators and chromatin remodeling complexes Histone modification is reversible some enzymes add these modifications other enzymes remove these modifications Figure 5-25 ECB5  Transcriptional regulators can alter chromatin structure Transcriptional regulators: -activators -> turn transcription ‘ON’ -repressors -> turn transcription ‘OFF’ Figure 8-11 ECB4 Tight packing of chromatin inhibits transcription Therefore, genes can be turned on and off by factors that influence chromatin regulatory sequence packing, such as: CHROMATIN REMODELING COMPLEXES HISTONE MODIFYING ENZYMES DNA METHYLATION  DNA methylation can affect chromatin structure CpG islands in mammals typically 300-3000 bases in length contain >50% CpG methylatio n will not ~70% of human genes have a affect base CpG island near their pairing promoter unmethylated unmethylated CpG islands recruit proteins that decondense chromatin activate gene expression methylated methylated CpG islands recruit proteins that condense chromatin repress gene repression Figure 8-23 ECB5  Today’s topics Mechanisms Generating of Maintaining specialized transcription cell identity cell types regulation  Combinations of a few transcriptional regulators can generate many cell types during development Figure 8-17 ECB4  The same transcriptional regulator may assemble into different complexes to regulate the expression of different genes Genes 1/2/3 could be turned on in different cell types, or in the same cell type. A single transcription factor can lead to the formation of an entire organ—the concept of a master regulator Loss of eyeless gene (eyeless mutation) results in the loss of eye (necessary) Eyeless is a homeodomain transcription factor Ectopic expression of eyeless wild typeeyeless mutant results in the formation of ectopic eye (sufficient) in antenna in leg Wild type Ectopic expression of eyeless  A single transcription factor can lead to the formation of an entire organ—the concept The of a master eyeless homolog regulator Expressing the in mice is also a mouse eyeless gene master regulator of in flies results in the eye development formation of ectopic Wild type eye Normal eye Normal eye mut/+ Small eye Ectopic eye in the antenna mut/mut No eye The function of the eyeless gene in eye development is evolutionarily conserved  Today’s topics Mechanisms Generating of Maintaining specialized transcription cell identity cell types regulation Combined actions of different transcriptional regulators (e.g. activators and repressors) and including specific master regulators cause cells to adopt specific fates  Today’s topics Mechanisms Generating of Maintaining specialized transcription cell identity cell types regulation  How do cells remember their developmental decisions and maintain cell type identity over time and through cell division? Positive feedback loops Histone modifications DNA methylation  Cell memory via positive feedback loops protein A activates transcription of itself (positive feedback) other genes that control cell fate Figure 8-22 ECB5  Cell memory via histone modifications Histone modification patterns can be passed on to daughter cells by the action of histone modifying enzymes Figure 5-25 ECB5  Cell memory via DNA methylation DNA methylation patterns can be passed on to daughter cells by the action of maintenance methyltransferase Figure 5-24 ECB5  Epigenetic inheritance Both histone modification and DNA methylation affect chromatin structure and patterns of gene expression without changing the nucleotide sequence. Epigenetic inheritance: patterns of gene expression are transmitted from parent to daughter cells without altering the actual nucleotide sequence of the DNA Figure 8-23 ECB4  Dosage compensation A mechanism to equalize the amount of X chromosome gene expression for males and females (i.e. XX and XY individuals have equal levels of expression of X-linked genes). Dosage compensation in mammals is via random inactivation of one of the X chromosomes in females. (Females are mosaics) X inactivation is irreversible and via an epigenetic mechanism. Rainbow (left) and her clone CC (right) A sex-linked color locus (C) has two alleles, O and B, for Orange and Black. Where an X chromosome bearing the O allele is inactivated, the melanocytes are black; where B is inactivated, the melanocytes are orange. Figure 5-28 ECB5 Next Lecture : Cell signaling I