Module 9 Flashcards
Epigenetic gene regulation are targeted by:
- DNA methylation
- Chromatin remodeling
- Covalent histone modification
- Localization of histone variants
- Feedback loop
Heterochromatin
Chromosomal regions that are stained during interphase, more compaction and inhibition and on periphery
Euchromatin
Chromosomal regions that are not stained during interphase; loop domains packed loosely together and are transcriptionally active and central to nucleus
Constitutive Heterochromatin
Same across all cell types, close to centromere/telomere, tandem repeats, highly methylated cytosines, histone modifications (H3K9me2)
Facultative Heterochromatin
Varies in location depending on cell type, located on multiple sites between centromere/telomere, LINE-type repeat sequences, methylation at CpG islands in gene regulatory regions (silences), histone modifications (H3K27me)
Reader Domains
Contained in specific proteins, used to bind particular posttranslational modifications to histone, has writer (+PTMs), eraser (-PTMs), and recruitment domains (recruits other proteins for chromatin remodeling)
HP1 Protein
Forms dimer that binds two nucleosomes with H3K9me3 modification, holding them in close proximity to silence transcription
Heterochromatin is maintained through cell divisions via:
DNA methylation (hemimethylation), histone modifications, DNA polymerase, and local chromatin structure
Phases of heterochromatin formation
- Nucleation
- Spreading
- Barriers
Epigenetic changes occur during development through:
Genomic imprinting (ex. Ig2f), X-chromosome inactivation (ex. Xci, Xist and Tsix), and formation of specific cell types (done through TrxG activation and PcG repression)
Epigenetic changes can be influenced by ____ and ____
diet (ex. Agouti mice with increased methylation, female bees consuming royal jelly to become queens) and environment (ex. vernalization in plants, which must be exposed to cold before flowering)
ncRNAs can bind to ____ and some have ____ binding sites
DNA, RNA, and proteins; multiple
ncRNAs function as/to:
- Scaffolds in complex formations
- Guides to bring molecules places
- Alter protein function/stability to interfere with catalytic properties
- Ribozyme
- Blocker to physically block cellular processes
- Decoy for other ncRNAs and sequester them to prevent their function
HOTAIR Gene Function
Hox Transcript Antisense Intergenic RNA (HOTAIR) alters chromatin structure and encodes long ncRNA which acts as a scaffold that guides two histone-modifying complexes to target genes
Fire and Mello Experiment Results
Found through injections into C. elegans gonads that antisense injections were only half-degraded, while both sense and antisense was fully-degraded, indicating the potency of dsRNA
RNA-Induced Silencing Complex (RISC)
A molecule produced from pre-miRNAs and pre-siRNAs by dicer, resulting in either inhibitory translation without degrading mRNA (remains in P body) or degradation of mRNA through cleavage by perfectly matching Argonaute protein
CRISPR-Cas provides antiviral defense for bacteria by:
- Adaptation: “spacer acquisition”, insertion of bacteriophage DNA into gene
- Expression: a second exposure event will result in expression of Crispr, tracr, and Cas9 genes (form tracrRNA-crRNA-Cas9 complex)
- Interference: crRNA acts as a guide causing tracrRNA-crRNA-Cas9 complex to bind to target bacteriophage DNA strand and Cas9 breaks it to prevent infection
cis Epigenetic Mutations
Maintained at a specific site, only affecting one copy of the gene (maintained through cell division)
trans Epigenetic Mutations
Maintained by diffusible (transcription) factors, affecting both copies
Heterochromatin plays a role in:
gene silencing, prevention of transposable element movement, and prevention of viral proliferation
RNA was the first molecule found in protobionts as it can ____, ____, and has ____
store info, self-replicate, and has catalytic activity
RNAi
RNA interference, how dsRNA causes mRNA silencing, mediated by microRNAs and siRNAs (both ncRNAs)
Provides viral defense in plants
snoRNAs
Small nucleolar RNAs, play a role in assembling rRNA to improve functionality, exists in C/D box and H/ACA box forms, each forming a small nucleolar ribonucleoprotein
____ (ncRNA) and ____ proteins are used to prevent ____ movement in germ-line cells
piRNA, PIWI, transposable element
piRITS
piRNA-induced transcriptional silencing, forms from piRNA and PIWI protein complex binding to specific TE and directs DNA methylation/trimethylation to prevent TE movement
piRISC
piRNA-induced silencing complex, directly inhibits RNA in cytosol via Argonaute protein
Methylated Igf2 gene is ____ during spermatogenesis, which occurs at the ____ (ICR) and the ____ (DCR), preventing CTCF from binding and ____ transcription
methylated, imprinting control region, differentially methylated region, promoting
