Module 9

Question 1

Epigenetic gene regulation are targeted by:

Answer 1

• DNA methylation
• Chromatin remodeling
• Covalent histone modification
• Localization of histone variants
• Feedback loop

Question 2

Heterochromatin

Answer 2

Chromosomal regions that are stained during interphase, more compaction and inhibition and on periphery

Question 3

Euchromatin

Answer 3

Chromosomal regions that are not stained during interphase; loop domains packed loosely together and are transcriptionally active and central to nucleus

Question 4

Constitutive Heterochromatin

Answer 4

Same across all cell types, close to centromere/telomere, tandem repeats, highly methylated cytosines, histone modifications (H3K9me2)

Question 5

Facultative Heterochromatin

Answer 5

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)

Question 6

Reader Domains

Answer 6

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)

Question 7

HP1 Protein

Answer 7

Forms dimer that binds two nucleosomes with H3K9me3 modification, holding them in close proximity to silence transcription

Question 8

Heterochromatin is maintained through cell divisions via:

Answer 8

DNA methylation (hemimethylation), histone modifications, DNA polymerase, and local chromatin structure

Question 9

Phases of heterochromatin formation

Answer 9

1. Nucleation
2. Spreading
3. Barriers

Question 10

Epigenetic changes occur during development through:

Answer 10

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)

Question 11

Epigenetic changes can be influenced by ____ and ____

Answer 11

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)

Question 12

ncRNAs can bind to ____ and some have ____ binding sites

Answer 12

DNA, RNA, and proteins; multiple

Question 13

ncRNAs function as/to:

Answer 13

1. Scaffolds in complex formations
2. Guides to bring molecules places
3. Alter protein function/stability to interfere with catalytic properties
4. Ribozyme
5. Blocker to physically block cellular processes
6. Decoy for other ncRNAs and sequester them to prevent their function

Question 14

HOTAIR Gene Function

Answer 14

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

Question 15

Fire and Mello Experiment Results

Answer 15

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

Question 16

RNA-Induced Silencing Complex (RISC)

Answer 16

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

Question 17

CRISPR-Cas provides antiviral defense for bacteria by:

Answer 17

1. Adaptation: “spacer acquisition”, insertion of bacteriophage DNA into gene
2. Expression: a second exposure event will result in expression of Crispr, tracr, and Cas9 genes (form tracrRNA-crRNA-Cas9 complex)
3. 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

Question 18

cis Epigenetic Mutations

Answer 18

Maintained at a specific site, only affecting one copy of the gene (maintained through cell division)

Question 19

trans Epigenetic Mutations

Answer 19

Maintained by diffusible (transcription) factors, affecting both copies

Question 20

Heterochromatin plays a role in:

Answer 20

gene silencing, prevention of transposable element movement, and prevention of viral proliferation

Question 21

RNA was the first molecule found in protobionts as it can ____, ____, and has ____

Answer 21

store info, self-replicate, and has catalytic activity

Question 22

RNAi

Answer 22

RNA interference, how dsRNA causes mRNA silencing, mediated by microRNAs and siRNAs (both ncRNAs)

Provides viral defense in plants

Question 23

snoRNAs

Answer 23

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

Question 24

____ (ncRNA) and ____ proteins are used to prevent ____ movement in germ-line cells

Answer 24

piRNA, PIWI, transposable element

Question 25

piRITS

Answer 25

piRNA-induced transcriptional silencing, forms from piRNA and PIWI protein complex binding to specific TE and directs DNA methylation/trimethylation to prevent TE movement

Question 26

piRISC

Answer 26

piRNA-induced silencing complex, directly inhibits RNA in cytosol via Argonaute protein

Question 27

Methylated Igf2 gene is ____ during spermatogenesis, which occurs at the ____ (ICR) and the ____ (DCR), preventing CTCF from binding and ____ transcription

Answer 27

methylated, imprinting control region, differentially methylated region, promoting