Genetics Test III Pt.2

Question 1

Epigenetics

Answer 1

change in gene expression not caused by changes in DNA sequence

Question 2

Chromatin

Answer 2

• the generic term for any complex of DNA and protein found in a nucleus of a cell
• 1/3 DNA, 1/3 histones, 1/3 nonhistone proteins

Question 3

Chromosome

Answer 3

the separate pieces of chromatin that behave as a unit during cell division

have a versatile, modular structure for packaging DNA that supports flexibility of form and function

Question 4

Histones

Answer 4

• Small, positively-charged, and highly conserved
• Bind to and neutralize negatively charged DNA
• Make up half of all chromatin protein by weight
• Five types - H1, H2A, H2B, H3, and H4

Question 5

Nonhistone Proteins

Answer 5

• 100s of other nonhistone proteins make up chromatin
• 200 – 200,000 molecules of each kind of nonhistone protein
• Large variety of functions
• Structural role – chromosome scaffold
• Chromosome replication – DNA polymerases
• Chromosome segregation – kinetochore proteins
• Active in transcription – largest group

Question 6

Nucleosome

Answer 6

condenses naked DNA 7-fold – DNA around histone octamer

Question 7

Super coiling

Answer 7

causes additional 6-fold compaction - Nucleosomes wound up

Question 8

Radial Loop-Scaffold

Answer 8

compaction to a rod-like mitotic chromosome – 3D packaging of Supercoiled DNA

Question 9

Heterochromatin

Answer 9

highly condensed, usually inactive transcriptionally

Question 10

Types of Heterochromatin

Answer 10

• Constitutive – condensed in all cells

* Facultative – condensed in only some cells and relaxed in other cells

Question 11

Euchromatin

Answer 11

relaxed, usually active transcriptionally

Question 12

Three major mechanisms can regulate chromatin patterns

Answer 12

1. Histone modifications – addition of methyl or acetyl groups

• N-terminal tails of histones H3 and H4 can be modified
• Methylation, acetylation, phosphorylation, and ubiquitination
• Can affect nucleosome interaction with other nucleosomes and with regulatory proteins
• Can affect higher-order chromatin structure

2. Remodeling complexes can alter nucleosome patterns
   • Change accessibility of promoter sequences
   • Remove or reposition promoter-blocking nucleosomes
3. Histone variants can cause different nucleosomal structures,

Question 13

DNA methylation

Answer 13

often occurs at C5 of cytosine in a CpG dinucleotide

Question 14

Chromatin hypercondensation

Answer 14

• results in silencing of transcription

* Examples: inactive X chromosome, centromeres, telomeres

Question 15

Genomic imprinting

Answer 15

• expression of a gene depends on whether it was inherited from the mother or father
• Occurs with some genes of mammals
• Results from transcriptional silencing
• Methylation of complementary strands of DNA causes genomic imprinting
• Epigenetic effect (no change in DNA sequence)
• Paternally imprinted gene is transcriptionally silenced if it was transmitted from the father, Maternal allele is expressed
• Maternally imprinted gene is transcriptionally silenced if it was transmitted from the mother, Paternal allele is expressed

Question 16

Conventional wisdom used to state: Epigenetic states are reset during meiosis

Answer 16

• Epigenetic states remain throughout the lifespan of the mammal
• In germ cells, epigenetic imprints are reset at each generation
• During meiosis, imprints are erased and new ones are set
• This is currently the subject of much debate

Question 17

Genomic imprinting and human disease

Answer 17

• Praeder-Willi syndrome occurs when the deletion is inherited from the father
• Angelman syndrome occurs when the deletion is inherited from the mother

Question 18

Transcription is controlled by chromatin structure and nucleosome position

Answer 18

• Spacing and structure of nucleosomes affect transcription

Question 19

Insulators limit what

Answer 19

chromatin region over which an enhancer can operate

Question 20

Regulatory non-coding RNA (ncRNA

Answer 20

Specialized RNAs that affect gene expression, several different sources and mechanisms

Question 21

Types of ncRNA

Answer 21

microRNA (miRNA)

Piwi-interacting RNA (piRNA)

Small-interfering RNA (siRNA)

Long non-coding RNA (lncRNA)

Promoter associated RNA (PAR)

    Enhancer RNA (eRNA)

Question 22

Basic Outline

Answer 22

RNA transcribed but not translated
often processed and associated with a protein or protein complex

The RNA part is complimentary
so can bind to DNA/RNA,

The protein has some function
affect local DNA,
bind other proteins

Question 23

microRNA (miRNA)

Answer 23

evolutionary conserved

Small 20 – 24 nt RNAs

Many regulate >50% of genes in a cell

Derive from transcripts that form hairpins

Associates with an RNA-induced silencing complex (RISC)

Question 24

miRNA processing MODEL

Answer 24

Primary transcripts containing miRNA are transcribed by RNA polymerase II from noncoding regions and generate short dsRNA hairpins

Drosha excises stem-loop from primary miRNA generates pre-miRNA of ~ 70 nt

Dicer processes excised stem loop to make a mature duplex miRNA

One strand is incorporated into miRNA-induced silencing complex (RISC)

May target the 3’UTR of mRNAs

Question 25

Two ways that miRNAs+ RISC can down-regulate expression of target genes

Answer 25

When complementarity - target mRNA is degraded When not exactly complementarity - translation of mRNA target is repressed

Question 26

Piwi-interacting RNA (piRNA)

Answer 26

Small 21-34 nt Bind to Piwi proteins of the Argonaute family In Drosophila these show complementarity to transposable and repetitive elements Suppress transposon activity during gametogenesis More than 90% of piRNA in mammals map to unique genome areas ````

Question 27

small interfering RNAs (siRNAs)

Answer 27

siRNAs detect and destroy foreign dsRNAs Two biological sources of dsRNAs that are precursors of siRNAs (pri-RNAs) Transcription of both strands of an endogenous genomic sequence Arise from exogenous virus pri-RNAs are processed by Dicer associate with RISC mediate post- transcriptional silencing siRNA pathway targets dsRNAs for degradation siRNAs are very useful experimental tools to selectively knock down expression of target genes

Question 28

Long non-coding RNA (lncRNA)

Answer 28

>200 nt Many are processed by splicing, polyadenylation, and other modifications Affect chromatin structure Transcription regulation Splicing Transcription Factor localization Precursors for siRNA

Question 29

Promoter associated RNA (PAR)

Answer 29

16-200 nt Function unclear Interact with proteins affect transcription

Question 30

Enhancer RNA (eRNA)

Answer 30

100-9000 nt Function mostly unknown Have a role in transcriptional gene activation

Question 31

Basic steps of RNA interference for Therapy

Answer 31

Develop siRNA for target Deliver siRNA to target / elicit RNAi Silence Gene

Question 32

Problems with RNA interference for Therapy

Answer 32

Specificity for target gene Off target silencing – your designed siRNA may stick to the wrong target and silence other genes Delivery to correct cell or tissues Durability of RNAi activity Ability to redoes if necessary Stability of target mRNA and target protein Vector associated immunological response

Question 33

Methods for Delivery

Answer 33

Viral vector Multiple possible to be immunogenic Bacterial vector E. coli – deliver to gut tissue Non-viral formulation Nanoparticle – self-assembling, requires specific knowledge and skills Stable nucleic acid lipid particle – systemic delivery Aptamer – target receptors Cholesterol – systemic delivery