The human genome, epigenetics and chromatine remodelling

Question 1

describe the composition of the human genome

Answer 1

about 50% repetitive, 1-1,4% exons, 24% introns, rest unique intergenic sequences
(about 50% unique)

Question 2

what are repetitive elements in the human genome?

Answer 2

retrotransposons, DNA-transposons, inverted repeats (hairpins, regulatory), highly repetitive DNA, telomeres, centromeres

Question 3

describe the size of the human genome

Answer 3

6 billion bases per cell (6x10^9), length of all DNA in the human body more than 500x the distance between earth and sun

Question 4

define “DNA”

Answer 4

macromolecule, contains all info necessary for development and function of a living organism

Question 5

define “gene”

Answer 5

unit of inheritance (promoter, exons and introns)

Question 6

define “chromosome”

Answer 6

organized structure of one long & coiled DNA (or two copies) and histones, visible in m-phase

Question 7

define “genome”

Answer 7

total hereditary information of an organism (chromosomes & mitoDNA)

Question 8

explain the structure of chromatin

Answer 8

naked DNA winding around histones=octamer - nucleosomes packed into 30 nm fiber (packed nucleosomes) - extended chromosome section (scaffolding proteins, form loops) - condensed chromosome section (condensin, loops form into coils), mitotic chromosome (cohesins - hold sister chromatides together)

Question 9

what is euchromatin?

Answer 9

open, more accessible to nucleases and transcription factors, rich in actively expressed genes, replicated early in S-phase

Question 10

what is heterochromatin?

Answer 10

closed, not accessible to TF, few genes, high content of repetitive DNA, replicated late in S-phase

Question 11

facultative heterochromatin

Answer 11

can differ by cell type & time: tissue specific genes, gene silencing (inactive x-chromosome)

Question 12

constitutive heterochromatin

Answer 12

same in all cell types, structural: telomeres, centromeres

Question 13

define “epigenetics”

Answer 13

heritable changes in gene expression, no changes in DNA sequence

Question 14

explain the function of DNA methylation

Answer 14

• silencing of genes: transcription repression of CpG-rich promoters & transposable elements
• > physically prevents binding of transcription factors, signal for other proteins to locate & silence genes, form heterochromatin

Question 15

de novo DNA methyltransferase

Answer 15

put initial pattern of methyl groups on DNA sequence in development

Question 16

maintenance DNA methyltransferase

Answer 16

copy methylation pattern from DNA template to new strand after replication in somatic cell division

Question 17

how are DNA methylation patterns inherited from mother cell to daughter cell?

Answer 17

DNMT1 recognizes 5-met-C on parental strand and adds a methylation on new strand

Question 18

active DNA demethylation

Answer 18

enzymatic process: TET-mediated oxidation of methyl group, base excision repair

Question 19

passive demethylation

Answer 19

lack of maintenance methylation during replication, inhibition of DNMT1

Question 20

what do histone tail modifications effect?

Answer 20

direct influence on overall chromatin structure, regulation of binding of effector molecules

Question 21

writers in histone tail modification, give example

Answer 21

add modification to histone tails/DNA e.g. methyltransferases, acetyltransferases

Question 22

readers in histone tail modification, give example

Answer 22

effector molecules that bind to modified histone tails e.g. chromodomain of HP1 binds to methylated region

Question 23

erasers in histone tail modification, give example

Answer 23

remove modification, e.g. demethylase, deacetylase

Question 24

describe histone methylation

Answer 24

lysine or arginine can be mono/di(tri)methylated, SAM as methyl donor, more repressive state

Question 25

describe histone acetylation

Answer 25

Histone acetyltransferases (HATs) use acetyl-CoA to acetylate lysine, removes positive charge, opens chromatine (facilitate transcription factor access at enhancers/promoters)

Question 26

describe the chromatin remodeling processes at the level of nucleosomes

Answer 26

enzyme-assisted, CRC=chromatin remodeling complexes for removal/insertion/sliding of nucleosomes, dimer exchange

Question 27

what decides the outcome of epigenetic marks?

Answer 27

interplay between DNA methylation, histone marks and nucleosome position

Question 28

how to epigentic modifications affect human disease in general?

Answer 28

abberant replacement of epigenetic marks and mutations in epigenetic machinery are involved in diseases like cancer, neurological disorders, autoimmunity

Question 29

give examples how alteration of DNA methylation patterns inactivates tumor suppressors

Answer 29

• methylated CpG islands
• unmethylated gene body (transcription starts internally)
• unmethylated repetitive sequence (retrotransposon jumps and destabilizes DNA)

Question 30

give an example of epigenetic therapy for cancer cells

Answer 30

HDAC inhibitors (messes around with specific gene expression outcome in cancer cells), for T-cell lymphoma

Question 31

where is DNA usually methylated?

Answer 31

C before G (CpG regions, p = phosphate)

Question 32

how can alterations in epigenetic modifications drive cancer development?

Answer 32

dysregulation of gene expression: upregulation of oncogenes and (most importantly) silencing of tumoursuppressors

Question 33

discuss important functions of the non-protein coding parts of the genome

Answer 33

regulatory (regulate chromatin structure, transcription, splicing), non-coding genes, functional, structural and regulatory RNA (tRNA, rRNA, miRNA), structural (centromers, telomers)