Genetics Test 3

1. Respond to environmental conditions

2. Express genes appropriate to developmental stages of life cycle

3. Express genes appropriate to cell type

1. Regulatory Transcription factors

2. Chromatin / Histone Modifications

3. DNA methylation

• required for binding of RNA pol to core promoter and progression to elongation stage

• necessary for basal transcription

• Recall TFIID, TFIIH, etc.

• regulate the rate of transcription of target genes

• influence ability of RNA pol to begin transcription of a particular gene

• **2-3% of human genes encode transcription factors

cis regulatory elements near the core promoter

proteins with DNA-binding motifs

• most upstream of promoter, within few hundred bps

• many orientation-independent

activators, enhancers

proteins with DNA-binding motifs

(repressor binds silencer)

• most upstream of promoter within a few hundred bps

• many-orientation dependent

• repressor - silencer

repressors, silencers

-Regulatory TF’s contain motifs that contribute to their activity

• DNA binding domain

• binding site for effector molecules

• dimerization domains

most regulatory TFs don’t bind directly to RNA poymerase

• Transcription activation occurs when activator complex recruits TFIID

• Transcription repression occurs when repressor inhibits binding of TFIID to core promoter

• Activation: activator protein + mediator, phosphorylation of C-terminal domain of RNA pol enhanced, GTFs released and RNA poly proceeds to elongation

• Repression: repressor protein + mediator, prevents phosphorylation of C-terminal domain of RNA pol, inhibits switch to elongation stage

produced by endocrine glands, secreted into the bloodstream, diffuse into cells

regulatory TFs that respond to steroid hormones

Enhancers where steroid receptors bind (near dozens of different genes)

• most signaling molecules can’t enter cells

• detected at surface, message relayed to TF’s inside the cell]

• ex. G-coupled protein receptors (cAMP levels)

activator - activated by increased cAMP levels and phosphorylation

enhancer

A region DNA whose nucleotide sequence encodes for a transcribed RNA and for those that go on to be translated to protein it typically contains exons and introns that will
be used to create primary RNA transcript

A region of DNA/RNA from the 5’ end to the position of the first codon used in translation initiation (post-transcriptional control)

A region of DNA/RNA from the 3’ end to the position of the last codon near the termination of transcription and used in translation for stability (post-transcriptional control)

A region or site of DNA to which transcription factor and co-activator binding occurs and regulates promoter availability

A region of DNA that binds negative regulatory elements for transcription suppression

A region of DNA on which transcription machinery assembles including RNA polymerase

A region of DNA that binds proteins to help define chromatin domains and protect genes from inappropriate signals, in human this is a CTCF binding site

• DNA is condensed/compact

• several levels of compaction

• space constraints

• organization of chromosomes into domains

• affects access to transcription machinery

DNA plus associated proteins

dynamic

histone proteins (nucleosome)

• 146 bps DNA in wrap

• linker DNA more accessible

2* H2A, H2B, H3, H4

H1

• basic(positively charged) proteins

• contain many Lys and Arg

• bind to phosphate in DNA backbone

• globular domain

• flexible, charged ‘tail’

30 nm fiber - histone H1 involved

• structure still not fully elucidated

chromatin structure is dynamic, and influences levels of gene expression

chromatin structure

• small local changes or large-scale

• multiprotein complexes move or modify nucleosomes

• this changes compaction level and accessibility to transcription

transcription levels

looser wrap

tighter wrap

histone modifications occur in patterns that are recognized by proteins

• pattern of modifications provide binding sites for proteins that specify alterations to be made to chromatin structure

• human genome contains over 70 histone genes

• most encode standard histones

• few have accumulated mutations

• found at the beginning and end of many genes

• less regularly distributed elsewhere

inaccessible protein

epigenetic modifications and methylation/acetylation

silences gene expression

DNA methyltransferase

methylated on cytosine

• CpG islands near promoters of many genes

silences gene expression

• methylation influences TF binding

• methyl-CpG-binding proteins recruit factors that increase chromatin compaction

• expressed in most cell types

• CpG islands unmethylated

• CpG islands unmethylated in tissues where expression is needed

• CpG islands methylated in non-target tissues

a. methylation inhibits the binding of an activator protein

b. Methyl-CpG-binding protein recruits proteins that close chromatin structure

heritable

• Methylated DNA sequences are inherited during cell division

• de novo methylation is infrequent, highly regulated

• genomic imprinting, epigenetics

multiple factors can contribute to regulation of one single gene

effectors, protein-protein interactions, covalent modification

nucleosomes near the promoter

preventing binding of the activator and recruiting proteins that compact chromatin

• regulatory TFs

• DNA methylation

• nucleosome location/composition

• small non-coding RNA

• RNA stability

• feedback inhibition

• covalent modifications

chemical modification of histones

true

false

false

False

True

False

True

False - it inhibits it

Between two genes

TFIID

DNA methylation

true

The cell will express different sets of genes than other cells in the same organism

True

structure is fluid and can be changed by modifications, evictions, variants

• Very few coding mutations discovered

• must mutations are SNPs lying in non-coding regions

repetitive DNA

enzymes that move discrete segments of DNA from one location in the genome to a new site

use RNA instead of DNA

bacterial cut and paste, inserts a fragment of DNA in a new location

• altered to carry and insert two double stranded adaptors

• changes in gene expression without change in DNA sequence

• passed from cell to cell

• can last lifetime of individual

• not permanent over multiple generations

• reversible

from parent to offspring

the markings that are placed ‘on’ the genome

• marks can be ON DNA itself (CpG islands)

• marks can be on the histones

• DNA methylation

• Chromatin remodeling

• Covalent histone modification

• Localization of histone variant

specific proteins bind to them

post-translational modifications

• binds methylated histones

• pulls nucleosomes closer together

• has a reader domain

• gene silencing

• prevent transposable element movement

• prevent viral proliferation

limit access to DNA-binding proteins

• random insertion in genes, can disrupt function

• block movement of these DNA regions

• viral DNA integrated on genome

• prevent viral activation/transcription

hemi-methylated DNA fully methylated via maintenance methylation

histones recruit chromatin-modifying/remodeling enzymes to new histones/nucleosomes

recruits chromatin-modifying complexes

• genetically programmed stages of development

• many changes maintained by epigenetic regulation

• occurs during gametogenesis

• offspring expresses allele from one parent only

• in germ cells, base imprint erased and reestablished based on sex of individual

• occurs during embryonic development of female mammals

• ‘count’ number of X chromosomes, silence all but 1

• inactivation occurs at X inactivation center

• dosage compensation

• Tsix expressed from both X chromosomes

• expression stimulated by pluripotency factors

• Tsix expression recruits DNA methyltransferase, silence Xist promoter