Chapter 15 Genetics

CpG islands

1,000 to 2,000 nucleotides long; contain high number or CpG sites

one way of orchestrating changes in chromatin structure

ATP-dependent chromatin remodeling

order of glucocorticoid hormone action

Binding of hormone to receptor, Release of HSP90 proteins, Entry of hormone into the nucleus

near promoters in vertebrates and plants, many genes contain

CpG islands

housekeeping genes

CpG islands are unmethylated; genes tend to be expressed in most cell types

hemimethylated DNA

DNA replication produces hemimethylated DNA which are then fully methylated by DNA methyltransferase

variant histone associated with Barr bodies

MacroH2A

enhancers/ upstream activation sequences may be located

a considerable distance from the promoter; will act in only one or a few cell types in multicellular eukaryote

de novo methylation

a highly regulated infrequent event

nuclear DNA resides in

a nucleosomal structure where approximately 146 base pairs of DNA are wound around a histone octamer consisting of 2 molecules of H2A, H2B, H3, and H4

enzyme cascade when extracellular signaling molecule (hormone, neurotransmitter, growth factor, etc) binds to plasma membrane receptor

activates G protein, which activates adenylyl cyclase, which activates cAMP with ATP, which activates protein kinase A, which phosphorylates CREB, which binds to DNA and stimulates transcription

proteins that directly interact with TFIID: activator protein, co-activator protein, repressor protein, histone deacetylase, mediator, RNA polymerase

activator protein, co-activator protein, repressor protein, mediator, RNA polymerase

transcriptional activation bia TFIID

activator/coactivator complex recruits TFIID to the core promoter and/or activates its function; transcription activated

chromatin immunoprecipitation sequencing (ChiP-Seq)

allows determination of where nucleosomes are located, where histone variants are found, and where covalent modifications of histones occur

pre-mRNA expression at the RNA processing level

alternative splicing, RNA editing

alternative splicing

alters exon choices

RNA editing

alters the base sequence of mRNAs

3D packing of chromatin is

an important parameter affecting gene expression

common ways to modulate transcription factors

binding of a small effector molecule such as a hormone; protein-protein interaction; covalent modification such as phosphorylation

what happens when glucocorticoid comes into the cell

binds to glucocorticoid receptor which already has heat shock proteins on it; HSP released when hormone binds; nuclear localization signal is exposed; formation of a homodimer

in transcriptional silencing via methylation, methyl groups

block binding of an activator protein to an enhancer element or the methyl-CpG-binding protein recruits other proteins that change the chromatin to a closed conformation

An insulator is a protein

false

Insulators prevent DNA looping

false

glucocorticoid receptors are membrane bound

false

glucocorticoid receptors bind to GRE elements which are present on newly synthesized mRNAs

false

presence of a NFR is sufficient for gene activation

false

steroid hormones are synthesized in the same cells where they function

false

protein expression at posttranslational modifications

feedback inhibition and covalent modifications

glucocorticoid response elements

function as enhancersl located near dozens of different genes, so hormone can activate many genes

protein-protein interaction

homodimers and heterodimers

strategies used in the ENCODE project

identify the sequence of RNA produced from genes, methylation sites, transcription factor binding sites, and histone modification sites

gonadocorticoids

include estrogen and testosterone; influence growth and function of gonads

glucocorticoids

influence nutrient metabolism in most cells; promote glucose utilization, fat mobilization, and protein breakdown

the 5 histone genes are

moderately repetitive; H1, H2A, H2B, H3, and H4

common pattern of nucleosome organization revealed by ChIp-Seq

nucleosome-free region found at beginning and end of many genes; nucleosomes tend to be precisely positioned near the beginning and end of a gene, but a less regularly distributed elsewhere

moving the histone octamer along DNA

one way to alter chromatin structure; nucleosome positions are known to change in a genes' regulatory region between transcriptionally active and inactive genes

modification of amino terminal tails of histones

over 50 enzymes that acetylate, methylate, or phosphorylate

histone code

pattern of modifications that are recognized in proteins; specify alterations to be made to chromatin structure; proteins bind based on code and affect transcription

difference between phosphorylated and unphosphorylated CREB

phosphorylated CREB binds to DNA and stimulates transcription; unphosphorylated CREB can bind to DNA, but cannot activate RNA pol

process not mediated by histone variants

phosphorylation

promoter-proximal elements

precede the promoter of a eukaryotic gene

eukaryotic cis-regulatory sequences

promoter-proximal elements and enhancers (or upstream activation sequences)

domains

regions in TF proteins that have specific functions (DNA binding domain, effector molecule binding domain

mechanism behind acetylation

removes positive charges of proteins, thereby reducing affinity between histones and DNA: RNA pol and transcription factors can more easily access promoter region

transcriptional repression via TFIID

repressor protein inhibits the binding of TFIID to the core promoter or inhibits its function; transcription is repressed

cAMP response element (CRE)

response element with consensus sequence 5'TGACGTCA3'

histone acetyltransferase (HAT)

responsible for adding acetyl groups to histone tails; various protein complexes recruited by transcriptional activators possess HAT activity

insulators

segments of DNA that insulates a gene from the regulatory effects of other genes; some act as barriers to chromatin remodeling; others block the effect of enhancers

mRNA expression at the translation level

small RNAs (miRNAs and siRNAs), phosphorylation of translational initiation factors, proteins that bind to 5' end of mRNA, RNA binding proteins

some histone variants are incorporated into a subset of nucleosomes to create

specialized chromatin

Glucocorticoids are ________ hormones secreted by ________ glands

steroid, endocrine

glucocorticoids activate genes that are involved in

synthesis of glucose, mobilization of fats, breakdown of proteins

ATP-dependent chromatin-remodeling complex can cause changes in nucleosome position either by

the relative positions of a few nucleosomes or the spacing of nucleosomes over a long distance

effect on transcription of gene A when transcriptional repressor that controls the transcription of gene A is not normally active unless bound by an effector molecule X and the domain of the repressor that binds X is mutated

transcription of gene A will increase

effect on transcription of gene A when transcriptional repressor that controls the transcription of gene A is not normally active unless bound by an effector molecule X and the domain of the repressor that binds to the silencer of gene A is mutated

transcription of gene A will increase

mediator stimulated by

transcriptional activator

mediator inhibited by

transcriptional repressor

Insulators can prevent an enhancer from working on a neighboring gene

true

ultimate action of a steroid hormone

to affect gene transcription

most histone modifications occur on

N-terminal basic tail domain

repressor protein at silencer

RNA polymerase and general transcription factors not at core promoter, RNA transcription is inhibited

activator protein at enhancer

RNA polymerase and general transcriptional factors at core promoter, RNA transcription increased

hyperacetylated histones

associated with the nucleosomes of transcriptionally active genes

hypoacetylated histones

associated with transcriptionally inactive genes

nucleosomes

basic unit of chromatin

why might all histone variants not be expressed by all cells

because some histones are not needed in certain cell types

small RNAs (miRNAs and siRNAs)

can degrade mRNA or silence translation

DNA methylation

can lead to a change in chromatin structure that silences gene expression, especially in vicinity of promoter; carried out by DNA methyltransferase

nucleosomes have been shown to change position in

cells that normally express a particular gene compared with cells in which the gene is inactive

potential effects of ATP-dependent chromatin-remodeling complex

change in nucleosome position, histone eviction, replacement with variant histones

nucleosome positioning changes for beta-globin

changes in the promoter region as part of gene activation

open conformation

chromatin is accessible to transcription factors; transcription can take place

closed conformation

chromatin is very tightly packed; transcription may be difficult or impossible

location of enhancer sequences

either upstream or downstream of promoter

transcriptional activation via a mediator

enables RNA pol to form a preinitiation complex, which then proceeds to the elongation phase of transcription

structural motifs found in TF proteins

helix-turn-helix, helix-loop-helix, zinc finger, leucine zipper

protein that does not directly interact with TFIID: activator protein, co-activator protein, repressor protein, histone deacetylase, mediator, RNA polymerase

histone deacetylase

modfications of amino terminal tails of histones affect level of transcription and may influence; occur in a

interactions between nucleosomes; occur in a histone code

N-terminal basic tail domains of core histones are involved in

involved in transcriptional regulation, replication, and chromatin condensation

in tissue-specific genes, methyl-CpG-binding proteins may recruit factors that

lead to compaction of chromatin

H1

linker histone that is an essential component of chromatin structure; links nucleosomes into higher order structure

ATP-dependent chromatin remodeling

makes the DNA more or less amenable to transcription; refers to dynamic changes in chromatin structure

human genome contains over 70 histone genes

most encode standard histones; a few of these genes have accumulated mutations that alters the amino acid sequence (variants)

packaging of DNA into chromatin means that

much of the DNA is not accessible to regulatory proteins and the transcriptional complex

steroid receptors

regulatory transcription factors that respond to steroid hormonesl hormone actually binds to the transcription factor

gene expression at transcription level

regulatory transcription factors, the arrangements and composition of nucleosomes, DNA methylation

CREB protein

regulatory transcriptional factor; cAMP response element-binding

histone deacetylases (HDTs)

remove acetyl groups from histone tails; associated with transriptional inactivation

Insulators can prevent chromatin remodeling proteins from working on a DNA region

true

an NFR is likely required for transcription to occur

true

estrogen is a gonadocorticoid

true

glucocorticoid receptor is active as a dimer

true

glucocorticoid receptors have a nuclear localization signal that is hidden until a glucocorticoid is bound

true

glucocorticoid response elements function as enhancers

true

nucleosome-free regions are often found at the beginning and end of a gene

true

the NFR is frequently flanked by variant histones

true

two glucocorticoid receptors function as a homodimer

true

energy of ATP in ATP-dependent chromatin remodeling

used to alter the structure of nucleosomes and thus make the DNA more accessible

chromatin structure

very dynamic that can alternate between closed and open conformations

motif

when a domain has a very similar structure in many different proteins