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
