Quiz 6 Flashcards
Cell specific gene expression
Different cell types in multicellular organisms require specific genes to be used; some genes only expressed under certain conditions or at certain times
How genes can ge regulated as DNA
Histone modification and chromatin remodeling
Gene regulation in transcription and translation
Transcription, post transcriptional modifications, nuclear export of mRNA, mRNA stability, mRNA localization in the cell before translation, translation, post-translational protein modifications
Chromosome territory
Each chromosome occupies a separate territory in nucleus during interphase
Interchromatin compartments
Channels between chromosomes
Transcriptionally active genes are located:
At the edges of the chromosome territories; during coordinated transcription when they’re brought together to transcription machinery
Postranscriptional modification occurs:
In the interchromatin compartment, which is connected to nuclear pores allowing the mRNA to then be transported out
Transcription factories
Enable efficient and coordinated transcription of genes (a few hundreds to thousands)
Located on the edge of a chromosome territory, contains a handful of RNA polymerase and many tran-acting factors
Dynamic structure
Different ways nucleosomes can be modified
Changing nucleosome composition, histone modification (adding or removing chemical groups), and chromatin remodeling (repositioning or removing nucleosomes on DNA)
Also DNA methylation
Changes in nucleosome composition
Affect transcription (ex: replacing histone 2A protein with H2A.Z, which makes nucleosome unstable; often found in association with promoter regions and enhancers of transcriptionally active genes)
Histone modification
Affects way DNA is wrapped around nucleosomes using chemical groups such as acetyl, phosphate, and methyl groups
Histone acetylation
Done using histone acetyltransferase (HAT) that can be recruited by trans-acting factors (activators), loosening interaction between histones and DNA making promoters and genes available for transcription
Increases transcription
Histone deacetylation
Done by histone deacetylases (HDACs) recruited by repressors that tighten DNA in nucleosomes, decreasing transcription
Chromatin remodeling
Repositioning or removal of nucleosomes from DNA; makes promoters and regulatory sequences accessible to RNA polymerase and other proteins involved in transcription
Chromatin remodeling complexes
Large protein complexes that use ATP for energy and alter nucleosome structure in several ways: loosening contact between DNA and histones (causing sliding), altering the DNA path around the nucleosome, remodeling the structure of the core nucleosome
DNA methylation
Adding methyl groups to DNA, most commonly on cytosone in CG doubles in CpG islands, found in the promoter regions of 70% of human genes
Evidence that DNA methylation affects gene expression
DNA methylation equals a decrease in gene expression, DNA methylation patterns are tissue specific and inherited to all daughter cells in the tissue, and base analogs that cannot be methylated cause a change in gene expression patterns
How DNA methylation inhibits transcription
Inhibits transcription factors binding to DNA and recruits HDACs and repressive chromatin remodeling complexes to regulatory regions
(Affects genes in some but not all eukaryotes)
Cis-acting DNA elements that regulate transcription in eukaryotes
Promoter is the DNA region to which RNA polymerase II and general transcription factors bind and as such acts as a recognition site for transcription machinery
Two components of eukaryotic promoters
Core promoter: minimum part of promoter needed for transcription initiation, about 80 nucleotides long
Proximal promoter elements: binds trans-acting factors that regulare efficiency of transcription (about 250 nucleotides upstream)
Two types of core promoters
Focused: transcription starts at a single site and genes are highly regulated
Dispersed: transcription starts at multiple sites, constitutively expressed genes
Core promoter elements:
Initiator element: -2 to 4, found in all focused core promoters
TATA box: -30 to -24, found in all focused core promoters
BRE (TFIIB recognition element): either upstream or downstream of TATA box, found in all focused core promoters
Proximal promoter elements
Upstream of TATA box and BRE
CAAT box: about 70 nucleotides upstream, found in many promoters
GC box: about 110 nucleotides upstream, found in many promoters
Enhancers
Found upstream, downstream, and in introns of genes, can be located close or far away, not required for transcription but increase its level (and are necessary for max), activators bind here; time and tissue specific
Insulators
Found in between an enhancer and promoter for a non-target gene, trans-acting factors bins here and stop enhancers from regulating wrong gene
Silencers
Found upstream, downstream, or within gene; trans-acting factors called repressors bind and exert negative regulation of transcription; involved in time and tissue specific negative regulation
Two fundamental components of transcription regulation
Locations in DNA close to genes (cis-acting regulatory sites) and proteins (trans-acting regulatory factors) that bind to cis acting sites
Cis-acting regulatory sites
Promoters, enhancers, silencers that bind transcription factors
Two types of transcription factors
General (essential, RNA polymerase can’t bind without them) and specific (activators and repressors)
Specific transcription factors
Some regulate many genes and are common, while some are very spherical and only regulate a few genes and are tissue/time specific
How specific transcription factors compete for same cis-acting element
Most numbers wins or the stronger bind wins
Fine tuning
Different transcription factors bind to enhancers and promoter elements of the same gene and interact with each other to alter timing and level of transcription initiation
Example of fine-tuning
hMTIIA (human metallothionein IIA gene) which is expressed when we’re exposed to heavy metals and encodes a protein that binds to the metals and reduces their toxic effect
Three modes of fine tuning
Basal levels of transcription, high levels, and repression; done by multiple promoter and enhancers elements and the transcription factors that bind to them
Basal level of the hMTIIA
Sp1 binds to the GC element to stimulate transcription at low levels, while AP1, 2, and 4 binds to ARE and BLE elements (which contains overlapping binding sites for 1 and 4 to provide selectivity in how 1 and 4 stimulate transcription in different cells)
High levels of the hMTIIA
MTF1 exists in cytoplamsm and is activated by heavy metal, causing an allosteric change that moves it to nucleus and binds to MREs
Glucocorticoid receptor is activated by the glucocorticoid hormone causing an allosteric change moving to nucleus to bind to GRE
Repression of hMTIIA
PZ120 binds to transcription starts region
Transcription factor domains
Part of a protein that gives the protein a unique function; two functional domains in transcription factors proteins: DNA binding domain where it binds to the cis-acting element, and the trans-activating domain where it interacts with the other proteins (stimulation or inhibition)
How cis-acting elements and transcription factors act to influence transcription:
The formation of the transcription pre-initiation complex (involving general transcription factors and RNA polymerase II) and the interactions between general transcription factors/RNA polymerase II with specific transcription factors
Formation of the preinitiation complex
General transcription factors (TFIIA, TFIIB, etc) bind RNA polymerase II to promoter and seamless it at the promoter in specific order to create PIC
TFIID binds to TATA box using binding protein TBP and TFIIA finds TFIID to bind; TFIIB binds to BRE, and RNA polymerase recruits TFIIF and mediator and TFIIE AND TFIIH bind
Mechanisms of transcription activation and repression
- Recruitment model: the DNA loops and enhancers and silencers are brought to promoter region, where specific transcription factors stimulate/inhibit PIC formation/stability or initiation; can involve coactivators that bridge between specific TFs and proteins at the promoter (called enhanceosomes)
- Chromatin alteration model: the DNA loops, stimulating/inhibiting transcription by producing chromatin alterations
- Nuclear relocation model: DNA loops of enhancers and repressors causes active genes to move to a nuclear region that is favorable or inhibitory to transcription
Alternative splicing
Posttranscriptional regulation; a gene has multiple exons, and different combinations of them can produce different mature mRNAs called spliceforms, which produce different proteins called isoforms
Types of alternative splicing
Cassette exons, alternative splice site, intron retention, mutually exclusive exons, alternative promoters, alternative polyadenylation
Regulation of alternative splicing
Splicing enhancers are cis-acting DNA elements where SR proteins bind and activate splicing; splicing silencers are where hnRNPs bind and inhibits splicing by blocking yhe formation of its machinery or excluding exons
Alternative splicing example
Sex determination in fruit flies; Sxl I’d only expressed in female embryos, while Tra is expressed in both; Sxl causes a female specific splicing of Tra; a third gene called Dsx produces Dsx F and Dsx M according to whether or not TRA protein is expressed
DsxF repressed genes that control male development, while DsxM activates genes that control male development and repressed genes that control female development
Human diseases caused by alternative splicing
Spliceopathies are genetic diseased caused by defective alternative splicing such as spinomuscular atrophy or myotonic dystrophy
Epigenetics
Heritable changes to gene expression that are not dependant on DNA sequence itself; mechanisms include DNA methylation, chemically modifying histone tails, and oncoming RNAs
Epigenome
Epigenetic modifications in a cell at a given time
Hyper vs hypomethylation
Increase vs decrease in DNA methylation
Methylome
All methylated Cs in a cell’s genome at a given time
Methylation is associated with:
Less gene expression; unmethylated means gene is expressed while methylated means gene is silenced because methyl groups protrude from where binding proteins bind
Methylation in heterochromatin
Where most methylation happens; for stability to prevent translocation and expression/movement of transposable elements
Two types of demethylation
Passive, where daughter strand is nit methylated after replication, and active, where methyl groups are removed
Histone modifications
Influence whether DNA is open (available for transcription) or closed (not available); more than 20 chemical modifications can be made; three classes of protein involved (writers that add, readers that interpret, and erasers that remove)
Histone acetylation
Adding of acetyl groups to histone tails by writers called histone acetyltransferases (HATs) that loosen interaction between histones and DNA; histone deacetylation is done by erasers called histone deacetylases (HDACs) that tighten the histones and DNA
