Transcription Regulation

what are the 2 factors that regulate transcription?

cis and trans acting factors

what are trans-acting factors?

• usually protein that interact with DNA

• transcription factors (or sigma factors)

• transcription activators/repressors

• transcriptional regulators

what do trans-acting factors do?

1. bind DNA directly or are recruited to DNA by other factors

2. Influence transcription (positively or negatively) either by directly recruiting polymerase (or blocking it), or indirectly by recruiting other factors

what are cis-acting elements?

• are within the DNA

• promoters

• enhances

• regulatory sites

• activators/repressor sites

• sequences on the DNA that are recognized and bound to by trans-factors

• can contain a single binding or a cluster of sites (ex enhancers)

• can be near the start site (ex promoters) or far away away (ex enhancers)

what happens if there is a mutation in the Cis-acting element?

occurs when a region only affects transcription of the DNA strand it is on (i.e. it cannot impact transcription of another DNA strand). Regulatory sites on the DNA act in cis

how it would look

trans-acting factor present and working how every cis-acting element is NOT, NO TRANSCRIPTION OF GENE X

2nd copy of Gene X

trans-acting factor binds to promoter → YES TRANSCRIPTION OF GENE X

what happens if there is a mutation in the Trans-acting factor

regulation in the trans occurs when a factor can affect transcription on any DNA strand. transcription factors act in trans

how it would look

cis-acting elemet present but the trans-acting factor is NOT = NO TRANSCRIPTION

2nd copy of Gene X

NO TRANSCRIPTION, the trans-acting isn’t working so its just not gonna bind to anything

what are repressors?

a transcription factor that negatively regulates transcription by competing with RNA pol of other activators for binding to the promotor

inhibits transcription

what are Activators

a transcription factor that positively regulate transcription by recruiting or enhancing recruitment of the transcription machinery to the promotor

facilitates transcription

Can transcription factors act from long distances?

YES

can bind to both or distant regions from the promotors and help to recruit transcription machinery to promotors

what is DNA looping

the loop formed when a transcription factor bound to an enhancer binds to the promotor

what are architectural regulators?

they bind to DNA at their sites (architectural regulator binding sites) and alter the structure of DNA/chromatin ]

which indirectly facilitates transcription by making it easier for distant transcriptional activators to reach the promotor

what are Cofactors (coactivators and corepressors)?

are proteins that do not bind to DNA directly

BUT can facilitate interactions that activate or repress transcription

what are Insulators aka boundary elements?

are cis-elements that block activators and repressors from being able to affect transcription from one side of the insulator to the other

they can be associated with more than 1 gene

what are Effectors?

are small molecule (not a protein) that can bind to transcriptional regulators and effect their function

what kind of things can effectors do to regulators?

• effectors can help to repress transcription (inhibitor) or they can help to activate transcription (inducers)

• are sometimes metabolites (molecules involved in metabolic pathways) produced by the gene they regulate and can act in a positive or negative feedback loop

what is the lac operon?

it is the group of genes that help produce lactose

What are the proteins in the lac operon that encode proteins that metabolize lactose?

lacZ

lacY

lacA

relies on lacl and lacO

What are the regulators in the lac operon when its expressed?

lacl and lacO

important for repressing lac operon expression

what does lacl encode?

encodes protein called lac repressor

the product acts in Trans

what does lacO encode for?

encodes for a binding site for lac repressor (operator)

lac repressor bind to the operator sequence to block lac expression

lacO acts in cis

Can the lac operon sense when lactose is present?

YES

in absence of lactose the lac repressor is blocks transcription

in the presence of lactose the lac repressor is blocked → allowing transcription

what is an Inducer?

a type of effector

binds to the lac repressor, blocking its function and allowing lac expression

it induces the operon

the inducer is..?

is allolactose hw

what is Alloactose?

a byproduct of lactose metabolism by the lac operon

*does’t get produced if lacY or lac Z isn’t there

How are do lac repressors work?

• there are 3 repressor binding sites: O1, O2, and O3

• O1 is the original and is the only one required

• lac repressors binds to the O1 and either O2 or O3, making a loop

• that loop physically blocks RNA polymerase

what is Cyclic AMP (cAMP)?

• it is overproduced when glucose is absent but turned off when glucose is abundant

• reflects the level of glucose for cells

what does cAMP bind to activate transcription?

binds to a protein called cAMP responsive protein (CRP)

What scenario provides the highest level of gene expression in the lac operon?

when glucose is low, cAMP high and lactose is present

when glucose is low, cAMP-CMP bind to the lac promotor, if lactose is high then the lac repressor is unbound and high transcription

what is chromatin remodeling controlled by

controlled by at least 3 mechanisms:

1. Nucleosome repositioning of the DNA

2. Histone variants

3. histone modification

What is nucleosome repositioning of the DNA

it is when chromatin remodeling complexes shift the position of nucleosomes so that the promoter is no longer is wrapped around a nucleosome

What are Histone Variants?

can be inserted to subsitute for the main histone subunits, altering DNA binding ability

what is Histone modification?

are modified by activation or methylation, altering DNA accessibility

what is acetylation?

associated with increasing accessibility and activating transcription

what are HATs (histone actyltransferabes) and HDACs (histone deacetylases)

they regulate histone acetylation

what is methylation?

associated with silencing transcription

what are SWI/SNF

chromatin remodeling complex that can reposition nucleosomes to free up the promotor

they are recruited to specific regions by transcription activators, thus the transcription activators must bind to their DNA sequences first

what are siRNA

short interfering RNA

they sequence is in the reverse complement of transcript and will hybridize with it to form double stranded RNA

typically created as single-stranded or double stranded RNA

what are Anti-sense RNA

an RNA whose sequence is in the reverse complement of another RNA (sense RNA)

both of these RNA will hybridize to form double-stranded RNA

what are the 2 ways miRNAs silence genes?

1. perfect or near perfect complementarity

2. partial complementarity

what are shRNA?

short hairpin RNA, created by researchers

when placed into a DNA plasmid, will get transcribed and form a short hairpin, which then will be processed by the miRNA machinery