B2.080 Basic Mechanisms of Gene Transcription in Humans

Question 1

what are the 4 eurkaryotic RNA polymerases?

Answer 1

I: rRNA
II: mRNA, miRNA
III: tRNA, rRNA, snRNA
mitochondrial: mitochondrial genome

Question 2

what are the 3 classes of DNA regulatory elements?

Answer 2

promoters
enhancers
silencers

Question 3

describe promoters

Answer 3

required for ANY transcription
bound by GTFs and RNA polymerase II
defines transcriptional start site

Question 4

describe the nature of enhancers and silencers

Answer 4

specific, conserved nucleotide sequence
regulatory elements can be: near, far, upstream downstream; within introns
each binds different transcription factors
transcription factors alter activity of associated promoters

Question 5

what are the 2 stages of transcriptional regulation?

Answer 5

access to info in DNA

recruitment of necessary factors (for facilitating access or enzymatic activities)

Question 6

how are enhancers accessed by factors?

Answer 6

TFs can bind to DNA within chromatin
OR
enhancers are marked w histone modifications reducing nucleosome occupancy

Question 7

once bound to an enhancer, what do TFs recruit?

Answer 7

enzymes that open chromatin
histone acetyltransferases (HATs)
chromatin remodeling complexes (CRC)

Question 8

what are the 3 ways that TFs bound to the enhancer interact w the promoter?

Answer 8

1. HATS and CRCs fold over and remodel chromatin
2. enhancer TFs recruit GTFs to promoter
3. enhancer TFs recruit kinase complex PtefB to phosphorylate RNA polymerase II (activate)

Question 9

what is an example of a co-repressor?

Answer 9

HDACs

Question 10

what are HATs CRCS and PtefB classified as?

Answer 10

co-activators

Question 11

how many co-activators/repressors exist?

Answer 11

> 100, some ubiquitous, some tissue specific

Question 12

how do silencers work?

Answer 12

bind TFs that recruit histone deacetylases (HDACs) and prevent recruitment of GTP to promoter

Question 13

how can silencers lead to “permanent” transcriptional silencing?

Answer 13

recruit DNA methyltransferases that methylate cytosines into CpG pairs
chromatin packed into heterochromatin