Lecture 19: Molecular Regulation

Question 1

Transcription Factor Target Finding

Answer 1

Rely on diffusion 3D and 1D
-binds to DNA in a non-specific transient way and then slides along the DNA to be able to find their recognition sequence

Question 2

HaloTag

Answer 2

Forms covalent bond with ligand and can be tracked by its ligand fusion with fluorescent dye

Question 3

Increase probability of TF to find their target

Answer 3

compartmentalization

Question 4

TF localization

Answer 4

Often localize within the nucleus forming puncta and contains hundreds and thousands of copies of the transcription proteins

Question 5

IDRs

Answer 5

Present in some transcription factors to product puncta
-IDR IDR interaction can occur
-Protein in IDR do not have a secondary structure

Question 6

liquid-liquid phase separation

Answer 6

The formation of the IDR regions in the cytoplasm

Question 7

Liquid-Liquid Phase Sep Examples

Answer 7

C. elegans P granulees

Question 8

Components of Transcription condensates

Answer 8

Transcription Factors
Polymerases
Cofactor

Question 9

Super Enhancers

Answer 9

Multiple enhancers clustered over a region of 10+kb

Question 10

Localization of RNA

Answer 10

MS2 binds MCP and can be fluoresced if MCP is fused as a fluorescent GFP protein
-Multiple copies integrated

Question 11

smFISH

Answer 11

alternative to MS2 for RNA localization
-Fixation step required so the cells are dead
-Fluorescently labelled DNA probes

Question 12

Transcription occurence

Answer 12

Transcription occurs in burst and increased transcription means that there is a increased frequency of the bursts (not size)