CPPS403 - GeneRegulation II - 2 Flashcards
(18 cards)
What influences gene expression?
Chromatin organization
Chromatin organization affects the accessibility of DNA for transcription.
What are the mechanisms that regulate chromatin accessibility and gene expression?
Epigenetic mechanisms
These include DNA methylation, histone modifications, and nucleosome occupancy.
How do transcription factors regulate downstream genes?
By binding to specific DNA sequences
Transcription factors often bind to transcription factor binding sites (TFBSs).
What is the role of pioneer transcription factors?
They initiate decompaction of heterochromatin
Pioneer transcription factors can bind to nucleosomes and recruit chromatin remodellers.
What is chromatin accessibility?
The degree to which nuclear proteins can contact DNA
It is determined by factors like nucleosome occupancy and histone modifications.
What is epigenetics?
Mechanisms affecting gene expression without changing the DNA sequence
Epigenetic changes are reversible and dynamically regulated.
What are post-translational modifications (PTMs) in histones?
Chemical modifications on histone tails
PTMs include methylation, acetylation, ubiquitination, and phosphorylation.
What is the function of histone methyltransferases?
To add methyl groups to histone lysine residues
They use S-adenosine methionine (SAM) as a substrate.
What does histone acetylation generally indicate?
Active gene expression
Acetylation is enriched at enhancer elements and promoter regions.
What are the two main mechanisms of histone modification?
Modifies chromatin structure and regulates binding of effector molecules
Effectors include chromatin modifying proteins and chromatin remodellers.
What is the role of HDACs in gene regulation?
Repress gene transcription by maintaining histone acetylation
HDAC inhibition can be cardioprotective in disease models.
How do transcription factors bind DNA?
By recognizing short stretches of DNA called transcription factor binding sites (TFBSs)
TFBSs are found in promoters and enhancers.
What is the effect of DNA methylation on transcription factors?
It can repress transcription by blocking binding
Methylated CpGs are usually associated with transcriptional repression.
What are pioneer transcription factors (PFs)?
Transcription factors that can bind to nucleosomes and initiate chromatin decompaction
PFs play a role in establishing cell fates and lineages.
What is ATAC sequencing used for?
To identify accessible chromatin regions
It uses Tn5 transposase to cut accessible DNA and insert sequencing primers.
What does ChIP-sequencing involve?
Cross-linking proteins with DNA and sequencing bound fragments
It allows for mapping where transcription factors or histone modifications are located.
What is the significance of H3K4me?
Associated with gene activation
Found at transcription start sites, promoters, and enhancers.
What is the impact of methylation on transcriptional activity?
Can be associated with both gene silencing and activation
It depends on the specific residue and type of methylation.
