Gene Regulation COPY Flashcards
What is the role of gene regulation in development?
In development, totipotent cells become pluripotent and then differentiate into unipotent cells.
How can specialized subtypes convert to another?
Specialized subtypes can convert to another by overexpressing transcription factors (TFs).
What errors can occur in gene regulation?
Errors in gene regulation can contribute to unregulated cell growth and division.
What is the overview of gene regulation in eukaryotes?
Regulating the synthesis of the primary transcript regulates everything downstream.
What are upstream regulators?
Upstream regulators modulate activity with enzymes, transcription factors, co-repressors, and co-activators.
Are transcription and translation coupled in eukaryotes?
Transcription and translation are not coupled in eukaryotes.
What is chromatin configuration?
Chromatin configuration refers to the structure of chromatin, including nucleosomes and modifications.
What is a nucleosome composed of?
A nucleosome is composed of a protein octamer (H2A, H2B, H3, H4) x2 and 146 bp of DNA.
What is euchromatin?
Euchromatin is loosely packed, allowing transcription factors to bind and transcription to be active.
What modifications occur in euchromatin?
Euchromatin features unmethylated cytosines and acetylated histones.
What is heterochromatin?
Heterochromatin is densely packed, preventing transcription factors from binding or initiating transcription.
What modifications occur in heterochromatin?
Heterochromatin contains methylated cytosines.
What are CpG islands?
CpG islands are regions in the promoter where methylation occurs, affecting gene expression.
What do DNA methyltransferases (DNMT) do?
DNMTs convert hemi-methylated DNA to fully methylated DNA, allowing the inheritability of the methylation pattern.
What are the mechanisms of DNA methylation?
Mechanisms include blocking transcription factor binding, recruiting other enzymes, and inducing mutations.
What is the role of MBD proteins?
MBD proteins are recruited to interact with histone deacetylases (HDAC) to alter chromatin structure.
What is the function of HDAC?
HDAC removes acetyl groups from histones, leading to deacetylation.
What are epigenetic modifications?
Epigenetic modifications alter chromatin state via DNA methylation and histone modifications.
What is a promoter?
A promoter is located immediately upstream of the 5’ end of a gene.
What is the TATA box?
The TATA box is a site for binding TATA-binding protein (TBP), initiating transcription.
What are promoter-proximal elements?
Promoter-proximal elements are within 200 bp of a gene and bind specific transcription factors.
What are enhancers and silencers?
Enhancers and silencers are distal regulatory regions that may be on different chromosomes.
What do general transcription factors do?
General transcription factors form a pre-initiation complex by binding to the promoter.
What is RNA polymerase II responsible for?
RNA polymerase II transcribes mRNA, miRNA, and snRNAs.
What is the function of miRNAs?
miRNAs regulate gene expression by repressing genes post-transcription.
What is the role of snRNAs?
snRNAs are involved in splicing mRNA via spliceosomes.
What does 5’ capping do?
5’ capping adds a guanosine triphosphate cap to pre-mRNA, protecting it from degradation.
What is polyadenylation?
Polyadenylation adds a poly-A tail to the 3’ end of mRNA, signaling the end of transcription.
What is RNA splicing?
RNA splicing involves spliceosomes removing introns and splicing together exons.
What is constitutive splicing?
Constitutive splicing generates a single isoform of mRNA.
What is alternative splicing?
Alternative splicing enables multiple isoforms from a single gene by rearranging exons.
What are hormone response elements (HRE)?
HREs are sites where hormones bind to nuclear receptors that then bind to DNA.
What is the function of AP-1?
AP-1 is regulated by growth factors, stress, and transmembrane signals.
What does CRE stand for?
CRE stands for cyclic AMP response element, which is regulated by cAMP and Ca.
What is the role of SP-1?
SP-1 regulates basal unregulated transcriptional activity.
What is the Ets family of transcription factors?
The Ets family regulates cellular proliferation, differentiation, and apoptosis.
What does NF-kB mediate?
NF-kB mediates inflammatory and immune responses and regulates cell survival.
What is the function of E2F?
E2F regulates genes in cell cycle progression, especially from G1 to S phase.
What are DNA binding domains?
DNA binding domains are regions in transcription factors that interact with specific DNA sequences.
What is a helix-turn-helix motif?
A helix-turn-helix motif consists of an alpha helix, a beta turn, and another alpha helix.
What is a zinc finger?
A zinc finger is a structural motif that coordinates a zinc ion with cysteine and histidine residues.
What is a leucine zipper?
A leucine zipper is formed by interdigitating alpha-helices that promote protein dimerization.
What is the transactivation domain?
The transactivation domain is a binding site for co-activators or co-repressors.
What is chromatin remodeling?
Chromatin remodeling involves recruiting chromatin-modifying enzymes to alter chromatin structure.
What is transcriptional repression?
Transcriptional repression blocks access to promoters and enhancers.
What is the decoy function of some transcription factors?
The decoy function prevents other transcription factors from binding to DNA.
What is the role of dimerization domains?
Dimerization domains allow transcription factors to form heterodimers that modulate transcription.
What is autoregulation in transcription factors?
Autoregulation occurs when a transcription factor binds to its own promoter.
What are AU-rich elements (AREs)?
AREs in the 3’ UTR of mRNA cause de-adenylation and degradation of the mRNA.
How does phosphorylation affect transcription factors?
Phosphorylation can activate or deactivate transcription factors.
What are early events in metastasis related to transcription factors?
Early events include cell fate misregulation, inflammation, and response to hypoxic conditions.
What is the role of Oct-4?
Oct-4 is expressed in pluripotent cells and regulates differentiation.
What do Sox2 and NANOG do?
Sox2 and NANOG interact with Oct-4 to regulate embryonic stem cell differentiation.
What are enhancer transcripts (eRNAs)?
eRNAs facilitate transcription factor binding to enhancers and core promoter regions.
What is the process of miRNA maturation?
miRNAs are processed in the nucleus, exported to the cytoplasm, and then bind to RISC.
What are long non-coding RNAs (lncRNAs)?
lncRNAs are greater than 200 nucleotides long and lack an open reading frame.
