Exam 4: Eukaryotic Gene Regulation Flashcards
Describe how eukaryotic DNA structure influences transcription
-Chromatin prevents transcription factors from interacting with DNA.
-Histone modification: Post-translational modifications, such as acetylation, methylation, and phosphorylation can occur on histones. Acetylation is associated with gene activation.
-DNA methylation: DNA methylation involves the addition of methyl groups to cytosine bases in the DNA sequence. Methylation is often associated with gene repression.
-Promoters
-Enhancers and silencers
Compare and contrast focused and dispersed promoters.
Great diversity exits in eukaryotic promoters, in structure and function
Focused promoters:
-Specific transcription initiation at start site
-Major type of initiation for lower eukaryotes
Dispersed promoters:
-2/3 of vertebrate promoters direct initiation from several weak transcriptional start sites
DIFFERENCES:
-Focused promoters have a more precise initiation site, leading to a more defined and uniform transcription start. Dispersed promoters exhibit a less defined initiation site, resulting in a more heterogeneous population of transcripts.
-Focused promoters often contain well-defined consensus sequences like the TATA box.
Briefly describe basic eukaryotic promoter structure including core and proximal promoter elements.
CORE PROMOTER STRUCTURE
-Initiator: encompasses the transcription start site
-TATA box
-TFIIB recognition element: immediately up- or downstream of TATA box
-Downstream promoter element
-Motif ten element (downstream element)
PROXIMAL PROMOTER STRUCTURE
-Promoters contain proximal-promoter elements
–Located upstream of TATA and BRE motifs
–Enhance levels of basal transcription
–Examples: CAAT and GC boxes
Compare and contrast enhancers, silencers, and insulators.
Cis-acting transcription regulatory elements
Enhancers:
-Located on either side of gene, some distance from gene, or even within gene
–Important in reaching maximum level of transcription
Silencers:
-Repress the level of transcription initiation
Insulator:
-DNA sequence that blocks or insulates the effect of enhancers in a position dependent manner
Describe the functional domains of transcription factors (ie proteins).
Transcription factors (proteins)
Have two functional domains (clusters of amino acids with a specific function):
– DNA-binding domain
Binds to specific DNA sequences in the cis-acting regulatory site
–Trans-activating domain
Activates or represses transcription by binding to other transcription factors or RNA polymerase
Briefly explain the role of pre-initiation complex formation.
-Required at promoter to initiate
basal or enhanced transcription
–Specific assembly of proteins forms
the pre-initiation complex (PIC)
TBP: TATA binding protein
TAF: TBP Associated Factors
Med: Mediator complex
-PIC provides platform for RNAP II
to recognize transcription start sites
Describe various types of post-transcriptional gene regulation.
–Control of alternative splicing
–Control of mRNA stability (5’ methyl capping and poly-A tail)
–Translation rate
–RNA silencing
Related alternative splicing to differences in genome and proteome size.
-Alternative splicing generates different forms of mature mRNA from identical pre-mRNA (increases number of proteins)
–Expression of one gene gives rise to numerous proteins with similar and different functions
-Crucial mechanism that contributes to the diversity of the proteome in eukaryotes. It allows for the production of multiple protein isoforms from a single gene, providing organisms with a means to increase functional complexity and adaptability without a proportional increase in genome size.
Describe the process of RNA-induced gene silencing and list the ways gene expression can be effected.
RNA interference (RNAi)
–Short, d-s RNA molecules regulate gene expression in the cytoplasm: repress translation, trigger mRNA degradation
-Phenomena known as RNA-induced gene silencing
siRNAs: Arise in cell due to virus infection, produce double-stranded RNA, which is recognized and cleaved by Dicer
–microRNAs: Noncoding RNAs that negatively regulate gene expression
Double-stranded RNA (dsRNA) is typically the trigger for RNA-induced gene silencing. This dsRNA can originate from various sources, including viruses, transposons, or artificially introduced dsRNA.
The dsRNA is processed into small RNA molecules, usually 21-25 nucleotides in length. This processing is catalyzed by an enzyme called Dicer.
The small RNA molecules are incorporated into an effector complex called the RNA-Induced Silencing Complex (RISC) or RITS.
Depending on the degree of complementarity between the small RNA and the target mRNA, gene silencing can occur through different mechanisms:
mRNA Cleavage: If there is near-perfect complementarity, the RISC complex can cleave the target mRNA, leading to its degradation.
Translation Inhibition: If complementarity is partial, the RISC complex can inhibit translation without causing mRNA degradation.
Explain some ways eukaryotic gene regulation is more complex than that in prokaryotes
-Eukaryotic DNA is organized into chromatin, which regulates gene accessibility.
-Post-translational modifications of histones and DNA methylation contribute to the control of gene expression.
-Introns and exons allow for alternative splicing
Two structural features of eukaryotes distinguish them from prokaryotes
1) Eukaryotic genes are situated on chromosomes within the nucleus
2) Eukaryotic DNA is combined with histones to form chromatin. This inhibits transcription.
Chromosome Territory
During interphase, each chromosome occupies a discrete domain and stays separate from other chromosomes
Interchromosomal domains:
Channels between chromosomes that contain little or no DNA
DNA Methylation
-Associated with decreased gene expression
-Cytosines are the typical nitrogenous base that gets methylated
-Methylation can repress transcription by inhibiting the binding of transcription factors to DNA
CpG Methylation:
-CpG islands are the regions that can get methylated (Chargaff’s Rule: C on both)
-Occurs on opposite strands
–Semi-conservative replication leads to a methylation mark on each
template.
–Methytransferases can
then perform “maintenance methylation” of the hemimethylated dsDNA
-Transmitted generally just within the cells of the organism
Promoters
-Nucleotide sequences that serve as recognition sites for transcription machinery
–Located immediately adjacent to regulatory genes
–Critical for transcription initiation
–Core promoter: Determines accurate initiation of transcription
– Proximal-promoter elements: Modulate efficiency of basal levels of transcription
Cis-acting sequence elements
Located on same chromosome as the gene that it regulates
Required for accurate regulated transcription of genes
-Promoters
-Enhancers
-Silencers
-Insulators
