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Questions and Answers
Which of the following levels of gene expression regulation involves changes to chromatin structure?
What is the primary role of DNA methylation in gene expression?
Which of the following best describes the process of X-inactivation?
What role do chromatin binding proteins play in transcription?
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How does the epigenetic profile affect transcriptional regulation?
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What is a characteristic of CpG islands related to gene regulation?
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What is a feature of transcription regulation at the post-transcriptional level?
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What impact do non-coding RNAs have on gene expression?
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What role does X inactivation specific transcript (XIST) play in gene regulation?
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Which mechanism is primarily responsible for transcriptional regulation at mammalian gene promoters?
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What is a characteristic of enhancers in gene expression?
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How do transcription factors interact with the transcription process?
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What is the significance of alternative promoters in mammalian genes?
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What is the role of p-TEFb in transcription elongation?
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How do non-coding RNAs (ncRNAs) influence transcription?
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What is one of the key features of Waddington’s epigenetic landscape?
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What condition is caused by mutations in the regulatory open reading frame upstream of the primary ORF in the TPO gene?
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How does the pRNA contribute to the silencing of rDNA loci?
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What type of genetic change results in atrichia with papular lesions?
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What is the role of PAPAS in rDNA silencing?
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Which of the following is NOT involved in the transcriptional regulation of gene expression in eukaryotes?
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Which type of RNA is primarily involved in the control of rRNA gene expression?
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What is one function of transcriptional corepressors mentioned in the context of TPO gene regulation?
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What is a common result of transcriptional regulation through non-coding RNAs?
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How does the antisense transcript ANRIL affect the CDKN2B–CDKN2A locus?
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Which of the following describes the function of HOX transcript antisense RNA (HOTAIR)?
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What role do splicing enhancers and suppressors play in alternative splicing?
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Which statement about the IRP/IRE system is correct?
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What is the impact of RNA-binding regulatory proteins on mRNA structure?
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Which mechanism is utilized by ncRNAs such as miRNAs to regulate gene expression?
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What kind of modifications can antisense transcripts make to their associated sense promoters?
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What effect do poison exons have in alternative splicing?
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Study Notes
Genome and Chromatin Structure
- Transcription takes place in euchromatic DNA.
- CTCF protein defines the boundaries between euchromatic and heterochromatic regions.
- Chromosome territories are positioned within the nucleus, with those closer to the nuclear envelope being silenced.
- Topologically associating domains (TADs) are distinct in different cell types, with different profiles of active and inactive TADs.
- Non-coding RNAs (ncRNAs) can bind to DNA and proteins that bind to DNA or RNA, impacting chromatin structure.
- ncRNAs can recruit chromatin remodeling complexes, which alter chromatin structure.
Epigenetic profile and imprinting
- Epigenetic mechanisms, including histone modifications, nucleosome positioning, and DNA methylation, play a role in gene expression.
- The epigenetic profile is linked to chromatin structure, with chemical modifications of histones creating various chromatin states with different transcriptional activity levels.
- Chromatin-binding proteins recognize epigenetic marks and contribute to establishing open or closed chromatin.
DNA Methylation
- DNA methylation (addition of methyl groups to cytosine bases in CpG dinucleotides) is associated with transcriptional repression.
- Methylated DNA cannot be bound by transcription factors.
- Specific proteins bind to methylated DNA, influencing chromatin organization and epigenetic maintenance.
- Epigenetic memory is transmitted through mitosis due to the action of DNA methyltransferase 1 (DNMT1).
- CpG islands in gene-rich areas remain unmethylated.
- During gametogenesis, the epigenome is reset to a totipotent state.
Imprinting
- Around 150 genes in humans exhibit imprinting, meaning they are differentially expressed depending on whether they are inherited from the mother or father.
- A common mechanism is methylation of the maternal differentially methylated region (DMR).
X-Inactivation
- During early embryogenesis, one of the X chromosomes in females undergoes X-inactivation, a process involving epigenetic modification.
- Random X inactivation occurs in the blastula stage to ensure balanced expression of X-linked genes.
- Epigenetic marks established during X inactivation persist through mitosis, contributing to the phenomenon of epigenetic memory.
- The X inactivation center (XIC) is a 1 Mb region on the X chromosome, containing a 19 kb non-coding RNA called X inactivation specific transcript (XIST) that plays a key role in X inactivation.
Transcriptional Regulation
- Promoters are often devoid of nucleosomes to enable the assembly of the pre-initiation complex (PIC).
- Chromatin remodeling complexes reposition nucleosomes, making promoters accessible to transcription machinery.
- Many mammalian genes have alternate promoters, contributing to the diversity of gene expression.
- Enhancers, often cell- and tissue-specific regulatory elements, can interact with promoters, contributing to precise gene control.
- DNA looping, facilitated by cohesin and mediator proteins, is essential for enhancer-promoter interactions.
- TAD structure can influence interactions between regulatory elements.
- A vast number of transcription factors (general and tissue-specific) contribute to development, cell identity, and gene expression.
- As cells differentiate, they exhibit increased epigenetic restriction.
Transcriptional Elongation
- Transcription factors can bind to promoters, but elongation may not proceed.
- TFIIH facilitates the access of DNA polymerase to the promoter.
- Phosphorylation of DNA polymerase by p-TEFb is required for efficient transcription elongation beyond abortive transcription.
Transcription Termination
- The polyadenylation signal (PAS) marks the termination site for RNA polymerase II.
- Many mammalian genes utilize alternative cleavage and polyadenylation sites.
Non-coding RNAs (ncRNAs) in Transcriptional Regulation
- Antisense and bidirectional transcription of ncRNAs can interfere with sense transcription, affect DNA methylation, modify the histone code, or induce heterochromatic states.
- ncRNAs also participate in the silencing of transposons.
Post-Transcriptional Regulation
- Alternative splicing: Enhancer and suppressor sequences modulate the strength of splice sites, leading to tissue-specific isoforms.
- RNA turnover: The degradation of mRNA can be influenced by various factors, impacting gene expression levels.
- RNA editing: Modifications to the RNA sequence, such as base substitutions or insertions, can alter the final protein product.
Regulation of Translation
- Leader peptides: Upstream open reading frames (uORFs) found in about one-third of human transcripts can influence translation initiation at the main ORF.
- mRNA structure: Stem-loop structures in mRNA can affect ribosome movement and contribute to translational regulation.
- RNA-binding proteins: These proteins can bind to mRNA and regulate translation initiation or elongation rates.
ncRNAs in Translational Regulation
- miRNAs, siRNAs, and piRNAs can repress the expression of target mRNAs.
- miRNAs can specifically bind to the 3’ UTR of target mRNAs, modulating their translation efficiency.
- Competition for binding sites on target mRNAs between different miRNAs creates a complex regulatory network of subtle effects.
Cellular Iron Homeostasis
- The iron responsive element (IRE)/iron regulatory protein (IRP) system plays a critical role in regulating cellular iron levels.
- IRP1 and IRP2 proteins bind to IREs in the 5' UTR or 3' UTR of mRNAs, influencing their translation and stability.
- In iron-deficient cells, IRPs bind to IREs in the 5' UTR, repressing translation.
- In the same scenario, binding to IREs in the 3' UTR stabilizes the mRNA.
- When iron levels are high, IRP binding is disrupted, leading to increased translation and mRNA degradation.
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Description
Test your knowledge on genome and chromatin structure, focusing on transcription, boundary definition by CTCF protein, and the impact of non-coding RNAs on chromatin. Explore the concepts of epigenetic profiles and imprinting, along with histone modifications and their role in gene expression.
