Gene Regulation Flashcards
Draw a gene with its main features
Promoter: a sequence that signals the start of transcription and recruits the RNA polymerase and other transcription factors2.
Exon: a coding region that is expressed or translated into amino acids5.
Intron: a non-coding region that is spliced out of the primary transcript.
Terminator: a sequence that signals the end of transcription and releases the RNA polymerase.
5’ UTR and 3’ UTR: untranslated regions at the ends of the mRNA that regulate translation, localization, and stability of the mRNA.
5’ cap and poly-A tail: modifications added to the ends of the mRNA that protect it from degradation and facilitate export and translation.
What are Exons and Introns? Describe their role in
Exons are the expressed or coding regions of a gene that are translated into amino acids5. Introns are the intervening or non-coding regions of a gene that are spliced out of the primary transcript6. Exons and introns play a role in:
Alternative splicing: a process that produces different mRNAs and proteins from the same pre-mRNA by selectively including or excluding different exons or introns7.
Regulation of gene expression: some introns contain cis-regulatory sequences that are recognized by transcription regulators or splicing factors that can enhance or repress transcription or splicing.
What are the main component of transcription activation?
Transcription activation is the process of initiating transcription of a gene by the RNA polymerase. The main components of transcription activation are:8
Transcription factors: proteins that bind to specific DNA sequences and recruit or activate the RNA polymerase and other transcription factors9.
Enhancers: cis-regulatory sequences that are located far from the promoter and can enhance transcription by looping the DNA and interacting with transcription factors and the mediator complex.
Mediator complex: a large protein complex that mediates the interaction between the RNA polymerase and the transcription factors and enhancers.
What is DNA methylation? How does it impact transcription?
DNA methylation is a covalent modification of the DNA that involves the addition of a methyl group (-CH3) to the 5’ carbon of cytosine residues, usually in CpG dinucleotides. DNA methylation impacts transcription by:
Repressing transcription: methylated CpGs are often associated with gene silencing, as they can inhibit the binding of transcription factors or recruit chromatin modifiers that compact the chromatin and prevent transcription.
Maintaining gene expression patterns: methylated CpGs can be inherited after cell division and preserve the gene expression state of the parent cell.
How is DNA methylation promoted?
DNA methylation is promoted by enzymes called DNA methyltransferases (DNMTs) that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to cytosine. There are two types of DNMTs:
De novo DNMTs: DNMT3A and DNMT3B, which add methyl groups to unmethylated DNA and establish new methylation patterns during development or differentiation10.
Maintenance DNMT: DNMT1, which copies the methylation pattern from the parent strand to the daughter strand after DNA replication and maintains the existing methylation state.
Describe a nucleosome and its modifications involved in transcription regulation
A nucleosome is the basic unit of chromatin, the complex of DNA and proteins that organizes and regulates the genome. A nucleosome consists of:1
Histones: proteins that have a positive charge and bind to the negatively charged DNA. There are four core histones: H2A, H2B, H3, and H4, which form an octamer that wraps around 147 bp of DNA11. There is also a linker histone: H1, which binds to the DNA between two nucleosomes and stabilizes the chromatin structure12.
Histone modifications: covalent modifications of the histone tails that affect the chromatin compaction and transcription. There are many types of histone modifications, such as methylation, acetylation, ubiquitination, and phosphorylation, that can have different effects depending on the histone and the amino acid residue modified. For example, methylation of H3K9 and H3K27 is associated with heterochromatin and transcription repression, while acetylation of H3K27 is associated with euchromatin and transcription activation.
Describe what is an enhancer
An enhancer is a cis-regulatory sequence that can enhance the transcription of a gene by looping the DNA and interacting with transcription factors and the mediator complex. An enhancer has the following characteristics:
Distance and orientation independent: an enhancer can be located upstream, downstream, or within a gene, and can act on the same or opposite strand of the DNA, as long as it can physically contact the promoter region.
Tissue and time specific: an enhancer can be activated or deactivated depending on the cell type, developmental stage, or environmental condition, by the binding of specific transcription factors or chromatin modifiers.
Combinatorial and cooperative: an enhancer can bind multiple transcription factors that work together to modulate the transcription rate of a gene.
What are repressor and activators of transcription?
Repressors and activators are transcription factors that bind to specific DNA sequences and regulate the transcription of a gene. Repressors and activators can control transcription by:134
Preventing or promoting the recruitment of RNA polymerase and other transcription factors: repressors can block the access of the RNA polymerase or other transcription factors to the promoter, while activators can recruit or stabilize the RNA polymerase or other transcription factors on the promoter2.
Preventing or promoting the recruitment of chromatin modifiers: repressors can recruit chromatin modifiers that compact the chromatin and inhibit transcription, while activators can recruit chromatin modifiers that open the chromatin and facilitate transcription.
Why there are so many regulators of transcription in the cell?
There are many regulators of transcription in the cell because:14
The genome is complex and diverse: the cell has to express different genes in different contexts, such as cell type, developmental stage, or environmental condition, and each gene has its own, often complex, collection of cis-regulatory sequences that require specific transcription regulators to recognize and activate or repress them15.
The transcription is dynamic and responsive: the cell has to adjust the transcription rate of genes in response to changes in condition or environment, such as stress, signaling, or nutrient availability, and this requires multiple transcription regulators that can sense and transduce these signals and modulate the transcription machinery accordingly.
What are the differences between heterochromatin and euchromatin?
Heterochromatin and euchromatin are two types of chromatin that differ in their compaction and transcriptional activity16. Heterochromatin is:17
Closed chromatin: it is tightly packed and inaccessible to the transcription machinery and other DNA-binding proteins.
Transcriptionally inactive: it contains mostly repetitive or silenced DNA sequences, such as centromeres, telomeres, or transposons, and few genes are expressed from it.
Marked by specific histone and DNA modifications: it is enriched in histone modifications that promote chromatin compaction and transcription repression, such as methylation of H3K9 and H3K27, and DNA methylation of CpG islands. Euchromatin is:3
Open chromatin: it is loosely packed and accessible to the transcription machinery and other DNA-binding proteins.
Transcriptionally active: it contains mostly gene-rich and regulatory DNA sequences, such as promoters, enhancers, or exons, and many genes are expressed from it.
Marked by specific histone and DNA modifications: it is enriched in histone modifications that promote chromatin opening and transcription activation, such as acetylation of H3K27, and DNA demethylation of CpG islands.
Describe the main steps of mRNA maturation
mRNA maturation is the process of modifying the primary transcript into a mature mRNA that can be exported and translated. The main steps of mRNA maturation are:18
5’ capping: the addition of a 7-methylguanosine cap to the 5’ end of the mRNA by a triphosphate linkage, which protects the mRNA from degradation and facilitates export and translation19.
Splicing: the removal of introns and the joining of exons by the spliceosome, a complex of small nuclear RNAs (snRNAs) and proteins, which produces different mRNAs and proteins by alternative splicing.
3’ polyadenylation: the cleavage of the mRNA by a ribonuclease after a AAUAAA sequence and the addition of a poly-A tail of 100-200 adenines by a poly-A polymerase, which protects the mRNA from degradation and facilitates export and translation.
What is alternative splicing? Draw an example
Alternative splicing is a process that produces different mRNAs and proteins from the same pre-mRNA by selectively including or excluding different exons or introns7. Alternative splicing can generate:
Exon skipping: the exclusion of one or more exons from the mRNA.
Mutually exclusive exons: the inclusion of only one of two or more alternative exons in the mRNA.
Alternative 5’ or 3’ splice sites: the use of different splice donor or acceptor sites within the same exon or intron in the mRNA.
Intron retention: the inclusion of one or more introns in the mRNA.
What is RNA decay?
RNA decay is the process of degrading the RNA molecules that are no longer needed or that are defective. RNA decay can occur in different ways, such as exonucleolytic decay from the 5’ or 3’ end, endonucleolytic cleavage in the middle, or decapping and deadenylation that remove the 5’ cap and the 3’ poly-A tail.
Describe at least 2 mechanism of translation regulation
Translation can be regulated at different levels, such as initiation, elongation, termination, and recycling. Some examples of translation regulation mechanisms are:
Cap-dependent initiation: the binding of the initiation factors and the small ribosomal subunit to the 5’ cap of the mRNA, and the scanning for the start codon. This process can be regulated by the availability of the initiation factors, the methylation of the cap, or the secondary structure of the mRNA.
IRES-dependent initiation: the binding of the initiation factors and the small ribosomal subunit to an internal ribosome entry site (IRES) in the mRNA, bypassing the need for the 5’ cap and the scanning. This process can be regulated by the structure of the IRES, the binding of IRES trans-acting factors (ITAFs), or the cellular stress conditions.
Which are the most important protein modification? How can they affect protein
functions?
Proteins can be modified after translation by the addition or removal of functional groups or proteins, or by the cleavage of peptide bonds. Some important protein modifications are:
Phosphorylation: the addition of a phosphate group to serine, threonine, or tyrosine residues, which can change the activity, localization, or interaction of the protein.
Ubiquitination: the addition of a ubiquitin protein to lysine residues, which can target the protein for degradation, alter its activity, or affect its interaction with other proteins.
Acetylation: the addition of an acetyl group to lysine residues, which can neutralize the positive charge of the lysine and affect the protein’s interaction with DNA or other proteins.
Methylation: the addition of a methyl group to lysine or arginine residues, which can affect the protein’s interaction with DNA or other proteins.
