RR6-8 (this one is good)

A multi-protein complex that plays a crucial role in eukaryotic transcription by facilitating the interaction between transcription factors, enhancers, and RNA polymerase II.

Mediator's ability to interact with activation domains and bring together different components of the transcription machinery, allowing for the formation of the pre-initiation complex.

The Mediator's ability to bring together different components of the transcription machinery facilitates interactions between different DNA regions, leading to the formation of chromatin loops.

A technique used to study actively transcribed RNA molecules in living cells by incorporating a reporter sequence into the 5' region of a gene of interest.

Transcription of highly transcribed genes often occurs in bursts, with periods of active transcription followed by periods of inactivity.

A model of gene expression that suggests that transcription occurs in bursts, with periods of high activity followed by periods of inactivity.

A model of gene expression that suggests that transcription occurs at a constant, steady rate.

A protein complex that forms in eukaryotic cells and plays a role in gene regulation.

A model of gene regulation that suggests that enhancers interact with promoters dynamically, like two objects kissing.

The complex of DNA and proteins that make up chromosomes in eukaryotic cells.

The tightly packed form of chromatin that is generally transcriptionally inactive.

The loosely packed form of chromatin that is generally transcriptionally active.

A type of gene silencing that is mediated by chromatin modifications.

A modification of histones that involves the removal of acetyl groups from lysine residues.

Stable heritable changes in gene expression that are not encoded by alterations in DNA sequence.

A 5' methylguanalate cap is added to the nascent mRNA as it emerges from the RNA exit channel and reaches a length of 25 nucleotides. This process is catalyzed by a dimeric capping enzyme that interacts with the CTD domain of RNA Pol II. The cap is added concurrently with elongation, facilitated by the exchange of the NELF complex for the PAF elongation complex in association with RNA Pol II.

The CTD (C-terminal domain) of RNA polymerase II (Pol II) is a protein tail with repeated amino acid sequences. Its length allows multiple proteins to bind simultaneously, providing a platform for coordinating various RNA processing events. Enzymes involved in adding the 5' cap, splicing, and polyadenylation associate with the phosphorylated CTD (pCTD).

hnRNPs (heterogeneous ribonucleoprotein particles) are nuclear proteins that bind to mRNAs from their emergence from RNA Pol II until their translocation to the cytoplasm. These proteins contain RNA-binding domains that allow them to associate with mRNAs and play roles in pre-mRNA splicing, mRNA transport out of the nucleus, and other processes.

Introns are non-coding sequences within a gene that are removed from the pre-mRNA during splicing. This process ensures that only exons, the coding sequences, are present in the mature mRNA. Intron removal and exon splicing occur after 3' cleavage and polyadenylation for shorter transcripts. In longer transcripts, splicing can begin before transcription is complete.

The spliceosome is a complex molecular machine responsible for removing introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) - U1, U2, U4, U5, and U6 - that transiently associate with each other and the splice sites on the pre-mRNA to form an active spliceosome (U2/U5/U6). The snRNA U1 interacts with the intron splice site border, while U2 binds to the branch point region, a motif essential for splicing.

Splicing involves two key transesterification reactions. First, the hydroxyl (OH) group at the branch point within the intron attacks the 5' phosphate at the first intron residue, forming a lariat structure, a lasso-shaped loop. Second, the 3' end of the upstream exon attacks the 5' end of the downstream exon, joining the exons together and releasing the intron lariat.

The splicing cycle involves a series of steps: 1) U1 and U2 snRNAs bind to the pre-mRNA. 2) U4, U5, and U6 snRNAs are recruited. 3) U1 and U4 are released, forming the active spliceosome. 4) The intron is removed, and exons are joined through transesterification reactions. 5) The released lariat is degraded. 6) The mature mRNA is ready for export to the cytoplasm for translation.

The spliceosome is a dynamic complex that changes its composition during the splicing cycle. It is essential for accurate intron removal and exon joining, ensuring the production of functional mature mRNAs. Defects in splicing can lead to various genetic disorders.

A DNA region that binds to proteins like RAP1 and SIR1, preventing gene expression in that area.

A protein that binds to the silencer region and plays a role in silencing genes.

A protein that works with RAP1 to secure the silencer region and keep genes silent.

A group of proteins involved in silencing genes by binding to hypoacetylated histone tails and recruiting SIR2.

A process where proteins bind to specific DNA regions, altering the structure of chromatin and silencing genes.

A complex of RNA and proteins that removes introns from pre-mRNA, ensuring the production of functional mRNA molecules.

Small nuclear ribonucleoproteins (snRNPs) are crucial components of the spliceosome complex. They bind to the pre-mRNA and facilitate the splicing process.

The process where introns are removed from pre-mRNA and exons are joined together, producing a mature mRNA ready for translation.

A specific configuration of the spliceosome that is formed during the splicing process, marked by the presence of particular snRNPs.

Chemical reactions that occur during splicing, involving the breaking and formation of bonds in the RNA molecule, leading to intron removal and exon joining.

The spliceosome is a complex molecular machine made up of five small nuclear RNAs (snRNAs) - U1, U2, U4, U5, and U6. These snRNAs work together to remove introns from pre-mRNA, ensuring correct gene expression.

U1 snRNA binds to the intron splice site border, while U2 snRNA interacts with the branch point region, a crucial sequence for splicing.

The first step involves the hydroxyl group (OH) on the branch point attacking the 5' phosphate of the first intron residue, forming a lariat structure. The second step involves the 3' end of the upstream exon attacking the 5' end of the downstream exon, effectively joining the exons together and releasing the lariat.

The spliceosome undergoes a series of steps, including binding of U1 and U2 snRNAs to the pre-mRNA, recruitment of additional snRNAs (U4, U5, and U6), formation of the active spliceosome, intron removal, exon joining, lariat degradation, and finally, mature mRNA export to the cytoplasm.

A specific region on yeast Chromosome III containing genes that determine mating type, where one of the three loci, MAT, is actively transcribed while the other two (HML and HMR) are transcriptionally silent.

The central mating type locus (MAT) on yeast Chromosome III is responsible for determining the mating type of the yeast cell.

The HML and HMR loci on yeast Chromosome III are silent versions of MAT genes, located near the telomeres of the chromosome.

A process where genetic information from the silent HMR or HML loci is transferred to the MAT locus, changing the mating type of the yeast cell.

A mechanism that prevents gene expression in specific DNA regions, often involving proteins binding to silencers and modifying chromatin structure.

A technique used to identify DNA regions bound to specific proteins, involving crosslinking, chromatin isolation, antibody addition, immunoprecipitation, DNA release, and analysis using either PCR or NGS.

The reversible binding of proteins to chromatin using chemicals, allowing the isolation of these interactions.

The process of isolating and breaking down chromatin into smaller fragments, allowing for better accessibility to the antibody.

Specific proteins are added to bind to the protein of interest, allowing for the isolation of the protein-DNA complexes.

The process of separating the antibody-protein-DNA complexes from the rest of the solution, enriching for the target protein.

RNA polymerase II has a C-terminal domain (CTD) with repeating amino acid sequences. The CTD is phosphorylated at specific serine residues, allowing different proteins to bind at different stages, facilitating mRNA processing.

The length of the CTD allows multiple proteins to bind to RNA polymerase II simultaneously. This creates a docking site for various enzymes involved in mRNA processing, such as those responsible for capping, polyadenylation, and splicing.

The CTD acts as a platform for recruiting different proteins, such as splicing factors and polyadenylation factors, to the pre-mRNA. This coordinated recruitment enables efficient mRNA processing.

Serine 2 phosphorylation of the CTD allows the recruitment of additional proteins involved in mRNA processing, including splicing factors, polyadenylation factors, and export factors. It acts like a signal indicating the proper time and place for these events.

The diagram emphasizes the sequential steps and associated proteins involved in CTD phosphorylation. It illustrates how different components work together, highlighting interactions between Pol II and various proteins at different stages of transcription.

The 5' cap is added by a dimeric capping enzyme that interacts with the CTD domain of RNA polymerase II (RNA Pol II).

The 5' cap protects the mRNA from degradation by nucleases, which are enzymes that break down nucleic acids.

The 5' cap is recognized by translation initiation factors, which are proteins that help ribosomes bind to mRNA and begin translation.

The 5' cap facilitates the export of mRNA from the nucleus to the cytoplasm, where protein synthesis takes place.

Acetylation of histone tails neutralizes their positive charge, weakening their interaction with negatively charged DNA and loosening DNA packaging. This allows for easier access of transcription factors and other regulatory proteins to the DNA, often promoting gene expression.

Deacetylation removes acetyl groups from histone tails, restoring their positive charge and strengthening their interaction with DNA. This leads to tighter packaging of DNA, restricting access for transcription factors and often resulting in gene silencing.

Proteins called histone acetyltransferases (HATs) add acetyl groups to histone tails, promoting open chromatin structure and enabling gene expression.

Proteins known as histone deacetylases (HDACs) remove acetyl groups from histone tails, leading to a closed chromatin configuration and silencing of genes.

Transcriptional activators (proteins) recruit HATs to specific DNA regions, leading to histone acetylation and increased accessibility for transcription factors, promoting gene expression. Repressors recruit HDACs to specific DNA regions, causing deacetylation, tightening chromatin structure and repressing gene expression.