Notes in i. Transcription and its Regulation

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Published	07/28/2024	The {{c1::HOX}} gene is a series of genes that when expressed define developmental patterns along the anteroposterior axis. The encoded {{c2…
Published	07/28/2024	The {{c1::Sonic hedgehog Shh}} is a secreted protein molecule that diffuses to form a concentration gradient starting at the {{c2::zone of p…
Published	07/28/2024	Synpolydactyly (SPD) is a disorder with an {{c1::autosomal dominant}} inheritance pattern.
Published	07/28/2024	Explain the cause of synpolydactyly
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Published	07/28/2024	PIC stands for {{c1::Pre-Initiation Complex}}
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Published	07/28/2024	An activator protein has 2 domains:
Published	07/28/2024	What is Chromatin Immunoprecipitation (ChIP) used for?
Published	07/28/2024	CRE stands for the {{c1::Cyclic-AMP Response Element}}
Published	07/28/2024	The {{c1::CRE}} is a cis-element, (a DNA sequence that regulates the transcription of a neighboring gene) that is located near many promoters for…
Published	07/28/2024	CREB stands for {{c1::Cyclic AMP Response Element-Binding protein}}
Published	07/28/2024	{{c1::CREB}} is a transcription factor that binds to the CRE cis element
Published	07/28/2024	CBP stands for {{c1::CREB bind protein}}
Published	07/28/2024	{{c1::CBP}} is a co-activator and histone acetylation writer that does not bind DNA but binds CREB when CREB is phosphorylated and increases transcrip…
Published	07/28/2024	A {{c1::mediator}} is a key protein connectivity complex that allows for many different transcription factors to communicate with the polymerase
Published	07/28/2024	By what 3 mechanisms can a repressor work?
Published	07/28/2024	{{c1::Co-activators/repressors}} do not themselves bind directly to DNA, but function to regulate transcription of genes via binding to the general tr…
Published	07/28/2024	For CBP to bind CREB, CREB must first be {{c1::phosphorylated}}
Published	07/28/2024	{{c1::Focused}} transcription initiation typically is regulated by a {{c2::TATA box}} in the promoter region
Published	07/28/2024	{{c1::Dispersed}} transcription initiation typically is regulated by {{c2::CpG islands}} in the promoter regions
Published	07/28/2024	Focused transcription is more commonly used for?
Published	07/28/2024	Dispersed transcription initiation is typically used for?
Published	07/28/2024	The histone octamer is typically composed of pairs of the following 4 subunits:
Published	07/28/2024	The acetylation of histone tails is associated with {{c1::active}} genes
Published	07/28/2024	HATs stands for {{c1::Histone aceyltransferases}}
Published	07/28/2024	HDACs stands for {{c1::Histone deacetylases}}
Published	07/28/2024	{{c1::Histone Acetyl Transferases}} acetylate histone tails
Published	07/28/2024	{{c1::HDACs}} de-acetylate histone tails
Published	07/28/2024	2 examples of HATs are:
Published	07/28/2024	Histone acetylation occurs at the {{c1::lysine}} residues of the histone tail thereby removing the positive charge of {{c1::lysine}} which reduce…
Published	07/28/2024	{{c1::CBP}} is an example of a histone acetylation {{c2::writer because it also has histone acylation activity along with the activity to bind to…
Published	07/28/2024	{{c1::HDACs}} are an example of histone acetylation {{c2::eraser}}
Published	07/28/2024	{{c1::bromo domain proteins}} are an example of a histone acetylation {{c2::reader}}
Published	07/28/2024	{{c1::bromodomains}} with reader complexes bind to specific acetylated lysine residues in specific histone sequences to recruit other associated chrom…
Published	07/28/2024	A {{c1::chromatin remodeler}} is an enzyme that is stimulated by the presence of DNA to hydrolyze ATP, which can then be used as energy source to…
Published	07/28/2024	A {{c1::histone chaperone}} is a family of proteins that binds to either a H2A-H2B dimer or to a H3-H4 tetramer to prevent inappropriate aggregat…
Published	07/28/2024	A {{c1::histone variant}} is a protein that is almost identical to one of the four core canonical histone genes with specific amino acid changes …
Published	07/28/2024	What is the function of the SWI/SNF chromatin remodeling complex?
Published	07/28/2024	{{c1::ATRX}} is a histone methylation reader at H3K9me3 and H3K4me0 that recruits the {{c2::DAXX}} histone chaperone to insert the variant histon…
Published	07/28/2024	The histone {{c1::H2A.Z}} facilitates TBP binding (TFIID subunit) and increases gene expression
Published	07/28/2024	The histone {{c1::H3.3}} is enriched near the promoter of some actively transcribing genes and represents the majority of H3K4me modified subunit…
Published	07/28/2024	The {{c1::SWR-C}} complex exchanges the variant histone {{c2::H2A.z for H2A}} at the promoter region
Published	07/28/2024	The {{c1::HIRA}} complex facilitates {{c2::H3.3}} deposition at both promoters and downstream particularly during muscle development (same a…
Published	07/28/2024	{{c1::lysine and arginine}} residues may be methylated during histone methylatation
Published	07/28/2024	{{c1::SUV39H1}} is a histone methylation (H3K9) writer and mutated in cases of {{c2::retinoblastoma}}
Published	07/28/2024	{{c1::JHDM}} is a demethylase (H3K9) (Histone methylation eraser); mutations of which are responsible for {{c2::male infertility}} and {{c3:…
Published	07/28/2024	DNA methylation occurs at the {{c1::C5}} position of {{c2::cytosine}} found in {{c3::CpG islands}}
Published	07/28/2024	5meC can spontaneously deaminate to form {{c1::thymine}}; hence CpGs are {{c2::under}}-represented compared to their expected frequency
Published	07/28/2024	Non-methylated CpGs typically overlap with {{c1::promoter regions}}
Published	07/28/2024	5meC's recruit {{c1::methyl binding domain proteins (MBDs)}} and other potential transcription inhibitory proteins to turn off the gene. The inhi…
Published	07/28/2024	{{c1::Rett syndrome}} is an x-linked neurodevelopmental syndrome due to mutations in the gene for {{c2::MeCP2 (Methyl-CpG-Binding Protein 2)}}
Published	07/28/2024	MeCP2 (a methyl binding domain protein) binds to {{c1::5meCs}} in selected CGIs and recruits transcription repression factors such as {{c2::…
Published	07/28/2024	{{c1::phosphorylation}} can cause MeCP2 dissociation and gene activation
Published	07/28/2024	Histone methylation on lysine {{c1::H3K4}} always activates the gene
Published	07/28/2024	Mono methylation on the histone lysine {{c1::H3K27}} will promote activation of the gene
Published	07/28/2024	How does DNA methylation play a role in genomic imprinting?
Published	07/28/2024	Rubinstein Tabi Syndrome is caused by a spontaneous deletion in the {{c1::CBP gene}}
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