Regulation of Transcription in Eukaryotes Molecular Biology

EXAM 2

Why is regulation in eukaryotic transcription more complex than transcriptional regulation in bacteria?

development and diverse types of cells, and additional levels of DNA/protein structure

What is the organization of the promoter regions in eukaryotes?

core and proximal elements

What are the major distal DNA regulatory elements?

enhancers, silencers, insulators, and locus control genes

What is the function of enhancers?

activators bind to increase the rate of transcription

What is the function of silencers?

repressors bind to decrease/stop transcription

What is the function of insulators?

often bound by CTCF to prevent promoter and enhancer interaction, or confine spreading of either activation or repression from chromatin locations

What is the fuction of locus control genes?

chromatin region that controls developmentally regulated expression of individual genes within a gene cluster

What is the chromatin hub?

a dynamic spatial organization or clustering of genes and chromatin regions that affect the transcriptional activity of the resident genes

What are the major characteristics of the transcription factors in eukaryotes?

molecular complexes with multiple subunits and/or domains, some for DNA binding, some for interaction with other factors to activate or repress transcription; regulation of transcription of different genes is achieved by working with unique combination of TBP and various TBP-associated factors

What is promoter-proximal-stalling?

RNAP that has just begun transcribing the
body of the gene becomes stalled at the position very close to the promoter region. It’s an important aspect of regulation of inducible genes

What is the organization of the nucleosome?

histone octamers wrapped around by DNA; N-terminal tails of the core histones are usually sites for modifications

What are the major types of histone modifications involved in regulation of transcription?

methylation, acetylation, poly(ADP)ribosylation, phosphorylation and ubiquitylation

What are the main types of proteins involved in the recognition and modification of histones?

writers, readers, and erasers

What is a bromodomain?

the domain that recognizes acetylated lysine residues

What is a chromodomain?

the domain that recognizes methylated residues

Where on the histone do most of the post-translational modifications (PTMs) occur?

N- or C-terminal tails

Examples of PTMs are associated with gene activation

H3K4me2/3, lysine acetylation

Examples of PTMs are associated with gene silencing

methylation of H3K9 and H3K27

What are the characteristics of distribution of nucleosomes with canonical histones and
histone replacement variants in the human genome?

2A.Z flanking NFR around the TSS,
H3.3 and H2ABbd association with active transcription; MacroH2A associated with
repressive transcription

What is poly(ADP)ribosylation?

enzymatic addition of ADP-ribose units or chains of such units to proteins

What is the enzyme that catalyzes polyADPribosylation reactions?

poly(ADP-ribose) polymerase 1, abbreviated as PARP-1

What are the main functions of PARP-1?

emergency responses (DNA damage detection
and repair), and housekeeping role (transcriptional regulation via a variety of mechanisms such as interaction with other regulators, with H1, affecting insulator activity and chromosome organization)

What is heterochromatin protein 1 (HP1) and its main function?

a protein with both a chromodomain and a chromo-shadow domain, is involved in both transcription
repression, via formation of highly compacted chromatin structure and association with HDACs and methylation enzymes), or repressor near the TSS, and transcription activation through interactions with transcriptional activators

Where is DNA methylation mostly found?

cytosine in CpG dinucleotides

What are CpG islands, and where are these islands often located?

genomic regions with high density of the dinucleotides. They are often located within promoters

What are the enzymes that are involved in methylating the DNA?

Dnmt1 for maintenance methylation; Dnmt3a and Dnmt3b for de novo methylation

Are most CpG dinucleotides methylated or demethylated in adult vertebrates?

70-80% CpGs are methylated

Is DNA demethylation the same as histone demethylation?

no, DNA demethylation is more complex, consisting of multiple steps including deamination, G:T mismatch detection and repair

What are the proteins that recognize and bind to the methylated DNA?

methyl-CpG-binding proteins such as MBD4 and MeCP2

What human disease can be caused by mutations in MECP2?

Rhett Syndrome

Why DNA methylation affect transcription?

DNA methylation is a major mechanism of
regulating gene expression. CpG islands often coincide with promoters. Methylation in the
promoter is recognized and bound by methyl-CpG binding proteins, which in turn can recruit repressors of gene transcription (histone deacetylases, histone methyl transferases) to inhibit transcription

What roles do lcRNAs play in the regulation of gene translation?

affect gene expression via interacting with activators, repressors, and/or affecting chromatin remodeling complexes