expressing the genome Flashcards
what is gene expression?
process by which the info from a gene is used to synthesis a functional gene product which is either a protein or a functional RNA
what are the 3 stages of gene expression? and what happens during each stages
initiation: basal transcription machinery assembles on the DNA at the promoter
elongation
termination
what are the 3 common features of most promoters?
transcription start site TATA box sequences bound by transcriptional regulators which includee: upstream activating sequences (UASs) enhancers upstream repressing sequences (URSs) silencers
what are core promoters?
start site+TATA box
what is basal transcription machinery?
RNA polymerase II+5 multi-subunit general transcription factors (TFIIB, D, E, H) which assemble sequentially
what is a transcription factor?
sequence specific DNA binding proteins that bind at or close to te core promoter and influence the efficiency of transcription initiation
what is DNA helicase?
subunit of TFIIH that uses energyy from the hydrolysis of ATP to open up the DNA double helix allowing RNA polymerase II to have access to the template strand
what is transcriptome?
total complement of mRNA molecules (or “transcripts”) produced in a specific cell or the population of cells comprising a tissue
what enzymes allows chromatin to be accessible?
chromatin-modifying enzymes
where does DNA methylation occur?
occurs at the 5 carbon position of the cytosine ring resulting in 5-methylcytosine
what does the methyl group after methylation do?
inhibits transcription
what is genomic imprinting?
form of epigenetic inheritance where DNA methylation ensures only one parental allele is expressed
when the paternal allele is expressed, the maternal copy is silenced and vice versa
what are the key modifications on histones? what do they do?
acetylation of lysine 27 –>promotes gene transcription
methylation of lysine 27 –> suppresses transcription and results in large regions of inactive chromatin
methylation of lysine 9 –> Di- or Tri- methylation silences gene promoters and prevents transcription
methylation of lysine 4 –> active promoters and gene expression
what is chromatin folding’s role?
it plays a role in enhancing transcript
what are the different chromatin folding?
chromosomal looping
topologically associating domains
chromosomal compartments
chromosomal territories
what are the different methods to determine genomic architecture?
CHIP-Seq
chromosome conformation capture (3C)
the encyclopaedia of DNA elements (ENCODE)
what is the regulome?
noncoding genomic regions that have significant elements for gene regulation
they include promoters, transcriptional regulatory sequences and regions of chromatin and histone modification which modulate the activity and expression of the protein-coding genes as well as other functions
what are the different layers of hierarchical structure of chromatin?
heterochromatin/euchromatin –> A and B compartments –> TADs and chromatin loops
what can be the result of the formation or disappearance of chromatin loops between enhancers and promoters?
gain or loss, respectively of enhancer function and can alter transcription factor binding in the genome and contribution to disease progression
what can TAD boundary deletions do?
can induce rewiring of promoter enhancer interactions allowing enhancers from neighbouring domains to ectopically activate other genes causing aberrant gene expression and disease
what can mis regulation of Wnt signalling result to?
various diseases including cancer
if no Wnt beta-catenin is phosphorylated and constitutively degraded
what are DNA methyltransferases (DNMTs)?
family of enzymes that have an important role in the inheritance of epigenetic markers
what does DNMT1 do?
DNMT1 maintains DNA methylation by identifying hemimethylated DNA (=CpG dinucleotides that are methylated on the original DNA strand but not the newly synthesised strand) and methylating the unmethylated cytosine at such sites
what is DNA demethylation? what are the 2 mechanisms of DNA demethylation?
removal of methyl group from DNA
the two mechanisms of DNA demethylation are:
1. active: through an enzymatic process that removes or modifies the methyl groupp from 5-methyl cytosine. the ten-eleven translocation (TET) family of enzymes are involved in active demethylation
2. passive: takes place on newly synthesised DNA strands in the absence of DNA methylation maintenance
