Cis regulatory elements Flashcards
cis regulatory elements
regions of DNA which regulate expression of a nearby gene or genes
- often binding sites for regulatory proteins like TFs
- TF binding sites are short (5-12bp)
- commonly in 5’ upstream region or 5’ of UTR
- also can be 5’UTR, 3’UTR, or introns
- within 5’ upstream – usually within a few hundred bases of transcription start site
- regulate time and patterns of gene expression
- size of cis-regulatory elements is highly variable
components of regulatory regions
- core promoters
- basal promoter
- site of assembly of transcription complex, not site of transcriptional regulation - transcription factor binding sites
- enhancers, repressors, others, sites of transcriptional regulation
detect cis regulatory elements
A. experimental - time consuming
deletion constructs: delete region/part and determine if it affects expression using reporter gene
- exact nucleotides can be identified by site directed mutagenesis
B. Computational - gives candidates for further ID
1. programs that use databases of known binding sites to scan for potential binding sites
- rapid ID of possible sites
- many of candidates have no biological function and are just matches
2. Comparisons with homologous chromosomal region from other species == “Phylogenetic Foot-printing”
- looks for conserved regions
- assumes nucleotides within binding sites are more likely to be conserved
- Advantage: ID previously unknown binding sites
- Disadvantage: can only ID highly conserved elements
- may have no regulatory function
conservation of regulatory element sequences
some highly conserved across distant related species
others evolve rapidly
mutations in regulatory element sequences
- can modulate or eliminate TF binding (common)
- can result in binding of different TF
- can generate de novo binding sites
- insertions/deletions can change spacing between binding sites that affect transcription
- new sequences acquired by transposition
- presence or absence of exon
- reorganization of regulatory region form other part of genome
gene duplication and cis elements
- if breakpoints of duplication do not include cis regulatory elements - gene likely Not expressed
- if SOME are included- may have altered transcription profile
- after duplication can gain/lose cis sequenes— divergence between them
- – results in different expression patterns, especially regulatory neofunctionalization
types of selection acting on Cis elements
Purifying = long term CONSERVE binding sites Positive = CHANGES in binding sites
evolutionary dynamics of 5’ cis regions
- substitution and insertion/deletions frequencies higher than coding, but lower than introns and non-regulatory intergenic regions
- many nucleotides are not part of regulatory elements and do not effect transcription
- – should evolve neutrally
selective sweep
which a new beneficial mutation that increases its frequency and becomes fixed in the population leads to the reduction or elimination of genetic variation
- region of low gene diversity
- ex maize tb1
trans regulatory elements
further away from gene
ex. lactase
- - located in introns of adjacent gene
genomic approaches to detecting cis elements
- ChIP seq or ChIP-ChIP - identify binding sites of particular TF
- DNase1-seq
- indentify protein binding sites that are potential cis elements
- identifies all TF binding sites but not TFs that bind them – complementary to ChIP
ChIP
followed by tiling array or illumina sequencing to analyze binding sites of individual TF
DNase1-seq
detect proteins bounding sites
- cut at open chromatin sites around where proteins are bound, but not at heterochromatin or sites protected by a protein
- Protein bound sites, typically TF, are removed and DNA is sequenced
regulatory networks
simple to very complex networks of gene products regulating expression of other genes, either positively or negatively
- many networks present in cells
- can evolve by changes in interactions
- can be linked to signal transduction
cis vs trans regulatory changes results from analysis
cis would be changes to regulatory elements themselves
trans would be changes to TFs
