BIOL 142 Chapter 19.3: Initiating Transcription- Regulatory Sequences and Proteins

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19.3%Initiating%Transcription:%Regulatory%Sequences%and%
Proteins%
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Regulatory+sequence:!any!segment!of!DNA!or!RNA!that!is!involved!in!controlling!the!expression!of!a!
specific!gene!by!binding!a!regulatory!transcription!factor!protein!or!other!protein!that!regulates!gene!
expression!
Eukaryotic!promoters!often!contain!two!or!three!conserved!regulatory+sequences!that!serve!as!
binding!sites!for!other!proteins!needed!to!start!transcription!
Core+promoter:!a!short!nucleotide!sequence!in!eukaryotic!DNA!that!binds!general!transcription!
factors!to!enable!RNA!polymerase!to!begin!transcription;!indicates!a!specific!sequence!where!RNA!
polymerase!binds!as!opposed!to!the!other!sequences!needed!for!regulation!of!transcription!
o Being!called!a!"core!promoter"!distinguishes!it!from!other!DNA!sequences!important!for!
transcription!initiation!
Once!a!core+promoter!that!contains!a!TATA+box!has!been!exposed!by!chromatin!remodeling,!
transcription!is!initiated!by!the!binding!of!the!TATA-binding+protein+(TBP)!
o TATA+box:!a!short!DNA!sequence!in!in!many!eukaryotic!promoters!that!is!important!for!
assembling!general!transcription!factors!and!RNA!polymerase!at!the!core!promoter;!located!
about!30!base!pairs!upstream!from!the!transcription!box!
o TATA-binding+protein+(TBP):!a!protein!that!binds!to!the!TATA!box!in!eukaryotic!promoters!
and!is!a!component!of!the!basal!transcription!complex!
Binding!of!TBP!or!any!of!its!relative!proteins!does!not!guarantee!that!a!gene!will!be!
transcribed!!there!are!other!factors!
!!
Promoter-Proximal+Elements+are+Regulatory+Sequences+Near+the+Core+Promoter!
Promoter-proximal+element:!in!eukaryotic!DNA,!a!regulatory!sequence!that!is!close!to!a!promoter!and!
can!bind!regulatory!transcription!factors;!have!sequences!that!are!unique!to!a!specific!set!of!genes!
Regulatory!proteins!bind!to!regulatory!sequences!located!just!upstream!from!the!core!promoter!
In!eukaryotes,!genes!that!need!to!be!regulated!together!each!have!the!same!regulatory!DNA!
sequence!that!binds!the!same!type!of!regulatory!protein!
o In!bacteria:!co-regulated!genes!are!clustered!into!a!single!operon!and!transcribed!into!a!
single!mRNA!
Unlike!the!core!promoter!itself,!promoter-proximal+elements!have!sequences!that!are!unique!to!a!
specific!set!of!genes!
o All!eukaryotic!cells!to!express!certain!genes!and!not!others!
!!
Enhancers+are+Regulatory+Sequences+Far+form+the+Core+Promoter!
History!–!finding!regulatory!sequences!within!an!intron!
Studied!a!gene!broken!into!many!introns!and!exons!
o Introns!–!spliced!out!of!the!primary!transcript!
o Exons!–!included!in!the!mature!RNA!once!splicing!is!complete!
Finding!was!remarkable!because:!
o The!regulatory!sequence!was!thousands!of!bases!away!from!the!promoter!
o It!was!downstream!of!the!promoter!
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Enhancers:!a!regulatory!sequence!in!eukaryotic!DNA!that!may!be!located!far!from!the!gene!it!controls!or!
within!introns!of!the!gene;!binding!of!specific!regulatory!transcription!factor!proteins!to!his!helps!the!
transcription!of!certain!genes!
Enhancers!can!be!more!than!100,000!bases!away!from!the!promoter!
o Can!be!located:!!
In!introns!!
In!un-transcribed!sequences!
On!either!the!5'!or!3'!end!of!the!gene!
Within!a!gene!
Like!promoter-proximal!elements,!there!are!many!types!of!enhancers!
Most!genes!have!more!than!one!enhancer!
Enhancers!have!different!binding!sites!for!more!than!one!type!of!regulatory!protein!
o Typically!contains!binding!sites!for!more!than!one!transcription!factors!
Enhancers!can!work!even!if!researchers!flip!their!normal!5'!-->!3'!orientation!or!move!them!to!a!
new!location!near!the!gene!
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Enhancers!and!promoter-proximal!elements!regulate!the!expression!of!eukaryotic!genes!
Promoter-proximal!elements!are!near!the!core!promoter!
Enhancers!are!located!farther!away!and!may!be…!
o Upstream!or!downstream!of!the!promoter!
o Within!introns!
!
!!
Regulatory!proteins!
Transcriptional+activator+(activator):!a!eukaryotic!regulatory!transcription!factor!that!binds!to!
regulatory!DNA!sequences!in!enhancers!or!promoter-proximal!elements!to!promote!the!initiation!
of!transcription;!protein!that!increases!the!frequency!of!transcription!
o Activators!bind!to!enhancers!to!begin!transcription!
o !Positive+control+–+enhancers+and+activators+are+like+a+gas+pedal!
Repressors:!in!eukaryotes,!a!protein!that!binds!to!a!silencer!sequence!in!DNA!to!prevent!or!reduce!
gene!transcription!
o Silencer:!a!regulatory!sequence!in!eukaryotic!DNA!to!which!repressor!proteins!can!bind,!
inhibiting!gene!transcription!
Eukaryotes!have!regulatory!sequences!similar!in!structure!and!characteristics!with!
enhancers!but!inhibit!transcription!
o !Negative+control+–+silencers+and+repressors+are+like+a+brake!
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The+Role+of+Transcription+Factors+in+Differential+Gene+Expression!
Transcription+factor:!general!term!for!a!protein!that!binds!to!a!DNA!regulatory!sequence!to!influence!
transcription;!includes!both!general!and!regulatory!transcription!factors!
Enhancers!and!silencers!are!binding!sites!for!activators!and!repressors!that!regulate!transcription!
!Different+types+of+cells+express+different+genes+because+they+have+different+transcription+
factors!
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