cis$regulatory$elements:$ $ - PowerPoint PPT Presentation

cis$regulatory$elements:$ $ Switches$to$modulate$the$expression$level$of$genes$ $ $ Sebas:aan$Meijsing$ Transcrip:onal$regula:on$group$ Berlin,$Germany$ meijsing@molgen.mpg.de$$

Outline$ Transcrip:on$ • $ Cis$regulatory$elements$ • $ Transcrip:on$factors$ • Chroma:n $ • $

Outline$ Transcrip:on$ • $ Cis$regulatory$elements$ • $ Transcrip:on$factors$ • Chroma:n $ • $

Transcrip:on$ DNA RNA Protein ! Central Dogma of Biology: DNA is transcribed into RNA which is translated into protein ! Only$≈$1%$of$genome$codes$for$proteins$

Transcrip:on$&$being$mul:cellular$ ! Different cell-types ! One genome:

Transcrip:on$&$being$mul:cellular$ ! Different transcriptomes ! One genome:

Transcrip:on$performed$by$RNA$polymerases$ RNA polymerase II ! Transcriptional Initiation ! Gene!X! Promoter ! Eukaryotic RNA polymerase-II alone is unable to bind DNA and relies on transcription factors & cis regulatory elements to initiate transcription 2 flavors: - General transcription factors (e.g. TATAA box binding protein (TBP) - Transcriptional regulatory factors that regulate the expression of individual genes !

Outline$ Transcrip:on$ • $ Cis$regulatory$elements$ • $ Transcrip:on$factors$ • Chroma:n $ • $

CisLregulatory$elements:$Different$flavors$ situated a Enhancer ( side of Promoter an gene b Silencer X long lating Promoter whereby c are Insulator X ing recent Promoter model which d Maston et al., Annu. Rev. Genom. Human Gent. (2006) Today$we$mostly$focus$on$cis$regulatory$elements$that$act$as$enhancers$

CisLregulatory$elements$ cis$vs$trans:$ Cis:$Directly$ac:ng$on$the$nearby$gene ! Gene!X! cis regulatory TATA/Promoter element !

CisLregulatory$elements$ cis$vs$trans:$ Transcription factor ! Trans:$ $Transcrip:on$factors$produced$$ $ $elsewhere$binding$to$cisLregulatory$$ $ $elements$to$control$gene$expression$ ! Gene!X! cis regulatory TATA/Promoter ! element

Transcrip:on$factors$and$transcrip:onal$regula:on$ Gene!X! enhancer TATA/Promoter ! Transcription factor ! Gene!X! enhancer TATA/Promoter ! RNA polymerase II ! Transcription factor ! Transcriptional Initiation ! Gene!X! enhancer TATA/Promoter !

Transcrip:on$&$being$mul:cellular$ ! Different transcriptomes ! One genome:

How$to$explain$:ssueLspecific$expression$ Liu et al., Dev. Bio. 2001 http://bioinfo2.weizmann.ac.il Muscle cell ! Brain cell(s) ! RNA Transcription polymerase II ! factor ! Transcriptional Initiation ! Gene!X! Gene!X! Cis regulatory TATA/Promoter Cis regulatory TATA/Promoter ! elements ! elements

How$to$explain$:ssueLspecific$expression$ Some factors are ubiquitously expressed yet target genes are tissue specific http://bioinfo2.weizmann.ac.il Liu et al., Dev. Bio. 2001 Microarrays$show$liRle$overlap$in$ transcrip:onal$regula:on$between$ different$cell$types !

TF$binding$sites$oTen$clustered$ Conservation analysis can be used to identify enhancers. Typically larger stretches of sequence conserved Cis-regulatory modules (enhanceasomes) ! Conservation score Petersen et al., Plos One (2009) Panne Curr. Opinion in Struc. Biol. (2008)

How$to$explain$:ssueLspecific$expressionLII$ RNA Transcription polymerase II ! ! factor Transcriptional Initiation ! Gene!X! Gene!X! Enhancer TATA/Promoter ! Enhancer TATA/Promoter ! Modular nature of CRM ! Different “switches” !

Distal$vs$promoter$proximal$ ± 1kb around TSS Nearby…..$ Gene!X! cis regulatory Promoter ! element Traditionally people looked at the promoter …… . For many TFs majority of binding occurs >10kb away from promoters ………… ! Nearby?$ y o r t a u l g e r s c i ! n t ≥ 1000kb from TSS e m e e l Gene!X! Promoter !

Muta:ons$in$cis$regulatory$elements$&$disease$ Table 1 Transcriptional regulatory elements involved in human diseases Regulatory Element Disease Mutation (bound factor) Affected Gene Reference Core promoter β -thalassemia TATA box, CACCC box, β -globin (4, 94, 109) DCE Proximal promoter Bernard-Soulier Syndrome 133 bp upstream of TSS GpIb β (117) (GATA-1) Charcot-Marie-T ooth disease 215 bp upstream of TSS connexin-32 (187) Congenital erythropoietic 70, 90 bp upstream of TSS uroporphyrinogen (167) porphyria (GATA-1, CP2) III synthase Familial 43 bp upstream of TSS (Sp1) low density lipoprotein (92) hypercholesterolemia receptor Familial combined 39 bp upstream of TSS lipoprotein lipase (195) hyperlipidemia (Oct-1) Hemophilia CCAAT box (C/EBP) factor IX (43) Hereditary persistence of ∼ 175 bp upstream of TSS A γ -globin (62) ß-Thalassemia fetal hemoglobin (Oct-1, GATA-1) Progressive myoclonus Expansion ∼ 70 bp upstream cystatin B (96) epilepsy of TSS Pyruvate kinase deficient 72 bp upstream of TSS PKLR (120) anemia (GATA-1) β -thalassemia CACCC box (EKLF) β -globin (130) δ -thalassemia 77 bp upstream of TSS δ -globin (125) (GATA-1) Treacher Collins syndrome 346 bp upstream of TSS TCOF1 (123) (YY1) Enhancer Preaxial polydactyly 1 Mb upstream of gene SHH (107) Van Buchem disease Deletion ∼ 35 kb downstream sclerostin (116) of gene X-linked deafness Microdeletions 900 kb POU3F4 (46) upstream Silencer Asthma and allergies 509 bp upstream of TSS TFG- β (78) (YY1) Fascioscapulohumeral Deletion of D4Z4 repeats 4q35 genes (66) muscular dystrophy Insulator Beckwith-Wiedemann CTCF binding site (CTCF) H19/Igf (147) syndrome LCR α -thalassemia 62 kb deletion upstream of α -globin genes (75) gene cluster β -thalassemia ∼ 30 kb deletion removing β -globin genes (52) 5 ′ HS2–5 Maston et al., Annu. Rev. Genom. Human Gent. (2006) Polydactyly

Outline$ Transcrip:on$ • $ Cis$regulatory$elements$ • $ Transcrip:on$factors$ • Chroma:n $ • $

CisLregulatory$elements:$contain$zip$codes$for$TFs$ Gene!X! cis regulatory TATA/Promoter ! element A$A$A$T$A$A$A$C$A$n$n$

Transcrip:on$factors$ Approx.$3000$in$human$genome$(approx$1/6 th $of$all$coding$genes) $ • $ Lots of switches allowing cells to run all sort of different “programs”. !

Transcrip:on$factors$ Fine tuning: Getting gene dosage just right is important Too much: Trisomy 21 (down syndrome) (X-inactivation woman) Copy number variation linked to various disease: au(sm,!schizophrenia,!systemic!lupus!erythematosis,!Crohn's!disease!and!psoriasis Too little: p53 and cancer !

Transcrip:on$factors$ Approx.$3000$in$human$genome$(approx$1/6 th $of$all$coding$genes) $ • $ Common feature: TFs recognize DNA using different types of DNA binding domains ! Basic leucine zipper domain Zinc finger domain Helix-turn-Helix !

Transcrip:on$factors$ DNA recognition: Specific contacts & non-specific contacts ! Specific contacts Non-specific contacts (recognize bases in major groove) (e.g. DNA backbone contacts) Sequence specific ! Not sequence specific ! K514 ! 3.5 ! G-4 ! G-3 !

TFs$in$turn$facilitate$RNA$polLII$recruitment$ 1: Directly interacts with RNA Pol-II ! Activation domain ! RNA polymerase II ! Transcriptional DNA binding Initiation ! domain ! Gene!X! Enhancers TATA/Promoter ! Maston et al., Annu. Rev. Genom. Human Gent. (2006)

TFs$in$turn$facilitate$RNA$polLII$recruitmentL2$ 2: recruits mediator ( ! RNA pol-II) ! Activation domain ! 1: Directly RNA polymerase II ! interacts with Transcriptional RNA Pol-II ! DNA binding Initiation ! domain ! Gene!X! Enhancers TATA/Promoter ! Maston et al., Annu. Rev. Genom. Human Gent. (2006)

TFs$in$turn$facilitate$RNA$polLII$recruitmentL3$ Co-activators: 3: recruits co- ! activators - Interact with Mediator - Interact with Pol-II - Chromatin modifying enzymes ! 2: recruits mediator ( ! RNA pol-II) ! Activation domain ! 1: Directly RNA polymerase II ! interacts with Transcriptional RNA Pol-II ! DNA binding Initiation ! domain ! Gene!X! Enhancers TATA/Promoter ! Maston et al., Annu. Rev. Genom. Human Gent. (2006)

TFs$in$turn$facilitate$RNA$polLII$recruitmentL4$ Activation domain ! RNA polymerase II ! Transcriptional DNA binding Initiation ! domain ! Gene!X! Enhancers TATA/Promoter ! 4. (Non-coding) RNAs (eRNAs) produced at enhancers facilitate interaction with promoter (e.g. by interacting with mediator or keeping Li et al., Nature 2013 chromatin “open”) ! Lai et al., Nature 2013

Muta:ons$in$transcrip:on$factors$&$disease$ 1: Mutations resulting in loss of expression 2: Mutations resulting in loss/change of function 3: Translocations directing TFs to wrong genomic location Developmental defects Cancer: cer r cer cer r You have access to different types of cancer either via the menu on the left or by clicking on a specific cancer name on the map below. Digits!in!wt!(le=)!and!Hoxd13!mutant!(right)!mice.!In!the!mutant! the!NFterminal!repeat!has!been!expanded!by!21!alanines! hIp://p53.free.fr/!