Embed Size (px)
Citation preview
M4 RNA Pol II genes promoters and enhancers
-----RNA Polymerase II (RNA Pol II) is located in the nucleoplasm It is responsible for the transcription of all protein-coding genes and some small nuclear RNA genes The pre-mRNAs must be processed after synthesis by cap formation at the 5rsquo-end of the RNA and poly (A) addition at the 3rsquo-end as well as removal of introns by splicing
Molecular Biology
TATA box
Transcription
Transcriptionalstart site
DNA
Coding-strand sequences TATAAAA
GC + CAAT boxesndash100
ndash50 ndash25 +1Py2CAPy5
Promoters
TATA box Many eukaryotic promoters contain a sequence called the TATA box around 25-35 bp upstream from the start site of transcription It has the 7 bp consensus sequence 5rsquo-TATA（ AT） A（ AT） -3rsquo although it is now known that the protein which binds to the TATA box TBP binds to an 8 bp sequence that includes an additional downstream base pair whose identity is not important
Initiator element The initiator element is located around the transcription strt site Many initiator elements have a C at -1 and A at +1
Molecular Biology
Upstream regulatory elements
These elements are found in many genes which vary widely in their levels of expression in different tissues Two common examples are SP1 box which is found upstream of many genes both with and without TATA boxes and the CCAAT box Promoters may have one both or multiple copies of these sequences These sequences which are often located within 100-200 bp upstream from the promoter are referred to as upstream regultory elements (UREs) and play an important role in ensuring efficient transcription from the promoter
Molecular Biology
Transcription from many eukaryotic promoters can be stimulated by control elements that are located many thousands of base pairs away from the transcription start site This kind of elements are called as enhancer Classically enhancers have the following general chracteristics
bull They exert strong activation of transcription of a linked gene from the correct start sitebullThey activate transcription when placed in either orientation with respect to linked genesbullThey are able to function over long distances of more than 1 kb whether from an upstream or downstream position relative to the start sitebullThey exert preferential stimulation of the closest of two tandem promoters
Enhancers
Molecular Biology
M5 General transcription factors and RNA Pol II initiation
RNA Pol II basal transcription fators A serial of nuclear transcription factors have been identified purified amd cloned These are required for basal trancription initiation from RNA Pol II promoter sequences in vitro and named as TFIIA TFIIB TFIIC TFIID They have been shown to assemble on basal promoters in a specific order and they may be subject to multiple levels of regulation
TFIID Inn promoters containing a TATA box the RNA Pol II transcription factor TFIID is responsible for binding to this key promoter element The binding of TFIID to the TATA box is the earliest stage in the formation of the RNA Pol II transcription initiation complex It seems that in mammalian cells TBP binds to the TATA box and is then joined by at least eight 由 TBP和 TAFIIs to form TFIID
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
TATA box
Transcription
Transcriptionalstart site
DNA
Coding-strand sequences TATAAAA
GC + CAAT boxesndash100
ndash50 ndash25 +1Py2CAPy5
Promoters
TATA box Many eukaryotic promoters contain a sequence called the TATA box around 25-35 bp upstream from the start site of transcription It has the 7 bp consensus sequence 5rsquo-TATA（ AT） A（ AT） -3rsquo although it is now known that the protein which binds to the TATA box TBP binds to an 8 bp sequence that includes an additional downstream base pair whose identity is not important
Initiator element The initiator element is located around the transcription strt site Many initiator elements have a C at -1 and A at +1
Molecular Biology
Upstream regulatory elements
These elements are found in many genes which vary widely in their levels of expression in different tissues Two common examples are SP1 box which is found upstream of many genes both with and without TATA boxes and the CCAAT box Promoters may have one both or multiple copies of these sequences These sequences which are often located within 100-200 bp upstream from the promoter are referred to as upstream regultory elements (UREs) and play an important role in ensuring efficient transcription from the promoter
Molecular Biology
Transcription from many eukaryotic promoters can be stimulated by control elements that are located many thousands of base pairs away from the transcription start site This kind of elements are called as enhancer Classically enhancers have the following general chracteristics
bull They exert strong activation of transcription of a linked gene from the correct start sitebullThey activate transcription when placed in either orientation with respect to linked genesbullThey are able to function over long distances of more than 1 kb whether from an upstream or downstream position relative to the start sitebullThey exert preferential stimulation of the closest of two tandem promoters
Enhancers
Molecular Biology
M5 General transcription factors and RNA Pol II initiation
RNA Pol II basal transcription fators A serial of nuclear transcription factors have been identified purified amd cloned These are required for basal trancription initiation from RNA Pol II promoter sequences in vitro and named as TFIIA TFIIB TFIIC TFIID They have been shown to assemble on basal promoters in a specific order and they may be subject to multiple levels of regulation
TFIID Inn promoters containing a TATA box the RNA Pol II transcription factor TFIID is responsible for binding to this key promoter element The binding of TFIID to the TATA box is the earliest stage in the formation of the RNA Pol II transcription initiation complex It seems that in mammalian cells TBP binds to the TATA box and is then joined by at least eight 由 TBP和 TAFIIs to form TFIID
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
Upstream regulatory elements
These elements are found in many genes which vary widely in their levels of expression in different tissues Two common examples are SP1 box which is found upstream of many genes both with and without TATA boxes and the CCAAT box Promoters may have one both or multiple copies of these sequences These sequences which are often located within 100-200 bp upstream from the promoter are referred to as upstream regultory elements (UREs) and play an important role in ensuring efficient transcription from the promoter
Molecular Biology
Transcription from many eukaryotic promoters can be stimulated by control elements that are located many thousands of base pairs away from the transcription start site This kind of elements are called as enhancer Classically enhancers have the following general chracteristics
bull They exert strong activation of transcription of a linked gene from the correct start sitebullThey activate transcription when placed in either orientation with respect to linked genesbullThey are able to function over long distances of more than 1 kb whether from an upstream or downstream position relative to the start sitebullThey exert preferential stimulation of the closest of two tandem promoters
Enhancers
Molecular Biology
M5 General transcription factors and RNA Pol II initiation
RNA Pol II basal transcription fators A serial of nuclear transcription factors have been identified purified amd cloned These are required for basal trancription initiation from RNA Pol II promoter sequences in vitro and named as TFIIA TFIIB TFIIC TFIID They have been shown to assemble on basal promoters in a specific order and they may be subject to multiple levels of regulation
TFIID Inn promoters containing a TATA box the RNA Pol II transcription factor TFIID is responsible for binding to this key promoter element The binding of TFIID to the TATA box is the earliest stage in the formation of the RNA Pol II transcription initiation complex It seems that in mammalian cells TBP binds to the TATA box and is then joined by at least eight 由 TBP和 TAFIIs to form TFIID
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
Transcription from many eukaryotic promoters can be stimulated by control elements that are located many thousands of base pairs away from the transcription start site This kind of elements are called as enhancer Classically enhancers have the following general chracteristics
bull They exert strong activation of transcription of a linked gene from the correct start sitebullThey activate transcription when placed in either orientation with respect to linked genesbullThey are able to function over long distances of more than 1 kb whether from an upstream or downstream position relative to the start sitebullThey exert preferential stimulation of the closest of two tandem promoters
Enhancers
Molecular Biology
M5 General transcription factors and RNA Pol II initiation
RNA Pol II basal transcription fators A serial of nuclear transcription factors have been identified purified amd cloned These are required for basal trancription initiation from RNA Pol II promoter sequences in vitro and named as TFIIA TFIIB TFIIC TFIID They have been shown to assemble on basal promoters in a specific order and they may be subject to multiple levels of regulation
TFIID Inn promoters containing a TATA box the RNA Pol II transcription factor TFIID is responsible for binding to this key promoter element The binding of TFIID to the TATA box is the earliest stage in the formation of the RNA Pol II transcription initiation complex It seems that in mammalian cells TBP binds to the TATA box and is then joined by at least eight 由 TBP和 TAFIIs to form TFIID
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
M5 General transcription factors and RNA Pol II initiation
RNA Pol II basal transcription fators A serial of nuclear transcription factors have been identified purified amd cloned These are required for basal trancription initiation from RNA Pol II promoter sequences in vitro and named as TFIIA TFIIB TFIIC TFIID They have been shown to assemble on basal promoters in a specific order and they may be subject to multiple levels of regulation
TFIID Inn promoters containing a TATA box the RNA Pol II transcription factor TFIID is responsible for binding to this key promoter element The binding of TFIID to the TATA box is the earliest stage in the formation of the RNA Pol II transcription initiation complex It seems that in mammalian cells TBP binds to the TATA box and is then joined by at least eight 由 TBP和 TAFIIs to form TFIID
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
TBP
TBP is present in all three enkaryotic transcription complexes and clearly plays a major role in transcription initiation TBP is a monomeric protein with a highly conserved C-terminal domains of 180 residues and this conserved domain functions as well as the full-length protein in in vivo transcription
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
TBP structure TBP has been shown to have saddle structure with an overall dyad symmetry but two halves of the molecule are not identical TBP interacts with DNA in the minor groove so that the inside of the saddle binds to DNA at the TATA box and the outside surface of the protein is available for interactions with other protein factors Binding of TBP deforms the DNA so that it is bent into the inside of the saddle unwound This results in a kink of about 45deg between the first two and last two base pariss of the 8 bp TATA element
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
TFIIA TFIIB and RNA polymearse binding
TFIIA TFIIA binds to TFIID and enhances TFIID binding to the TATA box stabilizing the TFIID-DNA complex TFIIA is made up of at least three subunits
TFIIB and RNA polymearse binding Once TFIID has bound to the DNA another transcription factor TFIIB binds to TFIID TFIIB can also bind to the RNA polymerase This seems to be an important step in transcription initiation since TFIIB asts as a bridging fator allowing recruitment of the polymerase to the complex togather with a further fator TFIIF
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
Factors binding after RNA polymerase
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex These proteins are necessary for transcription in vitro and associate with the complex in a defined order TFIIH is a large compex which is made up of at least five subunits TFIIJ remains to fully characterized
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
CTD phosphorylation by TFIIH
TFIIH is a large multicomponent protein compex which contains both kinase and helicase activity Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region TFIIH therefore seems to have a very important function in control of transcriptiom elongation
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
TFIID
TFIID TFIIB
TFIID
TFIIF
TATA box
TFIIB binds to TFIID
TFIIB acts as a bridge to bind toRNA polymerase IITFIIF
TFIIE and TFIIH bindto RNA polymerase II
RNA polymerase
TFIIB
TFIIA
TFIIA
TFIIA binds to TFIID and enhances TFIID binding to TATA box
Once TFIID has bound to the DNA TFIIB binds to TFIID
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
After RNA polymerase binding three other transcription factors TFIIE TFIIH and TFIIJ rapidly asociate with the compex
Activation of TFIIH results in phophorylation of the carboxyl-terminal domain (CTD) of the RNA polymerase This phosphorylation results on formation of a processive RNA polymerase complex and allows the RNA polymerase to leave the promoter region
Transcription factors
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
The initiator transcription complex
Many RNA Pol II promoters which do not contain a TATA box have an initiator element overlapping their start site It seems that at these promoters TBP is recruited to the promoter by a further DNA-binding protein which binds to the initiator element TBP the recruits the other transcription factors and RNA polymerase in a manner similar to that which occurs in TATA box promoters
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
Vmax = 50 nts sec
1048766 About 110th DNA polymerase1048766 Which needs to be fast1048766 Initiated at very few points1048766 Only ~ 10 DNA pol molecules cell
1048766 Each has to be very fast1048766 ~3000 molecules cell1048766 Transcription simultaneously at many points
RNA pol Speed
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
Error rate of ~ 10-4 to 10-51048766 Much greater than DNA pol1048766 Less than expected just from W-C base-pairing1048766 Suggests proof-reading Details of proof-reading not understood
RNA pol Fidelity
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
What about the dsDNA sequence tells RNA polymerase where to start
Be sure to be able to distinguish between prokaryotes and eukaryotes in your answer
Your homework
Molecular Biology
![Regulation of microRNA biogenesis and turnover by animals and … · 2013-05-10 · Most pri-miRNAs are transcribed by RNA polymerase II (Pol II) [37], however, a subset of miRNAs,](https://img.pdfslide.us/doc/110x75/5f8f978631c8ec19d945e274/regulation-of-microrna-biogenesis-and-turnover-by-animals-and-2013-05-10-most.jpg)
