Z box gene transcriptions: Difference between revisions

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"Mutation of the two conserved Z‐boxes (Z1, Z2) strongly reduced the specific binding complex [...]."<ref name=Burk/>
"Mutation of the two conserved Z‐boxes (Z1, Z2) strongly reduced the specific binding complex [...]."<ref name=Burk/>
{{clear}}
{{clear}}
==HY5 proteins==
"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of ''RbcS1A'' (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."<ref name=Song>{{ cite journal
|author=Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong
|title=DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins
|journal=Plant Physiology
|date=April 2008
|volume=146
|issue=4
|pages=1862–1877
|url=http://www.plantphysiol.org/content/plantphysiol/146/4/1862.full.pdf
|arxiv=
|bibcode=
|doi=10.1104/pp.107.113217
|pmid=
|accessdate=26 March 2019 }}</ref>


==Consensus sequences==
==Consensus sequences==
Line 59: Line 76:
"Snail-related and E2A factors bind to [...] (CAGGTG/A), termed Z-Box."<ref name=Spaderna/>
"Snail-related and E2A factors bind to [...] (CAGGTG/A), termed Z-Box."<ref name=Spaderna/>


"HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the [...], Z-box (ATACGGT), [...]."<ref name=Nawkar/>
"HY5 binds to [...], Z-box (ATACGGT), [...]."<ref name=Nawkar/>


"The HY5 protein interacts with [...] Z- (ATACGTGT) boxes [...]."<ref name=Song>
"The HY5 protein interacts with [...] Z- (ATACGTGT) boxes [...]."<ref name=Song/>
 
The more general Z-box consensus sequence accommodating these variations appears to be A(C/T)A(C/G)GT(A/G)T. But, it may be better to sample the three Z-boxes separately.
 
==HY5 proteins==
 
"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of ''RbcS1A'' (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."<ref name=Song>{{ cite journal
|author=Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong
|title=DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins
|journal=Plant Physiology
|date=April 2008
|volume=146
|issue=4
|pages=1862–1877
|url=http://www.plantphysiol.org/content/plantphysiol/146/4/1862.full.pdf
|arxiv=
|bibcode=
|doi=10.1104/pp.107.113217
|pmid=
|accessdate=26 March 2019 }}</ref>


==HY5 proteins==
The more general Z-box consensus sequence accommodating these variations appears to be A(C/T)A(C/G)GT(A/G)T:
# Negative strand, positive direction: ACAGGTGT at 1969, contains CAGGTG<ref name=Spaderna/>.
# Positive strand, positive direction: ACACGTGT at 2962.
# ci, positive strand, negative direction: ACACCTGT at 1131, ATACCTAT at 2996, ACACCTGT at 3970.


"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of ''RbcS1A'' (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."<ref name=Song>{{ cite journal
But neither ones found contain Z-box (ATACGGT, ACCGTAT)<ref name=Nawkar/> or (ATACGTGT, ACACGTAT)<ref name=Song/>. It may be better to sample the three Z-boxes separately:
|author=Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong
# CAGGT(A/G), (C/T)ACCTG,<ref name=Spaderna/> ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.<ref name=Mejlvang/>,
|title=DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins
# ATACGGT<ref name=Nawkar/> ZboxN, and
|journal=Plant Physiology
# ATACGTGT<ref name=Song/> ZboxSo.
|date=April 2008
|volume=146
|issue=4
|pages=1862–1877
|url=http://www.plantphysiol.org/content/plantphysiol/146/4/1862.full.pdf
|arxiv=
|bibcode=
|doi=10.1104/pp.107.113217
|pmid=
|accessdate=26 March 2019 }}</ref>


==SIP1-mediated Epithelial Mesenchymal Transition (EMT)==
==SIP1-mediated Epithelial Mesenchymal Transition (EMT)==
Line 118: Line 109:
Three "Z-boxes with coordinates -1014 to -1010 (Z-box 1); -857 to -853 (Z-box 2); and -300 to -290 (Z-box 3) are occupied by SIP1 in [doxorubicin (DOX)] DOX-stimulated cells. In contrast, neither sequences upstream of Z-box 1 [...], nor sequences containing Z-boxes 4 and 5 located at the first exon/intron boundary (-390 to -409) [...] were detected in association with SIP1."<ref name=Mejlvang/>
Three "Z-boxes with coordinates -1014 to -1010 (Z-box 1); -857 to -853 (Z-box 2); and -300 to -290 (Z-box 3) are occupied by SIP1 in [doxorubicin (DOX)] DOX-stimulated cells. In contrast, neither sequences upstream of Z-box 1 [...], nor sequences containing Z-boxes 4 and 5 located at the first exon/intron boundary (-390 to -409) [...] were detected in association with SIP1."<ref name=Mejlvang/>


Z-boxes 1-3 contain 5'-AGGTG-3'.<ref name=Mejlvang/>
Z-boxes 1-3 contain AGGTG.<ref name=Mejlvang/>


The "mutation of Z-boxes 1–3 markedly activated reporter activity in SIP1-expressing cells [...]."<ref name=Mejlvang/>
The "mutation of Z-boxes 1–3 markedly activated reporter activity in SIP1-expressing cells [...]."<ref name=Mejlvang/>
Line 128: Line 119:
# A1BG has no Z boxes in either promoter.
# A1BG has no Z boxes in either promoter.


==Samplings==
==General Z-box (ZboxG) samplings==


Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in [[A1BG gene transcriptions]] revealed no occurrence of either.
Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in [[A1BG gene transcriptions]] revealed no occurrence of either.


For the Basic programs testing consensus sequence 3'-A(C/T)A(C/G)GT(A/G)T-5' (starting with SuccessablesZbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
For the Basic programs testing consensus sequence A(C/T)A(C/G)GT(A/G)T (starting with SuccessablesZbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesZbox--.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 0.
# Negative strand, negative direction: 0.
# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesZbox-+.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 1, 3'-ACAGGTGT-5' at 1969.
# Negative strand, positive direction: 1, ACAGGTGT at 1969.
# positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesZbox+-.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 0.
# Positive strand, negative direction: 0.
# positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesZbox++.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 1, 3'-ACACGTGT-5', 2962.
# Positive strand, positive direction: 1, ACACGTGT at 2962.
# complement, negative strand, negative direction is SuccessablesZboxc--.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 0.
# inverse complement, negative strand, negative direction: 0.
# complement, negative strand, positive direction is SuccessablesZboxc-+.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 1, 3'-TGTGCACA-5', 2962.
# inverse complement, negative strand, positive direction: 0.
# complement, positive strand, negative direction is SuccessablesZboxc+-.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 0.
# inverse complement, positive strand, negative direction: 3, ACACCTGT at 3970, ATACCTAT at 2996, ACACCTGT at 1131.
# complement, positive strand, positive direction is SuccessablesZboxc++.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 1, 3'-TGTCCACA-5', 1969.
# inverse complement, positive strand, positive direction: 0.
# inverse complement, negative strand, negative direction is SuccessablesZboxci--.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
 
# inverse complement, negative strand, positive direction is SuccessablesZboxci-+.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
===ZboxG (4560-2846) UTRs===
# inverse complement, positive strand, negative direction is SuccessablesZboxci+-.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 3, 3'-ACACCTGT-5', 1131, 3'-ATACCTAT-5', 2996, 3'-ACACCTGT-5', 3970.
 
# inverse complement, positive strand, positive direction is SuccessablesZboxci++.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
# Positive strand, negative direction: ACACCTGT at 3970, ATACCTAT at 2996.
# inverse negative strand, negative direction is SuccessablesZboxi--.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 3, 3'-TGTGGACA-5', 1131, 3'-TATGGATA-5', 2996, 3'-TGTGGACA-5', 3970.
 
# inverse negative strand, positive direction is Successableszboxi-+.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 1, 3'-TGTGCACA-5', 2962.
===ZboxG negative direction (2596-1) distal promoters===
# inverse positive strand, negative direction is Successableszboxi+-.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 0.
 
# inverse positive strand, positive direction is SuccessablesAboxi++.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 0.
# Positive strand, negative direction: ACACCTGT at 1131.
 
===ZboxG positive direction (4050-1) distal promoters===
 
# Negative strand, positive direction: ACAGGTGT at 1969.
# Positive strand, positive direction: ACACGTGT at 2962.
 
==Z-box (ZboxSp) samplings==
 
CAGGT(A/G), (C/T)ACCTG,<ref name=Spaderna/> ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.<ref name=Mejlvang/>,
 
For the Basic programs testing consensus sequence CAGGT(A/G) (starting with SuccessablesZboxSp.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# Negative strand, negative direction: 0.
# Negative strand, positive direction: 0.
# Positive strand, negative direction: 0.
# Positive strand, positive direction: 0.
# inverse complement, negative strand, negative direction: 0.
# inverse complement, negative strand, positive direction: 0.
# inverse complement, positive strand, negative direction: 0.
# inverse complement, positive strand, positive direction: 0.
 
===AAA (4560-2846) UTRs===
 
===AAA negative direction (2846-2811) core promoters===
 
===AAA positive direction (4445-4265) core promoters===
 
===AAA negative direction (2811-2596) proximal promoters===
 
===AAA positive direction (4265-4050) proximal promoters===
 
===AAA negative direction (2596-1) distal promoters===
 
===AAA positive direction (4050-1) distal promoters===
 
==ZboxSp random dataset samplings==
 
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
 
===RDr arbitrary (evens) (4560-2846) UTRs===
 
===RDr alternate (odds) (4560-2846) UTRs===
 
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
 
===RDr alternate negative direction (odds) (2846-2811) core promoters===
 
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
 
===RDr alternate positive direction (evens) (4445-4265) core promoters===
 
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
 
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
 
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
 
===RDr alternate negative direction (odds) (2596-1) distal promoters===
 
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
 
===RDr alternate positive direction (evens) (4050-1) distal promoters===
 
==ZboxSp analysis and results==
{{main|Complex locus A1BG and ZNF497#ZboxSps}}
CAGGT(A/G).<ref name=Spaderna/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || negative || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || positive || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
 
Comparison:
 
The occurrences of real ZboxSps are greater than the randoms. This suggests that the real ZboxSps are likely active or activable.
 
==Z-box (ZboxN) samplings==
 
For the Basic programs testing consensus sequence ATACGGT (starting with SuccessablesZboxN.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# Negative strand, negative direction: 0.
# Negative strand, positive direction: 0.
# Positive strand, negative direction: 0.
# Positive strand, positive direction: 0.
# inverse complement, negative strand, negative direction: 0.
# inverse complement, negative strand, positive direction: 0.
# inverse complement, positive strand, negative direction: 0.
# inverse complement, positive strand, positive direction: 0.
 
===AAA (4560-2846) UTRs===
 
===AAA negative direction (2846-2811) core promoters===
 
===AAA positive direction (4445-4265) core promoters===
 
===AAA negative direction (2811-2596) proximal promoters===
 
===AAA positive direction (4265-4050) proximal promoters===
 
===AAA negative direction (2596-1) distal promoters===
 
===AAA positive direction (4050-1) distal promoters===
 
==ZboxN random dataset samplings==
 
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
 
===RDr arbitrary (evens) (4560-2846) UTRs===
 
===RDr alternate (odds) (4560-2846) UTRs===
 
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
 
===RDr alternate negative direction (odds) (2846-2811) core promoters===
 
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
 
===RDr alternate positive direction (evens) (4445-4265) core promoters===
 
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
 
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
 
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
 
===RDr alternate negative direction (odds) (2596-1) distal promoters===
 
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
 
===RDr alternate positive direction (evens) (4050-1) distal promoters===
 
==ZboxN analysis and results==
{{main|Complex locus A1BG and ZNF497#ZboxNs}}
ATACGGT.<ref name=Nawkar/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || negative || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || positive || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
 
Comparison:
 
The occurrences of real ZboxNs are greater than the randoms. This suggests that the real ZboxNs are likely active or activable.
 
==Z-box (ZboxSo) samplings==
 
For the Basic programs testing consensus sequence ATACGTGT (starting with SuccessablesZboxSo.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# Negative strand, negative direction: 0.
# Negative strand, positive direction: 0.
# Positive strand, negative direction: 0.
# Positive strand, positive direction: 0.
# inverse complement, negative strand, negative direction: 0.
# inverse complement, negative strand, positive direction: 0.
# inverse complement, positive strand, negative direction: 0.
# inverse complement, positive strand, positive direction: 0.
 
===AAA (4560-2846) UTRs===


===Zbox distal promoters===
===AAA negative direction (2846-2811) core promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, positive direction: ACAGGTGT at 1969.


Positive strand, positive direction: ACACGTGT at 2962.
===AAA positive direction (4445-4265) core promoters===


===Zbox random dataset samplings===
===AAA negative direction (2811-2596) proximal promoters===
 
===AAA positive direction (4265-4050) proximal promoters===
 
===AAA negative direction (2596-1) distal promoters===
 
===AAA positive direction (4050-1) distal promoters===
 
==ZboxSo random dataset samplings==


# RDr0: 0.
# RDr0: 0.
Line 179: Line 461:
# RDr9ci: 0.
# RDr9ci: 0.


===RDr UTRs===
===RDr arbitrary (evens) (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
 
===RDr alternate (odds) (4560-2846) UTRs===
 
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
 
===RDr alternate negative direction (odds) (2846-2811) core promoters===
 
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
 
===RDr alternate positive direction (evens) (4445-4265) core promoters===
 
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
 
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
 
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
 
===RDr alternate negative direction (odds) (2596-1) distal promoters===
 
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
 
===RDr alternate positive direction (evens) (4050-1) distal promoters===
 
==ZboxSo analysis and results==
{{main|Complex locus A1BG and ZNF497#ZboxSos}}
ATACGTGT.<ref name=Song/>


===RDr core promoters===
{|class="wikitable"
{{main|Core promoter gene transcriptions}}
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || negative || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Core || positive || 0 || 2 || 0 || 0
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}


===RDr proximal promoters===
Comparison:
{{main|Proximal promoter gene transcriptions}}


===RDr distal promoters===
The occurrences of real ZboxSos are greater than the randoms. This suggests that the real ZboxSos are likely active or activable.
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==
Line 213: Line 566:


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Revision as of 19:43, 20 November 2022

Editor-In-Chief: Henry A. Hoff

This female specimen is a zebrafish (Danio rerio) breed with fantails. Credit: Azul.{{free media}}

"Both miRNAs [miR‐141 and miR‐200c] map closely on human chromosome 12p13.31 and the stem–loop sequences are separated by only a 338‐base‐pair spacer sequence [...]. This spacer and the putative promoter 600 bp upstream from the hsa‐miR‐200c stem–loop contain six putative binding sequences for [zinc‐finger E‐box binding homeobox 1] ZEB1, two of which were restricted to ZEB factors (Z‐box 1 and 2, CAGGTA)."[1]

The "overall miRNA gene structure and the two Z‐boxes, as well as E‐box 2, are highly conserved in evolution from zebrafish to human [...]."[1]

"Mutation of the two highly conserved Z‐boxes showed that Z‐box 2 confers the strongest repressive function by ZEB1 [...] and also made the promoter activity insensitive to stable knockdown of ZEB1 [...]. A direct binding of ZEB1 to the two conserved ZEB1 sites (Z‐boxes) was shown by electromobility shift assay by using recombinant DNA‐binding domain of ZEB1 and nuclear extracts from SW480 colorectal cancer cells [...]. By applying chromatin immunoprecipitation (ChIP) with chromatin from SW480 or HCT116 colorectal cancer cells, we could show that endogenous ZEB1 binds to the native promoter region [...]. These data indicate that the transcriptional repressor ZEB1 can directly suppress expression of both miR‐141 and miR‐200c by binding to their putative common promoter."[1]

"The absolute transcriptional activity of the promoter was 55‐fold higher than the activity of the spacer sequence. [Mutations] (mut) of the Z‐boxes render the promoter less sensitive to suppression by ZEB1."[1]

"Mutation of the two conserved Z‐boxes (Z1, Z2) strongly reduced the specific binding complex [...]."[1]

HY5 proteins

"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of RbcS1A (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."[2]

Consensus sequences

"Snail-related and E2A factors bind to a consensus E-box promoter element (CANNTG), whereas ZEB factors bind to a related, but not necessarily identical sequence (CAGGTG/A), termed Z-Box. We detected 2 potential binding sites for Snail-related and E2A factors (E-box 1 and 2) and 3 for ZEB factors (E-box 2 and Z-box 1 and 2) in the human lama3a promoter [...]. Furthermore, sequence comparison of 1000 nucleotides upstream of the translation start site of the human and mouse lama3 gene showed that these sites are located in a highly conserved region of approximately 210 nucleotides, whereas further upstream sequences were not conserved [...]. Three of the 4 potential repressive elements were conserved between mouse and human, indicating their functional relevance."[3]

"HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."[4]

"Snail-related and E2A factors bind to [...] (CAGGTG/A), termed Z-Box."[3]

"HY5 binds to [...], Z-box (ATACGGT), [...]."[4]

"The HY5 protein interacts with [...] Z- (ATACGTGT) boxes [...]."[2]

The more general Z-box consensus sequence accommodating these variations appears to be A(C/T)A(C/G)GT(A/G)T:

  1. Negative strand, positive direction: ACAGGTGT at 1969, contains CAGGTG[3].
  2. Positive strand, positive direction: ACACGTGT at 2962.
  3. ci, positive strand, negative direction: ACACCTGT at 1131, ATACCTAT at 2996, ACACCTGT at 3970.

But neither ones found contain Z-box (ATACGGT, ACCGTAT)[4] or (ATACGTGT, ACACGTAT)[2]. It may be better to sample the three Z-boxes separately:

  1. CAGGT(A/G), (C/T)ACCTG,[3] ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.[5],
  2. ATACGGT[4] ZboxN, and
  3. ATACGTGT[2] ZboxSo.

SIP1-mediated Epithelial Mesenchymal Transition (EMT)

In vivo SIP1, or Zinc finger E-box-binding homeobox 2 (ZEB2), binds "to potential SIP1-binding sites (Z-boxes) located in the vicinity of the cyclin D1 transcription start site."[5]

Three "Z-boxes with coordinates -1014 to -1010 (Z-box 1); -857 to -853 (Z-box 2); and -300 to -290 (Z-box 3) are occupied by SIP1 in [doxorubicin (DOX)] DOX-stimulated cells. In contrast, neither sequences upstream of Z-box 1 [...], nor sequences containing Z-boxes 4 and 5 located at the first exon/intron boundary (-390 to -409) [...] were detected in association with SIP1."[5]

Z-boxes 1-3 contain AGGTG.[5]

The "mutation of Z-boxes 1–3 markedly activated reporter activity in SIP1-expressing cells [...]."[5]

"SIP1 represses cyclin D1 transcriptional activity via direct interaction with Z-boxes 1–3 in the cyclin D1 promoter."[5]

Hypotheses

  1. A1BG has no Z boxes in either promoter.

General Z-box (ZboxG) samplings

Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in A1BG gene transcriptions revealed no occurrence of either.

For the Basic programs testing consensus sequence A(C/T)A(C/G)GT(A/G)T (starting with SuccessablesZbox.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. Negative strand, negative direction: 0.
  2. Negative strand, positive direction: 1, ACAGGTGT at 1969.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 1, ACACGTGT at 2962.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 3, ACACCTGT at 3970, ATACCTAT at 2996, ACACCTGT at 1131.
  8. inverse complement, positive strand, positive direction: 0.

ZboxG (4560-2846) UTRs

  1. Positive strand, negative direction: ACACCTGT at 3970, ATACCTAT at 2996.

ZboxG negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: ACACCTGT at 1131.

ZboxG positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ACAGGTGT at 1969.
  2. Positive strand, positive direction: ACACGTGT at 2962.

Z-box (ZboxSp) samplings

CAGGT(A/G), (C/T)ACCTG,[3] ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.[5],

For the Basic programs testing consensus sequence CAGGT(A/G) (starting with SuccessablesZboxSp.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. Negative strand, negative direction: 0.
  2. Negative strand, positive direction: 0.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

ZboxSp random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

ZboxSp analysis and results

Main article: Complex locus A1BG and ZNF497 § ZboxSps

CAGGT(A/G).[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ZboxSps are greater than the randoms. This suggests that the real ZboxSps are likely active or activable.

Z-box (ZboxN) samplings

For the Basic programs testing consensus sequence ATACGGT (starting with SuccessablesZboxN.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. Negative strand, negative direction: 0.
  2. Negative strand, positive direction: 0.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

ZboxN random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

ZboxN analysis and results

Main article: Complex locus A1BG and ZNF497 § ZboxNs

ATACGGT.[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ZboxNs are greater than the randoms. This suggests that the real ZboxNs are likely active or activable.

Z-box (ZboxSo) samplings

For the Basic programs testing consensus sequence ATACGTGT (starting with SuccessablesZboxSo.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. Negative strand, negative direction: 0.
  2. Negative strand, positive direction: 0.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

ZboxSo random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

ZboxSo analysis and results

Main article: Complex locus A1BG and ZNF497 § ZboxSos

ATACGTGT.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ZboxSos are greater than the randoms. This suggests that the real ZboxSos are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Ulrike Burk, Jörg Schubert, Ulrich Wellner, Otto Schmalhofer, Elizabeth Vincan, Simone Spaderna, Thomas Brabletz (1 June 2008). "A reciprocal repression between ZEB1 and members of the miR‐200 family promotes EMT and invasion in cancer cells". EMBO Reports. 9 (6): 582–589. doi:10.1038/embor.2008.74. Retrieved 15 November 2018.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. Retrieved 26 March 2019.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Simone Spaderna, Otto Schmalhofer, Falk Hlubek, Geert Berx, Andreas Eger, Susanne Merkel, Andreas Jung, Thomas Kirchner, Thomas Brabletz (September 2006). "A Transient, EMT-Linked Loss of Basement Membranes Indicates Metastasis and Poor Survival in Colorectal Cancer". Gastroenterology. 131 (3): 830–840. doi:10.1053/j.gastro.2006.06.016. Retrieved 15 November 2018.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 Ganesh M. Nawkar, Chang Ho Kanga, Punyakishore Maibam, Joung Hun Park, Young Jun Jung, Ho Byoung Chae, Yong Hun Chi, In Jung Jung, Woe Yeon Kim, Dae-Jin Yun, and Sang Yeol Lee (21 February 2017). "HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis" (PDF). Proceedings of the National Academy of Sciences USA. 114 (8): 2084–89. doi:10.1073/pnas.1609844114. Retrieved 24 June 2021.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 Jakob Mejlvang, Marina Kriajevska, Cindy Vandewalle, Tatyana Chernova, A. Emre Sayan, Geert Berx, J. Kilian Mellon, and Eugene Tulchinsky (November 2007). "Direct Repression of Cyclin D1 by SIP1 Attenuates Cell Cycle Progression in Cells Undergoing an Epithelial Mesenchymal Transition". Molecular Biology of the Cell. 18 (11): 4615–4624. doi:10.1091/mbc.e07-05-0406. Retrieved 15 November 2018.

External links

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