Middle sporulation element gene transcriptions: Difference between revisions

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|pmid = 8524222
|pmid = 8524222
| pmc = 230910
| pmc = 230910
| doi = 10.1128/MCB.15.12.6572 }}</ref> The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.<ref name=Lamoureux>{{ cite journal
| doi = 10.1128/MCB.15.12.6572 }}</ref> The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.<ref name=Lamoureux>{{ cite journal
| vauthors = Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN
| vauthors = Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN
| title = Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
| title = Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
Line 31: Line 31:
| pmid = 5
| pmid = 5
| doi = 10.1016/0006-291x(75)90508-2 }}</ref>
| doi = 10.1016/0006-291x(75)90508-2 }}</ref>
Direct "binding of Ndt80 to the [mid sporulation element CRCAAAA/T (Ozsarac et al. 1997)] MSE is necessary for activating transcription of the middle sporulation genes."<ref name=Chu>{{ cite journal
| author = Shelley Chu and Ira Herskowitz
| title = Gametogenesis in Yeast Is Regulated by a Transcriptional Cascade Dependent on Ndt80
| journal = Molecular Cell
| volume = 1
| issue = 5
| pages = 685–96
| date = April 1, 1998
| pmid = 9660952
| doi = 10.1016/S1097-2765(00)80068-4 }}</ref>
"The midsporulation gene ''SPR3'' [...] is expressed only in sporulating cells (20), during both divisions of meiosis. It is therefore regulated in a developmentally specific manner and provides an example of a sporulation gene suited to analysis of midsporulation control. The 5'-flanking region contains several potential regulatory motifs, including an ABFI element which was shown to be essential to the regulation of SPR3 (33)."<ref name=Ozsarac/>
"The SPR3 gene contains four potential TATA boxes, with the most proximal one adjacent to the transcription start sites identified previously (33). The MSE is located 43 to 102 bp upstream of these TATA boxes, locating the sporulation-specific element very close to the site for assembly of the general transcription machinery."<ref name=Ozsarac/>


==Human genes==
==Human genes==
Line 36: Line 51:
== Interactions ==
== Interactions ==


==Consensus sequences==
==MSE consensus sequences==


The Ndt80 protein recognizes and binds to the middle sporulation element (MSE) 5'-C(A/G)CAAA(A/T)-3' in the promoter region of stage-specific genes that are required for progression through meiosis and sporulation.<ref name=Xu/><ref name=Chu>{{ cite journal
Of the midsporulation element (MSE), "a minimal element, CRCAAA(A/T), is sufficient for sporulation specificity."<ref name=Ozsarac>{{ cite journal
| vauthors = Chu S, Herskowitz I
| author = Nesrin Ozsarac, Melissa J. Straffon, Hazel E. Dalton, and Ian W. Dawes
| title = Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80
| title = Regulation of Gene Expression during Meiosis in ''Saccharomyces cerevisiae'': ''SPR3'' Is Controlled by both ABFI and a New Sporulation Control Element
| journal = Molecular Cell
| volume = 1
| issue = 5
| pages = 685–96
| date = April 1998
| pmid = 9660952
| doi = 10.1016/S1097-2765(00)80068-4 }}</ref><ref name=Ozsarac>{{ cite journal
| vauthors = Ozsarac N, Straffon MJ, Dalton HE, Dawes IW
| title = Regulation of gene expression during meiosis in Saccharomyces cerevisiae: SPR3 is controlled by both ABFI and a new sporulation control element
| journal = Molecular and Cellular Biology
| journal = Molecular and Cellular Biology
| volume = 17
| volume = 17
Line 81: Line 87:


For the Basic programs testing consensus sequence ACACAAA (starting with SuccessablesMSEB.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 ACACAAA (starting with SuccessablesMSEB.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, looking for AAAAAAAA, 0.
# negative strand, negative direction, looking for ACACAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for ACACAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for ACACAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for ACACAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for TGTGTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TGTGTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TGTGTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TGTGTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTGTGT, 2, TTTGTGT at 3513, TTTGTGT at 1541.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTGTGT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTGTGT, 1, TTTGTGT at 2835.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTGTGT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for AAACACA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAACACA, 2, AAACACA at 3513, AAACACA at 1541.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAACACA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAACACA, 1, AAACACA at 2835.
 
===MSE (Branco) (4560-2846) UTR gene transcriptions===
 
# Negative strand, negative direction: TTTGTGT at 3513
 
===MSE (Branco) negative direction (2596-1) distal promoters===
 
# Negative strand, negative direction: TTTGTGT at 1541.
 
===MSE (Branco) positive direction (4050-1) distal promoters===
 
# Positive strand, positive direction: TTTGTGT at 2835.
 
==MSE (Branco) random dataset samplings==
 
# MSEBr0: 0.
# MSEBr1: 0.
# MSEBr2: 0.
# MSEBr3: 0.
# MSEBr4: 2, ACACAAA at 1970, ACACAAA at 1775.
# MSEBr5: 0.
# MSEBr6: 0.
# MSEBr7: 0.
# MSEBr8: 0.
# MSEBr9: 0.
# MSEBr0ci: 0.
# MSEBr1ci: 0.
# MSEBr2ci: 0.
# MSEBr3ci: 0.
# MSEBr4ci: 0.
# MSEBr5ci: 1, TTTGTGT at 323.
# MSEBr6ci: 1, TTTGTGT at 4365.
# MSEBr7ci: 0.
# MSEBr8ci: 0.
# MSEBr9ci: 0.
 
===MSEBr arbitrary (evens) (4560-2846) UTRs===
 
# MSEBr6ci: TTTGTGT at 4365.
 
===MSEBr alternate positive direction (evens) (4445-4265) core promoters===
 
# MSEBr6ci: TTTGTGT at 4365.
 
===MSEBr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# MSEBr4: ACACAAA at 1970, ACACAAA at 1775.
 
===MSEBr alternate negative direction (odds) (2596-1) distal promoters===
 
# MSEBr5ci: TTTGTGT at 323.
 
===MSEBr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# MSEBr5ci: TTTGTGT at 323.
 
===MSEBr alternate positive direction (evens) (4050-1) distal promoters===
 
# MSEBr4: ACACAAA at 1970, ACACAAA at 1775.


===AAA UTR gene transcriptions===
==MSE (Branco) analysis and results==
{{main|UTR promoter gene transcriptions}}
{{main|Complex locus A1BG and ZNF497#MSE (Branco)s}}
"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."<ref name=Branco/>


===AAA core promoters===
{|class="wikitable"
{{main|Core promoter gene transcriptions}}
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--1,+-0)
|-
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.05
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0.05
|-
| 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 || 1 || 10 || 0.1 || 0.05
|-
| 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 || 1 || 2 || 0.5 || 0.5 ± 0.5 (--1,+-0)
|-
| Randoms || Distal || arbitrary negative || 2 || 10 || 0.2 || 0.015
|-
| Randoms || Distal || alternate negative || 1 || 10 || 0.1 || 0.15
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1)
|-
| Randoms || Distal || arbitrary positive || 1 || 10 || 0.1 || 0.15
|-
| Randoms || Distal || alternate positive || 2 || 10 || 0.2 || 0.15
|}


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


===AAA distal promoters===
The occurrences of real MSE (Branco)s are greater than the randoms. This suggests that the real MSE (Branco)s are likely active or activable.
{{main|Distal promoter gene transcriptions}}


==MSE (Xu) samplings==
==MSE (Ozsarac) samplings==


Copying a responsive elements consensus sequence C(A/G)CAAA(A/T) and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
Copying a responsive elements consensus sequence C(A/G)CAAA(A/T) and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence C(A/G)CAAA(A/T) (starting with SuccessablesMSEX.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 C(A/G)CAAA(A/T) (starting with SuccessablesMSEX.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, looking for AAAAAAAA, 0.
# negative strand, negative direction, looking for C(A/G)CAAA(A/T), 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for C(A/G)CAAA(A/T), 2, CACAAAA at 3767, CGCAAAA at 164.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for C(A/G)CAAA(A/T), 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for C(A/G)CAAA(A/T), 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for G(C/T)GTTT(A/T), 2, GTGTTTT at 3767, GCGGGGG at 164.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for G(C/T)GTTT(A/T), 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for G(C/T)GTTT(A/T), 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for G(C/T)GTTT(A/T), 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for (A/T)TTTG(C/T)G, 1, TTTTGTG at 3512.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for (A/T)TTTG(C/T)G, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for (A/T)TTTG(C/T)G, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for (A/T)TTTG(C/T)G, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for (A/T)AAAC(A/G)C, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for (A/T)AAAC(A/G)C, 1, AAAACAC at 3512.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for (A/T)AAAC(A/G)C, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for (A/T)AAAC(A/G)C, 0.


===AAA UTR gene transcriptions===
===MSE (Ozsarac) UTR gene transcriptions===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
Negative strand, negative direction: TTTTGTG at 3512


===AAA core promoters===
Positive strand, negative direction: CACAAAA at 3767
{{main|Core promoter gene transcriptions}}


===AAA proximal promoters===
===MSE (Ozsarac) distal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Positive strand, negative direction: CGCAAAA at 164


===AAA distal promoters===
==MSE (Ozsarac) random dataset samplings==
{{main|Distal promoter gene transcriptions}}
 
# MSEXr0: 2, CGCAAAT at 2807, CACAAAT at 1788.
# MSEXr1: 3, CGCAAAA at 4408, CACAAAA at 3175, CGCAAAA at 1775.
# MSEXr2: 1, CACAAAA at 4322.
# MSEXr3: 1, CGCAAAT at 3362.
# MSEXr4: 2, CACAAAA at 1971, CACAAAA at 1776.
# MSEXr5: 1, CGCAAAA at 752.
# MSEXr6: 4, CACAAAT at 3077, CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
# MSEXr7: 2, CGCAAAT at 2393, CGCAAAT at 660.
# MSEXr8: 2, CACAAAT at 3714, CGCAAAA at 2111.
# MSEXr9: 1, CACAAAT at 4053.
# MSEXr0ci: 0.
# MSEXr1ci: 1, TTTTGTG at 282.
# MSEXr2ci: 2, TTTTGTG at 4487, TTTTGCG at 37.
# MSEXr3ci: 1, ATTTGCG at 3972.
# MSEXr4ci: 2, TTTTGCG at 2429, TTTTGCG at 1426.
# MSEXr5ci: 3, ATTTGTG at 3880, TTTTGTG at 322, TTTTGCG at 276.
# MSEXr6ci: 1, TTTTGTG at 2653.
# MSEXr7ci: 2, ATTTGTG at 4226, TTTTGTG at 493.
# MSEXr8ci: 1, ATTTGCG at 2528.
# MSEXr9ci: 1, TTTTGTG at 470.
 
===MSEXr arbitrary (evens) (4560-2846) UTRs===
 
# MSEXr2: CACAAAA at 4322.
# MSEXr6: CACAAAT at 3077.
# MSEXr8: CACAAAT at 3714.
# MSEXr2ci: TTTTGTG at 4487.
 
===MSEXr alternate (odds) (4560-2846) UTRs===
 
# MSEXr1: CGCAAAA at 4408, CACAAAA at 3175.
# MSEXr3: CGCAAAT at 3362.
# MSEXr9: CACAAAT at 4053.
# MSEXr5ci: ATTTGTG at 3880.
# MSEXr7ci: ATTTGTG at 4226.
 
===MSEXr arbitrary positive direction (odds) (4445-4265) core promoters===
 
# MSEXr1: CGCAAAA at 4408.
 
===MSEXr alternate positive direction (evens) (4445-4265) core promoters===
 
# MSEXr2: CACAAAA at 4322.
 
===MSEXr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
# MSEXr0: CGCAAAT at 2807.
# MSEXr6ci: TTTTGTG at 2653.
 
===MSEXr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
# MSEXr9: CACAAAT at 4053.
# MSEXr7ci: ATTTGTG at 4226.
 
===MSEXr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# MSEXr0: CACAAAT at 1788.
# MSEXr4: CACAAAA at 1971, CACAAAA at 1776.
# MSEXr6: CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
# MSEXr8: CGCAAAA at 2111.
# MSEXr2ci: TTTTGCG at 37.
# MSEXr4ci: TTTTGCG at 2429, TTTTGCG at 1426.
# MSEXr8ci: ATTTGCG at 2528.
 
===MSEXr alternate negative direction (odds) (2596-1) distal promoters===
 
# MSEXr1: CGCAAAA at 1775.
# MSEXr5: CGCAAAA at 752.
# MSEXr7: CGCAAAT at 2393, CGCAAAT at 660.
# MSEXr1ci: TTTTGTG at 282.
# MSEXr5ci: TTTTGTG at 322, TTTTGCG at 276.
# MSEXr9ci: TTTTGTG at 470.
# MSEXr7ci: TTTTGTG at 493.
 
===MSEXr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# MSEXr1: CACAAAA at 3175, CGCAAAA at 1775.
# MSEXr3: CGCAAAT at 3362.
# MSEXr5: CGCAAAA at 752.
# MSEXr7: CGCAAAT at 2393, CGCAAAT at 660.
# MSEXr1ci: TTTTGTG at 282.
# MSEXr5ci: ATTTGTG at 3880, TTTTGTG at 322, TTTTGCG at 276.
# MSEXr9ci: TTTTGTG at 470.
# MSEXr7ci: TTTTGTG at 493.
 
===MSEXr alternate positive direction (evens) (4050-1) distal promoters===
 
# MSEXr0: CGCAAAT at 2807, CACAAAT at 1788.
# MSEXr4: CACAAAA at 1971, CACAAAA at 1776.
# MSEXr6: CACAAAT at 3077, CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
# MSEXr8: CACAAAT at 3714, CGCAAAA at 2111.
# MSEXr2ci: TTTTGCG at 37.
# MSEXr4ci: TTTTGCG at 2429, TTTTGCG at 1426.
# MSEXr8ci: ATTTGCG at 2528.
 
==MSE (Ozsarac) analysis and results==
{{main|Complex locus A1BG and ZNF497#MSE (Ozsarac)s}}
Of the midsporulation element (MSE), "a minimal element, CRCAAA(A/T) [C(A/G)CAAA(A/T)], is sufficient for sporulation specificity."<ref name=Ozsarac/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 2 || 2 || 1 || 1 ± 0 (--1,+-1)
|-
| Randoms || UTR || arbitrary negative || 4 || 10 || 0.4 || 0.5
|-
| Randoms || UTR || alternate negative || 6 || 10 || 0.6 || 0.5
|-
| 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 || 1 || 10 || 0.1 || 0.1
|-
| Randoms || Core || alternate positive || 1 || 10 || 0.1 || 0.1
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary negative || 2 || 10 || 0.2 || 0.1
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0.1
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 2 || 10 || 0.2 || 0.1
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.1
|-
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)
|-
| Randoms || Distal || arbitrary negative || 11 || 10 || 1.1 || 1.0
|-
| Randoms || Distal || alternate negative || 9 || 10 || 0.9 || 1.0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 12 || 10 || 1.2 || 1.3
|-
| Randoms || Distal || alternate positive || 14 || 10 || 1.4 || 1.3
|}
 
Comparison:
 
The occurrences of real MSE (Ozsarac) UTRs are greater than the randoms, negative distals are within the randoms. This suggests that the real MSE (Ozsarac)s are likely active or activable.
 
==HAP2 consensus sequences==
 
"The HAP2 motif [CCAATCA] binds a heterotrimeric transcription factor, HAP2/3/4, involved in the derepression of respiratory genes in cells growing on nonfermentable carbon sources (34)."<ref name=Ozsarac/>
 
==HAP2 samplings==
{{main|Model samplings}}
Copying a responsive elements consensus sequence CCAATCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
 
For the Basic programs testing consensus sequence CCAATCA (starting with SuccessablesHAP.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, looking for CCAATCA, 0.
# positive strand, negative direction, looking for CCAATCA, 0.
# positive strand, positive direction, looking for CCAATCA, 0.
# negative strand, positive direction, looking for CCAATCA, 0.
# complement, negative strand, negative direction, looking for GGTTAGT, 0.
# complement, positive strand, negative direction, looking for GGTTAGT, 0.
# complement, positive strand, positive direction, looking for GGTTAGT, 0.
# complement, negative strand, positive direction, looking for GGTTAGT, 0.
# inverse complement, negative strand, negative direction, looking for TGATTGG, 0.
# inverse complement, positive strand, negative direction, looking for TGATTGG, 0.
# inverse complement, positive strand, positive direction, looking for TGATTGG, 0.
# inverse complement, negative strand, positive direction, looking for TGATTGG, 0.
# inverse negative strand, negative direction, looking for ACTAACC, 0.
# inverse positive strand, negative direction, looking for ACTAACC, 0.
# inverse positive strand, positive direction, looking for ACTAACC, 0.
# inverse negative strand, positive direction, looking for ACTAACC, 0.


==Acknowledgements==
==Acknowledgements==

Latest revision as of 00:16, 5 September 2023

Associate Editor(s)-in-Chief: Henry A. Hoff

Ndt80 is a meiosis-specific transcription factor required for successful completion of meiosis and spore formation.[1] The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.[2] Ndt80 also competes with the repressor SUM1 for binding to promoters containing MSEs.[3]

Direct "binding of Ndt80 to the [mid sporulation element CRCAAAA/T (Ozsarac et al. 1997)] MSE is necessary for activating transcription of the middle sporulation genes."[4]

"The midsporulation gene SPR3 [...] is expressed only in sporulating cells (20), during both divisions of meiosis. It is therefore regulated in a developmentally specific manner and provides an example of a sporulation gene suited to analysis of midsporulation control. The 5'-flanking region contains several potential regulatory motifs, including an ABFI element which was shown to be essential to the regulation of SPR3 (33)."[5]

"The SPR3 gene contains four potential TATA boxes, with the most proximal one adjacent to the transcription start sites identified previously (33). The MSE is located 43 to 102 bp upstream of these TATA boxes, locating the sporulation-specific element very close to the site for assembly of the general transcription machinery."[5]

Human genes

Interactions

MSE consensus sequences

Of the midsporulation element (MSE), "a minimal element, CRCAAA(A/T), is sufficient for sporulation specificity."[5]

"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."[6]

Middle sporulation elements (MSE) motif has the consensus sequence 5'-ACACAAA-3'.[6]

MSE (Branco) samplings

Copying apparent core consensus sequences for the MSEs of ACACAAA and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ACACAAA (starting with SuccessablesMSEB.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, looking for ACACAAA, 0.
  2. positive strand, negative direction, looking for ACACAAA, 0.
  3. positive strand, positive direction, looking for ACACAAA, 0.
  4. negative strand, positive direction, looking for ACACAAA, 0.
  5. complement, negative strand, negative direction, looking for TGTGTTT, 0.
  6. complement, positive strand, negative direction, looking for TGTGTTT, 0.
  7. complement, positive strand, positive direction, looking for TGTGTTT, 0.
  8. complement, negative strand, positive direction, looking for TGTGTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTGTGT, 2, TTTGTGT at 3513, TTTGTGT at 1541.
  10. inverse complement, positive strand, negative direction, looking for TTTGTGT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTGTGT, 1, TTTGTGT at 2835.
  12. inverse complement, negative strand, positive direction, looking for TTTGTGT, 0.
  13. inverse negative strand, negative direction, looking for AAACACA, 0.
  14. inverse positive strand, negative direction, looking for AAACACA, 2, AAACACA at 3513, AAACACA at 1541.
  15. inverse positive strand, positive direction, looking for AAACACA, 0.
  16. inverse negative strand, positive direction, looking for AAACACA, 1, AAACACA at 2835.

MSE (Branco) (4560-2846) UTR gene transcriptions

  1. Negative strand, negative direction: TTTGTGT at 3513

MSE (Branco) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTTGTGT at 1541.

MSE (Branco) positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: TTTGTGT at 2835.

MSE (Branco) random dataset samplings

  1. MSEBr0: 0.
  2. MSEBr1: 0.
  3. MSEBr2: 0.
  4. MSEBr3: 0.
  5. MSEBr4: 2, ACACAAA at 1970, ACACAAA at 1775.
  6. MSEBr5: 0.
  7. MSEBr6: 0.
  8. MSEBr7: 0.
  9. MSEBr8: 0.
  10. MSEBr9: 0.
  11. MSEBr0ci: 0.
  12. MSEBr1ci: 0.
  13. MSEBr2ci: 0.
  14. MSEBr3ci: 0.
  15. MSEBr4ci: 0.
  16. MSEBr5ci: 1, TTTGTGT at 323.
  17. MSEBr6ci: 1, TTTGTGT at 4365.
  18. MSEBr7ci: 0.
  19. MSEBr8ci: 0.
  20. MSEBr9ci: 0.

MSEBr arbitrary (evens) (4560-2846) UTRs

  1. MSEBr6ci: TTTGTGT at 4365.

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

  1. MSEBr6ci: TTTGTGT at 4365.

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

  1. MSEBr4: ACACAAA at 1970, ACACAAA at 1775.

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

  1. MSEBr5ci: TTTGTGT at 323.

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

  1. MSEBr5ci: TTTGTGT at 323.

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

  1. MSEBr4: ACACAAA at 1970, ACACAAA at 1775.

MSE (Branco) analysis and results

Main article: Complex locus A1BG and ZNF497 § MSE (Branco)s

"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."[6]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
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 1 10 0.1 0.05
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 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms Distal arbitrary negative 2 10 0.2 0.015
Randoms Distal alternate negative 1 10 0.1 0.15
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 1 10 0.1 0.15
Randoms Distal alternate positive 2 10 0.2 0.15

Comparison:

The occurrences of real MSE (Branco)s are greater than the randoms. This suggests that the real MSE (Branco)s are likely active or activable.

MSE (Ozsarac) samplings

Copying a responsive elements consensus sequence C(A/G)CAAA(A/T) and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence C(A/G)CAAA(A/T) (starting with SuccessablesMSEX.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, looking for C(A/G)CAAA(A/T), 0.
  2. positive strand, negative direction, looking for C(A/G)CAAA(A/T), 2, CACAAAA at 3767, CGCAAAA at 164.
  3. positive strand, positive direction, looking for C(A/G)CAAA(A/T), 0.
  4. negative strand, positive direction, looking for C(A/G)CAAA(A/T), 0.
  5. complement, negative strand, negative direction, looking for G(C/T)GTTT(A/T), 2, GTGTTTT at 3767, GCGGGGG at 164.
  6. complement, positive strand, negative direction, looking for G(C/T)GTTT(A/T), 0.
  7. complement, positive strand, positive direction, looking for G(C/T)GTTT(A/T), 0.
  8. complement, negative strand, positive direction, looking for G(C/T)GTTT(A/T), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/T)TTTG(C/T)G, 1, TTTTGTG at 3512.
  10. inverse complement, positive strand, negative direction, looking for (A/T)TTTG(C/T)G, 0.
  11. inverse complement, positive strand, positive direction, looking for (A/T)TTTG(C/T)G, 0.
  12. inverse complement, negative strand, positive direction, looking for (A/T)TTTG(C/T)G, 0.
  13. inverse negative strand, negative direction, looking for (A/T)AAAC(A/G)C, 0.
  14. inverse positive strand, negative direction, looking for (A/T)AAAC(A/G)C, 1, AAAACAC at 3512.
  15. inverse positive strand, positive direction, looking for (A/T)AAAC(A/G)C, 0.
  16. inverse negative strand, positive direction, looking for (A/T)AAAC(A/G)C, 0.

MSE (Ozsarac) UTR gene transcriptions

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTTTGTG at 3512

Positive strand, negative direction: CACAAAA at 3767

MSE (Ozsarac) distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: CGCAAAA at 164

MSE (Ozsarac) random dataset samplings

  1. MSEXr0: 2, CGCAAAT at 2807, CACAAAT at 1788.
  2. MSEXr1: 3, CGCAAAA at 4408, CACAAAA at 3175, CGCAAAA at 1775.
  3. MSEXr2: 1, CACAAAA at 4322.
  4. MSEXr3: 1, CGCAAAT at 3362.
  5. MSEXr4: 2, CACAAAA at 1971, CACAAAA at 1776.
  6. MSEXr5: 1, CGCAAAA at 752.
  7. MSEXr6: 4, CACAAAT at 3077, CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
  8. MSEXr7: 2, CGCAAAT at 2393, CGCAAAT at 660.
  9. MSEXr8: 2, CACAAAT at 3714, CGCAAAA at 2111.
  10. MSEXr9: 1, CACAAAT at 4053.
  11. MSEXr0ci: 0.
  12. MSEXr1ci: 1, TTTTGTG at 282.
  13. MSEXr2ci: 2, TTTTGTG at 4487, TTTTGCG at 37.
  14. MSEXr3ci: 1, ATTTGCG at 3972.
  15. MSEXr4ci: 2, TTTTGCG at 2429, TTTTGCG at 1426.
  16. MSEXr5ci: 3, ATTTGTG at 3880, TTTTGTG at 322, TTTTGCG at 276.
  17. MSEXr6ci: 1, TTTTGTG at 2653.
  18. MSEXr7ci: 2, ATTTGTG at 4226, TTTTGTG at 493.
  19. MSEXr8ci: 1, ATTTGCG at 2528.
  20. MSEXr9ci: 1, TTTTGTG at 470.

MSEXr arbitrary (evens) (4560-2846) UTRs

  1. MSEXr2: CACAAAA at 4322.
  2. MSEXr6: CACAAAT at 3077.
  3. MSEXr8: CACAAAT at 3714.
  4. MSEXr2ci: TTTTGTG at 4487.

MSEXr alternate (odds) (4560-2846) UTRs

  1. MSEXr1: CGCAAAA at 4408, CACAAAA at 3175.
  2. MSEXr3: CGCAAAT at 3362.
  3. MSEXr9: CACAAAT at 4053.
  4. MSEXr5ci: ATTTGTG at 3880.
  5. MSEXr7ci: ATTTGTG at 4226.

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

  1. MSEXr1: CGCAAAA at 4408.

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

  1. MSEXr2: CACAAAA at 4322.

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

  1. MSEXr0: CGCAAAT at 2807.
  2. MSEXr6ci: TTTTGTG at 2653.

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

  1. MSEXr9: CACAAAT at 4053.
  2. MSEXr7ci: ATTTGTG at 4226.

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

  1. MSEXr0: CACAAAT at 1788.
  2. MSEXr4: CACAAAA at 1971, CACAAAA at 1776.
  3. MSEXr6: CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
  4. MSEXr8: CGCAAAA at 2111.
  5. MSEXr2ci: TTTTGCG at 37.
  6. MSEXr4ci: TTTTGCG at 2429, TTTTGCG at 1426.
  7. MSEXr8ci: ATTTGCG at 2528.

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

  1. MSEXr1: CGCAAAA at 1775.
  2. MSEXr5: CGCAAAA at 752.
  3. MSEXr7: CGCAAAT at 2393, CGCAAAT at 660.
  4. MSEXr1ci: TTTTGTG at 282.
  5. MSEXr5ci: TTTTGTG at 322, TTTTGCG at 276.
  6. MSEXr9ci: TTTTGTG at 470.
  7. MSEXr7ci: TTTTGTG at 493.

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

  1. MSEXr1: CACAAAA at 3175, CGCAAAA at 1775.
  2. MSEXr3: CGCAAAT at 3362.
  3. MSEXr5: CGCAAAA at 752.
  4. MSEXr7: CGCAAAT at 2393, CGCAAAT at 660.
  5. MSEXr1ci: TTTTGTG at 282.
  6. MSEXr5ci: ATTTGTG at 3880, TTTTGTG at 322, TTTTGCG at 276.
  7. MSEXr9ci: TTTTGTG at 470.
  8. MSEXr7ci: TTTTGTG at 493.

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

  1. MSEXr0: CGCAAAT at 2807, CACAAAT at 1788.
  2. MSEXr4: CACAAAA at 1971, CACAAAA at 1776.
  3. MSEXr6: CACAAAT at 3077, CACAAAA at 1779, CACAAAA at 970, CGCAAAT at 362.
  4. MSEXr8: CACAAAT at 3714, CGCAAAA at 2111.
  5. MSEXr2ci: TTTTGCG at 37.
  6. MSEXr4ci: TTTTGCG at 2429, TTTTGCG at 1426.
  7. MSEXr8ci: ATTTGCG at 2528.

MSE (Ozsarac) analysis and results

Main article: Complex locus A1BG and ZNF497 § MSE (Ozsarac)s

Of the midsporulation element (MSE), "a minimal element, CRCAAA(A/T) [C(A/G)CAAA(A/T)], is sufficient for sporulation specificity."[5]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 0 (--1,+-1)
Randoms UTR arbitrary negative 4 10 0.4 0.5
Randoms UTR alternate negative 6 10 0.6 0.5
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 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 2 10 0.2 0.1
Randoms Proximal alternate negative 0 10 0 0.1
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.1
Randoms Proximal alternate positive 0 10 0 0.1
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 11 10 1.1 1.0
Randoms Distal alternate negative 9 10 0.9 1.0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 12 10 1.2 1.3
Randoms Distal alternate positive 14 10 1.4 1.3

Comparison:

The occurrences of real MSE (Ozsarac) UTRs are greater than the randoms, negative distals are within the randoms. This suggests that the real MSE (Ozsarac)s are likely active or activable.

HAP2 consensus sequences

"The HAP2 motif [CCAATCA] binds a heterotrimeric transcription factor, HAP2/3/4, involved in the derepression of respiratory genes in cells growing on nonfermentable carbon sources (34)."[5]

HAP2 samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CCAATCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCAATCA (starting with SuccessablesHAP.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, looking for CCAATCA, 0.
  2. positive strand, negative direction, looking for CCAATCA, 0.
  3. positive strand, positive direction, looking for CCAATCA, 0.
  4. negative strand, positive direction, looking for CCAATCA, 0.
  5. complement, negative strand, negative direction, looking for GGTTAGT, 0.
  6. complement, positive strand, negative direction, looking for GGTTAGT, 0.
  7. complement, positive strand, positive direction, looking for GGTTAGT, 0.
  8. complement, negative strand, positive direction, looking for GGTTAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGATTGG, 0.
  10. inverse complement, positive strand, negative direction, looking for TGATTGG, 0.
  11. inverse complement, positive strand, positive direction, looking for TGATTGG, 0.
  12. inverse complement, negative strand, positive direction, looking for TGATTGG, 0.
  13. inverse negative strand, negative direction, looking for ACTAACC, 0.
  14. inverse positive strand, negative direction, looking for ACTAACC, 0.
  15. inverse positive strand, positive direction, looking for ACTAACC, 0.
  16. inverse negative strand, positive direction, looking for ACTAACC, 0.

Acknowledgements

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

See also

References

  1. ↑ Xu L, Ajimura M, Padmore R, Klein C, Kleckner N (December 1995). "NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae". Molecular and Cellular Biology. 15 (12): 6572–81. doi:10.1128/MCB.15.12.6572. PMC 230910. PMID 8524222.
  2. ↑ Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN (November 2002). "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA". The EMBO Journal. 21 (21): 5721–32. doi:10.1093/emboj/cdf572. PMC 131069. PMID 12411490.
  3. ↑ Hendrickson WA, Ward KB (October 1975). "Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin". Biochemical and Biophysical Research Communications. 66 (4): 1349–56. doi:10.1016/0006-291x(75)90508-2. PMID 5.
  4. ↑ Shelley Chu and Ira Herskowitz (April 1, 1998). "Gametogenesis in Yeast Is Regulated by a Transcriptional Cascade Dependent on Ndt80". Molecular Cell. 1 (5): 685–96. doi:10.1016/S1097-2765(00)80068-4. PMID 9660952.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Nesrin Ozsarac, Melissa J. Straffon, Hazel E. Dalton, and Ian W. Dawes (March 1997). "Regulation of Gene Expression during Meiosis in Saccharomyces cerevisiae: SPR3 Is Controlled by both ABFI and a New Sporulation Control Element". Molecular and Cellular Biology. 17 (3): 1152–9. doi:10.1128/MCB.17.3.1152. PMC 231840. PMID 9032242.
  6. ↑ 6.0 6.1 6.2 J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda (August 2017). "Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance". Clinical Microbiology and Infection. 23 (8): 575.e1–575.e8. doi:10.1016/j.cmi.2017.02.002. PMID 28196695. Retrieved 5 September 2020.

External links

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