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=Introduction=
'''Editor-In-Chief:''' Henry A. Hoff


'''Nucleohyaloplasm''' is the [[cytosol]] within the [[nucleus]], without the [[microfilaments]] and the [[microtubules]]. This liquid part contains [[enzyme]]s and intermediate [[metabolite]]s. Many substances such as [[nucleotide]]s (necessary for purposes such as the [[DNA replication|replication of DNA]] and production of [[Messenger RNA|mRNA]]) and enzymes (which direct activities that take place in the nucleus) are dissolved in the nucleohyaloplasm.
On recent contributions:
{{AE}} Henry A. Hoff


As a cytosol, it consists mostly of [[water]], dissolved ions, small molecules, and large water-soluble molecules (such as [[protein]]). It contains about 20% to 30% protein. It has a high concentration of K⁺ ions and a low concentration of Na⁺ ions. Normal human cytosolic [[pH]] ranges between 7.3 - 7.5, depending on the [[cell type]] involved.<ref name=Roos>{{cite journal |author=Roos A, Boron WF |title=Intracellular pH |journal=Physiol. Rev. |volume=61 |issue=2 |pages=296–434 |year=1981 |month=April |pmid=7012859 |url=http://physrev.physiology.org/cgi/pmidlookup?view=long&pmid=7012859}}</ref>
==Human genes==


=Small particles=


Small particles (< 30 kDa) are able to pass through the [[nuclear pore]] complex by [[passive transport]]. The majority of the non-protein molecules have a [[molecular mass]] of less than 300&nbsp;[[Atomic mass unit|Da]].<ref name=Goodacre>{{cite journal |author=Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB |title=Metabolomics by numbers: acquiring and understanding global metabolite data |journal=Trends Biotechnol. |volume=22 |issue=5 |pages=245–52 |year=2004 |month=May |pmid=15109811 |doi=10.1016/j.tibtech.2004.03.007 |url=http://personalpages.manchester.ac.uk/staff/roy.goodacre/learning/metabprof/Goodacre-TibTech2004.pdf|format=PDF}}</ref> This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the [[metabolite]]s) is immense. For example up to 200,000 different small molecules might be made in plants, although not all these will be present in the same species, or in a single cell.<ref name=Weckwerth>{{cite journal |author=Weckwerth W |title=Metabolomics in systems biology |journal=Annu Rev Plant Biol |volume=54 |issue= |pages=669–89 |year=2003 |pmid=14503007 |doi=10.1146/annurev.arplant.54.031902.135014}}</ref> Estimates of the number of metabolites in a single cell of ''[[Escherichia coli|E. coli]]'' or [[Saccharomyces cerevisiae|baker's yeast]] predict that under 1,000 are made.<ref name=Reed>{{cite journal |author=Reed JL, Vo TD, Schilling CH, Palsson BO |title=An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) |journal=Genome Biol. |volume=4 |issue=9 |pages=R54 |year=2003 |pmid=12952533 |pmc=193654 |doi=10.1186/gb-2003-4-9-r54 |url=http://genomebiology.com/1465-6906/4/R54}}</ref><ref name=Förster>{{cite journal |author=Förster J, Famili I, Fu P, Palsson BØ, Nielsen J |title=Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network |journal=Genome Res. |volume=13 |issue=2 |pages=244–53 |year=2003 |month=February |pmid=12566402 |pmc=420374 |doi=10.1101/gr.234503 |url=http://www.genome.org/cgi/pmidlookup?view=long&pmid=12566402}}</ref>
==Gene expressions==
{{main|Gene expressions}}


[[Miscibility|Miscible]] molecules such as O<sub>2</sub>, CO<sub>2</sub> and NH<sub>3</sub> occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions.
==Interactions==


Relative to the outside of a cell, the concentration of Ca<sup>2+</sup> is low.<ref name=Berridge>{{cite journal |author=Berridge MJ |title=Elementary and global aspects of calcium signalling |journal=J. Physiol. (Lond.) |volume=499 ( Pt 2) |issue= |pages=291–306 |year=1997 |month=March |pmid=9080360 |pmc=1159305 |url=http://www.jphysiol.org/cgi/pmidlookup?view=long&pmid=9080360}}</ref> In addition to sodium and potassium ions the nucleohyaloplasm also contains Mg<sup>2+</sup><ref name=Langelier>{{ cite journal |author=Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B |title=The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II |journal=Nucleic Acids Res. |volume=33 |issue=8 |pages=2629-39 |year=2005 |month=May |pmid=15886393 }}</ref>. Some of these magnesium ions are associated with incoming ribonucleoside triphosphate (NTP) as they enter the catalytic center for transcription by RNA polymerase (RNAP) II.<ref name=Langelier/> The remaining typical ions found in any cytosol include chloride and bicarbonate.<ref name=Lodish>{{cite book |author=Lodish, Harvey F. |title=Molecular cell biology |publisher=Scientific American Books |location=New York |year=1999 |pages= |isbn=0-7167-3136-3 |oclc=174431482}}</ref>


Intranuclear posttranscriptional modifications such as m[[RNA editing]] convert cytidine to uridine within some mRNA.<ref name=Ashkenas>{{ cite journal |author=Ashkenas J |title=Gene regulation by mRNA editing |journal=Am J Hum Genet. |volume=60 |issue=2 | pages=278-83 |month=Feb |year=1997 |pmid=9012400 }}</ref> This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia<ref name=3.5.4.5>{{cite web | title = NiceZyme View of ENZYME: EC 3.5.4.5| url = http://www.expasy.org/cgi-bin/nicezyme.pl?3.5.4.5| accessdate = }}</ref> or produces ammonium in solution. This enzyme is Zn<sup>2+</sup> dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate.<ref name=c100269>{{cite web | title = NCBI Conserved Domains: cytidine_deaminase-like Super-family| url = http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=119679| accessdate = }}</ref>
==Consensus sequences==


Cells also maintain an intracellular iron ion (Fe<sup>2+</sup>) homeostasis.<ref name=Mukhopadhyay>{{ cite journal |author=Mukhopadhyay CK, Attieh ZK, Fox PL |title=Role of ceruloplasmin in cellular iron uptake |journal=Science. |volume=279 |issue=5351 |pages=714-7 |month=Jan |year=1998 |pmid=9445478 }}</ref> Cu<sup>2+</sup> serves as a cofactor.<ref name=1.16.3.1>{{cite web | title = NiceZyme View of ENZYME: EC 1.16.3.1 | url = http://www.expasy.org/cgi-bin/nicezyme.pl? 1.16.3.1 | accessdate = }}</ref>


When a nucleotide is incorporated into a growing [[DNA]] or [[RNA]] strand by a [[polymerase]], [[pyrophosphate]] (PPi) is released. The pyrophosphate anion has the structure P<sub>2</sub>O<sub>7</sub><sup>4&minus;</sup>, and is an [[acid]] [[anhydride]] of [[phosphate]]. It is unstable in [[aqueous solution]] and rapidly [[hydrolysis|hydrolyze]]s into inorganic phosphate HPO<sub>4</sub><sup>2&minus;</sup> (orthophosphate).
==Binding site for==


The average mass range for amino acids: 75 - 204 Da. By comparison a water molecule is 18 Da. Nucleotides range in size from 176 Da (OMP) to 523 Da (GTP). The lateral speed of biological molecules in passive diffusion in water is on the order of 500 - 50 nm/sec. But in cytosol such as the nucleohyaloplasm: ~120 - 10 nm/sec due to crowding and collisions with large molecules.
==Complement copies==
{{main|Complement copy gene transcriptions}}


=Large particles=
==Inverse copies==
{{main|Inverse copy gene transcriptions}}


=Structures=
==Complement-inverse copies==


=Human nucleohyaloplasm=
 
==Enhancer activity==
 
 
==Promoter occurrences==
 
 
==Hypotheses==
{{main|Hypotheses}}
# A1BG has no regulatory elements in either promoter.
# A1BG is not transcribed by a regulatory element.
# No regulatory element participates in the transcription of A1BG.
 
==Response element samplings==
 
Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 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===
 
==Response element 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===
 
==Response element analysis and results==
{{main|Complex locus A1BG and ZNF497#Name of response elements}}
The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing.<ref name=Zhang>{{ cite journal
|author=Bosen Zhang, Liwei Song, Jiali Cai, Lei Li, Hong Xu, Mengying Li, Jiamin Wang, Minmin Shi, Hao Chen, Hao Jia, and Zhaoyuan Hou
|title=The LIM protein Ajuba/SP1 complex forms a feed forward loop to induce SP1 target genes and promote pancreatic cancer cell proliferation
|journal=Journal of Experimental and Clinical Cancer Research
|date=17 May 2019
|volume=38
|issue=
|pages=205
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525466/
|arxiv=
|bibcode=
|doi=10.1186/s13046-019-1203-2
|pmid=31101117
|accessdate=27 February 2021 }}</ref>
 
{|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 responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences 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 [http://www.wikiversity.org Wikiversity].
 
Initial content for this page in some instances came from [http://www.wikipedia.org Wikipedia].
 
Initial content for this page in some instances incorporates text from the [https://www.ncbi.nlm.nih.gov/gene United States National Library of Medicine].
 
==See also==
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element gene transcriptions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
{{Div col end}}
 
==References==
{{reflist|2}}
 
==External links==
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
 
<!-- footer templates -->
{{Gene project}}{{tlx|Phosphate biochemistry}}{{Transcription factors and intracellular receptors}}
 
<!-- footer categories -->
 
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* [https://en.wikipedia.org/wiki/User:Marshallsumter Wikipedia]
 
* [http://en.wikiquote.org/wiki/User:Marshallsumter Wikiquote]
 
* [http://en.wikisource.org/wiki/User:Marshallsumter Wikisource]
 
* [http://species.wikimedia.org/wiki/User:Marshallsumter Wikispecies]
 
* [http://en.wikiversity.org/wiki/User:Marshallsumter Wikiversity]
 
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Latest revision as of 05:24, 29 January 2023

Editor-In-Chief: Henry A. Hoff

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

Human genes

Gene expressions

Main article: Gene expressions

Interactions

Consensus sequences

Binding site for

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

Complement-inverse copies

Enhancer activity

Promoter occurrences

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

Response element samplings

Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 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

Response element 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

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § Name of response elements

The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing.[1]

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 responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences 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.

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

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. ↑ Bosen Zhang, Liwei Song, Jiali Cai, Lei Li, Hong Xu, Mengying Li, Jiamin Wang, Minmin Shi, Hao Chen, Hao Jia, and Zhaoyuan Hou (17 May 2019). "The LIM protein Ajuba/SP1 complex forms a feed forward loop to induce SP1 target genes and promote pancreatic cancer cell proliferation". Journal of Experimental and Clinical Cancer Research. 38: 205. doi:10.1186/s13046-019-1203-2. PMID 31101117. Retrieved 27 February 2021.

External links

{{Phosphate biochemistry}}


This user is also an author, contributor, and editor at

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