Myocyte enhancer factor gene transcriptions: Difference between revisions
Line 100: | Line 100: | ||
# MYOr1: 0. | # MYOr1: 0. | ||
# MYOr2: 2, CTAAATTTAG at 2521, TTAAATTTAG at 1772. | # MYOr2: 2, CTAAATTTAG at 2521, TTAAATTTAG at 1772. | ||
# | # MYOr3: 0. | ||
# | # MYOr4: 2, TTAATATTAA at 4164, TTATATTTAA at 3724. | ||
# | # MYOr5: 0. | ||
# | # MYOr6: 1, TTAAATATAA at 2239. | ||
# RDr7: 0. | # RDr7: 0. | ||
# RDr8: 0. | # RDr8: 0. | ||
Line 118: | Line 118: | ||
# RDr9ci: 0. | # RDr9ci: 0. | ||
=== | ===MYOr arbitrary (evens) (4560-2846) UTRs=== | ||
# MYOr4: TTAATATTAA at 4164, TTATATTTAA at 3724. | |||
===RDr alternate (odds) (4560-2846) UTRs=== | ===RDr alternate (odds) (4560-2846) UTRs=== | ||
Line 136: | Line 138: | ||
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters=== | ===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters=== | ||
=== | ===MYOr alternate positive direction (evens) (4265-4050) proximal promoters=== | ||
# MYOr4: TTAATATTAA at 4164. | |||
===MYOr arbitrary negative direction (evens) (2596-1) distal promoters=== | ===MYOr arbitrary negative direction (evens) (2596-1) distal promoters=== | ||
# MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772. | # MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772. | ||
# MYOr6: TTAAATATAA at 2239. | |||
===RDr alternate negative direction (odds) (2596-1) distal promoters=== | ===RDr alternate negative direction (odds) (2596-1) distal promoters=== | ||
Line 149: | Line 154: | ||
# MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772. | # MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772. | ||
# MYOr4: TTATATTTAA at 3724. | |||
# MYOr6: TTAAATATAA at 2239. | |||
==Myocyte enhancer factor analysis and results== | ==Myocyte enhancer factor analysis and results== |
Revision as of 18:16, 26 July 2022
Associate Editor(s)-in-Chief: Henry A. Hoff
Mef2 was originally identified as a transcription factor complex through promoter analysis of the muscle creatine kinase (mck) gene to identify nuclear factors interacting with the mck enhancer region during muscle differentiation.[1]
Three human mRNA coding sequences designated RSRF (Related to Serum Response Factor) were cloned and shown to dimerize, bind a consensus sequence similar to the one present in the MCK enhancer region, and drive transcription.[2] RSRFs were subsequently demonstrated to encode human genes now named Mef2A, Mef2B and Mef2D.
Myocyte enhancer factor-2 (MEF2) proteins are a family of transcription factors which through control of gene expression are important regulators of cellular differentiation and consequently play a critical role in embryonic development.[3] In adult organisms, Mef2 proteins mediate the stress response in some tissues.[3]
Human genes
Vertebrates have at least four versions of the Mef2 gene (human versions are denoted as Myocyte-specific enhancer factor 2A (MEF2A), MEF2B, MEF2C, and MEF2D), all expressed in distinct but overlapping patterns during embryogenesis through adulthood.[4]
Interactions
Consensus sequences
"The current study delineates the conformational paradigm, clustered recognition, and comparative DNA binding preferences for MEF2A and MEF2B-specific MADS-box/MEF2 domains at the YTA(A/T)4TAR consensus motif."[5] Y = (C/T) and R = (A/G). The consensus sequence is (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G).[5]
Myocyte enhancer factor samplings
Copying an apparent consensus sequence for the TTATAT or CTAATT and putting it in "⌘F" finds two (TTATAT) located between ZSCAN22 and one (CTAATT) between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G) (starting with SuccessablesMYO.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 (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G), 2, TTATTATTAA at 4226, CTATATATAA at 1601.
- positive strand, negative direction, looking for (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G), 0.
- positive strand, positive direction, looking for (C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G), 1, CTAATATTAA at 4169.
- negative strand, positive direction, looking for(C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G), 1, CTAATTTTAA at 2443.
Inverse complement is the same as the direct myocyte enhancer factor.
MEF UTR gene transcriptions
- Negative strand, negative direction: TTATTATTAA at 4226.
MEF proximal promoters
- Positive strand, positive direction: CTAATATTAA at 4169.
MEF distal promoters
- Negative strand, negative direction: CTATATATAA at 1601.
- Negative strand, positive direction: CTAATTTTAA at 2443.
Myocyte enhancer factor random dataset samplings
- MYOr0: 0.
- MYOr1: 0.
- MYOr2: 2, CTAAATTTAG at 2521, TTAAATTTAG at 1772.
- MYOr3: 0.
- MYOr4: 2, TTAATATTAA at 4164, TTATATTTAA at 3724.
- MYOr5: 0.
- MYOr6: 1, TTAAATATAA at 2239.
- 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.
MYOr arbitrary (evens) (4560-2846) UTRs
- MYOr4: TTAATATTAA at 4164, TTATATTTAA at 3724.
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
MYOr alternate positive direction (evens) (4265-4050) proximal promoters
- MYOr4: TTAATATTAA at 4164.
MYOr arbitrary negative direction (evens) (2596-1) distal promoters
- MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772.
- MYOr6: TTAAATATAA at 2239.
RDr alternate negative direction (odds) (2596-1) distal promoters
RDr arbitrary positive direction (odds) (4050-1) distal promoters
MYOr alternate positive direction (evens) (4050-1) distal promoters
- MYOr2: CTAAATTTAG at 2521, TTAAATTTAG at 1772.
- MYOr4: TTATATTTAA at 3724.
- MYOr6: TTAAATATAA at 2239.
Myocyte enhancer factor analysis and results
"The current study delineates the conformational paradigm, clustered recognition, and comparative DNA binding preferences for MEF2A and MEF2B-specific MADS-box/MEF2 domains at the YTA(A/T)4TAR consensus motif."[5]
Reals or randoms | Promoters | direction | Numbers | Strands | Occurrences | Averages (± 0.1) |
---|---|---|---|---|---|---|
Reals | UTR | negative | 1 | 2 | 0.5 | 0.5 |
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 | 1 | 2 | 0.5 | 0.5 |
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 |
Randoms | Distal | arbitrary negative | 0 | 10 | 0 | 0 |
Randoms | Distal | alternate negative | 0 | 10 | 0 | 0 |
Reals | Distal | positive | 1 | 2 | 0.5 | 0.5 |
Randoms | Distal | arbitrary positive | 0 | 10 | 0 | 0 |
Randoms | Distal | alternate positive | 0 | 10 | 0 | 0 |
Comparison:
The occurrences of real myocyte enhancer factors are greater than the randoms. This suggests that the real myocyte enhancer factors are likely active or activable.
See also
References
- ↑ Gossett LA, Kelvin DJ, Sternberg EA, Olson EN (1 November 1989). "A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes". Mol. Cell. Biol. 9 (11): 5022–33. doi:10.1128/MCB.9.11.5022. PMC 363654. PMID 2601707.
- ↑ Pollock R, Treisman R (1991). "Human SRF-related proteins: DNA-binding properties and potential regulatory targets". Genes Dev. 5 (12a): 2327–41. doi:10.1101/gad.5.12a.2327. PMID 1748287.
- ↑ 3.0 3.1 Potthoff MJ, Olson EN (December 2007). "MEF2: a central regulator of diverse developmental programs". Development. 134 (23): 4131–40. doi:10.1242/dev.008367. PMID 17959722. Unknown parameter
|s2cid=
ignored (help) - ↑ McKinsey TA, Zhang CL, Olson EN (2002). "MEF2: a calcium-dependent regulator of cell division, differentiation and death". Trends Biochem. Sci. 27 (1): 40–7. doi:10.1016/S0968-0004(01)02031-X. PMID 11796223.
- ↑ 5.0 5.1 5.2 Ayisha Zia, Muhammad Imran, and Sajid Rashid (7 February 2020). "In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity". Journal of Chemical Information and Modeling. 60 (3): 1892–1909. doi:10.1021/acs.jcim.0c00008. Retrieved 10 September 2020.