Epigenetics Theoretical Limits of Synthetic Genomes: the cases of Artificials Caulobacter(C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII

-In (Venetz et al., 2019), authors rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Then, they reduced the native Caulobacter crescentus native Caulobacter NA1000 genome sequence real genome (4042929 bp ) to the 785,701-bp reduced synthetic genome. Here we demonstrate the existence of a palindromic-like mirror structure that exists in real genomes and disappears totally in the synthetic genome. This biomathematic meta-organization is based on characteristic proportions of Fibonacci numbers between DNA single strand nucleotides proportions TC/AG on the one hand and TG/AC on the other hand. In both cases, we suggest that this meta-structure enhances the three-dimensional cohesion of the two DNA strands of the genome. We then generalize this study to the different synthetic genomes and synthetic cells published by the Craig Venter Institute on Mycoplasma Mycoides JCVI-syn1.0 (in 2010), JCVI-syn3.0 (in 2016) and JCVI-syn3A (in 2019). Finally, in the discussion section, we extend this study to synthetic genomes of E-Coli and Yeast chromosome XII.

Introduction he story which led to the development of the first synthetic genome JCVI-syn1.0 has its origins as far back as 1995, when Venter and his team published the sequence of Mycoplasma genitalium (Fraser, 1995) and (Sleator, 2010). In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. (Gibson, 2010). In 2016, Hutchinson et al design, build, and test cycle to reduce this Mycoplasma mycoides genome to 531 kb (473 genes). JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function. Since 2012 the Synthetic Yeast Genome Project (Sc2.0 http://synthetic yeast.org/sc2-0/) results from a worldwide partnership, « Sc2.0 International Consortium team », members spanning 4 continents to provide remote mentorship and solve challenges associated with synthetic individual chromosome design features and assembly (Jee Loon Foo 2018). Read the analysis in §Discussion. In January 2019, Breuer et al. published a synthetic cell resulting from the synthetic genome JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, providing a versatile platform to study the basics of life. Simultaneously, in 2019, Venetz et al. reduced the native Caulobacter crescentus NA1000 genome sequence real genome (4042929 bp) to the 785,701-bp reduced synthetic genome Caulobacter ethensis-2.0 (C. eth-2.0). Finally, also in 2019 (Fredens, 2019), researchers published a synthetic genome of E COLI changing systematically genetic code equivalent codons. They replaced every occurrence of the serine codon TCG with AGC, every TCA (also serine) with AGT, and every TAG (stop) with TAA. Read the analysis in § Discussion.
In a completely different field, 30 years ago, we had just published the first 2 French books on Artificial Intelligence (AI) neural networks (Perez, 1988;Perez, 1989;Perez, 1990a). It is the exploration of our network FRACTAL CHAOS (Perez 1990c), (Pellionisz et al, 2012), , which will reveal a hypersensitivity of this network to successive ratios of Here we demonstrate the existence of a palindromic-like mirror structure that exists in real genomes and disappears totally in the synthetic genome. This biomathematic meta-organization is based on characteristic proportions of Fibonacci numbers between DNA single strand nucleotides proportions TC/AG on the one hand and TG/AC on the other hand. In both cases, we suggest that this meta-structure enhances the threedimensional cohesion of the two DNA strands of the genome. We then generalize this study to the different synthetic genomes and synthetic cells published by the Craig Venter Institute on Mycoplasma Mycoides JCVI-syn1.0 (in 2010), JCVI-syn3.0 (in 2016) and JCVI-syn3A (in 2019). Finally, in the discussion section, we extend this study to synthetic genomes of E-Coli and Yeast chromosome XII. Fibonacci numbers, for example 34/21 (Perez, 1990b). While the big project of sequencing of the human genome "HUGO" just begins, we have the intuition to look for ratios of Fibonacci numbers between the contiguous proportions of TCAG nucleotides of genes and small genomes available at that time (like HIV, mtDNA, viruses, bacteria, or small genes). We published a first article in 1991 (Perez, 1991;Marcer, 1992) demonstrating the evidence of such biomathematic structures (Perez, 1991). This discovery was completely published 22 years ago in the book "DNA decrypted" (Perez, 1997). This method, which the Nobel prize winner Luc Montagnier called "DNA supracode" (Fleaux, 1995), was used to search exaustively in DNA searched exhaustively in DNA sequences for remarkable proportions of Fibonacci numbers (https://en.wikipedia. org/wiki/Fibonacci_number) between nucleotides called "resonances": for example if a contiguous sequence of 377 bases TCAG is subdivided into 233 (C + A) and 144 (T + G), there is a resonance of CA / TG of length 377 (where 144, 233 and 377 are three Fibonacci numbers). In (Perez, 2017a), it is precisely such resonances CA / TG that characterize this optimality of the mtDNA genome of humans. It is still such resonances that are affected during mutations associated with cancers. In particular, we have analyzed this type of resonance in the 3 respective mtDNA genomes of humans, mice, and the famous naked mole rat as well as in more than a dozen other mammalian species.
In a comprehensive analysis of all (ALL) listed mutations of the human mitochondrial mtDNA genome associated with cancers : effectively, multiple mutations associated with the mitochondrial genome of tumor cells have been reported. An open question is whether these mutations are only the CONSEQUENCE of the cancer process or if, on the contrary, they would be a possible ORIGINAL CAUSE of the cancer genesis process. In a paper in preparation (Perez, 2019) we'll propose a generic and universal law (of a numerical nature) allowing us to detect and classify these mutations at the early stage of the genesis of the tumors. Finally, in (Perez 2019) we will present a generic law of prediction and classification of tumors by the simple analysis of the DNA SUPRACODE of the mitochondrial genomes associated with these tumors. In this upcoming article, we analyse all known somatic mutations listed all cancers combined. We then discover a global strategy of mutation of all these basic somatic mutations materialized by a numerical score which systematically increases in ALL the cases of elementary somatic mutations related to 91 referenced cases involved in 9 different cancers (prostate, pancreatic, colon, thyroid, bladder, breast, head § neck, meduloblastoma, ovarian) with a success rate of 100%. This predictive method should make it possible to categorize and classify the potential pathogenicity of tumors from the early stage.
Particularly, we find an interesting symmetric property of resonances with very short periods: for example, the resonances 3 (1 TC 2AG) and 3 (2TC 1AG) correspond to the symmetrical beginnings of the Fibonacci and Lucas sequences. Similarly, the resonances 5 (2 TC, 3AG) and (3TC 2AG) correspond to the symmetrical beginnings of the Fibonacci and FibLuc 1 2 sequences. By looking for these resonances in all the known tumor mutations of human mtDNA genomes applied to the genomes inherited by evolution of the RSRS mother sequence (EVE), it appears the functional role of such local resonances whose repercussion on the global scale of the genome becomes a indicator of early diagnosis of tumors.
It is this type of symmetry that we will generalize in this article by extending it to longer Fibonacci, and Lucas sequences.

Experimental Section
Part I: Genomes analysed We will analyze 8 bacterial genomes, 3 real reference genomes, one transgenic genome, and four synthetic genomes.  29 47 76 For any contiguous sequence of nucleotides, one will search for "resonance" or exact proportions of the TG / CA types then mainly TC / AG.

==>
For example, if 34 TCAG bases are subdivided exactly into 13 TC bases and 21 AG bases, we will consider having discovered a TC / AG resonance of length 34. We will do the same for the search for Lucas resonances. The whole genome is explored by taking each of the positions as successive exploration points. On the other hand, the genome being circular, the analysis from the last pivots at the end of the sequence is looped back to the positions of the start nucleotides.
We We will therefore consider very significant: The forward / backward ratios. Forward-backward spreads. Since the lengths of real and synthetic genomes are generally very different, we will weight the forwardbackward differences by the respective lengths of the real or synthetic genomes.
The actual NA1000 genome being about 5 times longer than the synthetic genome C. eth-2.0, one might think that the comparison of these 2 genomes is skewed. However, in all the above results, we had already incorporated this difference by weighting the results by the length of the respective genomes.   In the figure on the left, the average ratio of weighted distances by genome length between real genome and synthetic genome is 14   processes such as transcription and translation, but also contains 149 genes of unknown function. In the following section, we compare 6 (six) genomes : two reference real strain mycoplasma genomes including CAPRI strain, one transgenic building strain and the 3 strong JCV Labs ; synthetic genomes.   In summary of this double analysis it seems obvious that synthetic genomes disturb and destroy a characteristic dimension of real genomes. This property could concern the mathematical topology of the genome (Rapoport, 2018) and probably its fractal, dynamic, evolution, and three-dimensional structures.
Having not yet obtained the synthetic genome from the authors, we have limited here our study to the concatenation of all wild type PCRTags on the one hand and synthetic ones on the other hand. For example: Forward wild type PCRTag : TGCTTGAACTGCAAATACAGGCCCACTC Forward synthetic PCRTag : AGCTTGGACAGCGAAAACTGGACCTGAT They published particularly all the wild type and synthetic PCR Tags. The full PCR Tags are available online: http://syntheticyeast.org/wpcontent/uploads/2016/10/synXII_PCRtag.txt Details: PCRTags « PCRTags are alterations incorporated into most open reading frames (ORFs) (on average one per ORF, as some ORFs are too small and others contain multiple PCRTags). These are made by recoding a ~20bp segments of the coding region of an ORF to a different DNA sequence encoding the same amino acid sequence. PCR primer pairs can then be designed that will selectively amplify only the synthetic or wild type sequences. In this way, transformants that have incorporated a synthetic segment can be quickly scanned to ascertain that a complete substitution of the segment has occurred. PCRTags can also be used to monitor for the deletion of non-essential segments post-SCRaMbLE induction. » (from http://syntheticyeast.org/designs/alterations/pcrtags/).
We analysed 681 PCRTags of each 28 bp from wild YEAST XII and artificial SYN XII chromosomes. Then only resonances < 28 bp are to be considered in the following analysis. We run 3 analysis :

Conclusions
In all the cases analyzed here, we find that the real genomes or chromosomes have a property of coherence, consistency and unity that our method highlights. This property disappears in almost all (ALL) studied cases of synthetic genomes or chromosomes. In our article (Perez, 2010) These two observations about the role of transposons already partly explain the digital disharmony that we prove in this article. These famous transposons disrupt the functioning of synthetic genomes, so we delete them (!). On the contrary, we believe that these same transposons constitute a major piece of genome stability.
The creation by men of SYNTHETIC genomes leads to a paradox on which I invite you now to think about: On the one hand, NATURAL DNA is a luxury of REDUNDANCY and SYMMETRY ...
On the other hand, SYNTHETIC DNA manipulation and synthesis technologies rely on and exploit the same luxury of REDUNDANCY and symmetries ... Thus; Sometimes the technology will try to EXPLOIT SYMMETRY and REDUNDANCY: this is the case of CRISPR technology based on DNA PALINDROMES, so on SYMMETRY and REDUNDANCY. Sometimes the technology will try to DESTROY symmetry and REDUNDANCY: Such is the case of mutations and alterations of transposons (Breuer, 2019) in order to fight against these transposons which will alter the SYNTHETIC genome. This is also the case when one tries to reduce the REDUNDANCE of the universal genetic code by reducing it from 64 to 61 codons (Fredens, 2019). By our different research on the biomathematics of DNA, we have on the contrary demonstrated that this REDUNDANCY and this symmetry contribute to the UNITY and INTEGRITY of genes, chromosomes and genomes: When a Meta-code unifies DNA, RNA and amino acids (Perez, 2009: Perez, 2011Perez, 2015;Perez, 2018d); When this master code unifies the genomic and proteomic meta structures of a gene (Perez, 2000; 2017e; Perez, 2017f; Perez, 2017g; Perez 2017h); When the multiple repetition of the same gene as DUF1220 is associated with mammalian brain properties via a kind of «FibLuc sequence» digital standing waves of its DNA (Sikela, 2006;Weiss, 2006;Parayon, 2011;Perez, 2017b); When we prove the existence of a UNITY of Fibonacci sequences on the scale of an whole human chromosome such as chromosome4 (Perez, 2017c); When we demonstrate how numerical proportions characterize the DNA of whole genomes of viruses, bacteria or Euchariotes (Perez 2013); When we highlight the UNITY of the 3 billion base pairs of the entire human genome (Perez, 2010;Perez, 2017d); When this whole human genome UNITY is destroyed by Cancer mutations (Perez, 2018a; Perez, 2018b; Perez, 2018c); When there is an evidence that these numerical structures (Petoukhov, 2019) of the genomes, particularly SYMMETRY and REDUNDANCY, are of TOPOLOGICAL nature (Rapoport 2016). This topological unified hyper structure of whole genomes is based particularly on Fibonacci Numbers, Golden ratio (Friedman, 2018), and Klein bottle (Rapoport §Perez, 2018).
We can not manipulate the genomes "no matter how". Thus, transposons certainly play a key role in the stability and epigenetics of genomes.
To conclude we will finally notice that the REAL genomes of bacteria analyzed obey two simultaneous numerical constraints of Phi and Phi * 2 (where Phi = 1.618 is the golden ratio and Phi * 2 = 2.618). For example, for a contiguous sequence of 21 TCAGs, we have simultaneously: This double strong constraint on REAL genomes almost disappears in the case of SYNTHETIC genomes.
Manipulation technologies (CRISPR) and especially of artificial creation of genomes will have to respect these laws of nature.
In (Strecker et al., 2019) by using DNA sequences referred to as transposons, or "jumping genes" (genes that can change their position within the genome), a team from MIT led by NYSCF -Robertson Stem Cell Investigator Dr. Feng Zhang has created a new version of CRISPR (called CRISPR-associated transposase, or "CAST") that can insert functional DNA sequences into the genome without making cuts, which can often lead to unintended damage.
What about for the FUTURE ? There are theoretical new background for Biology and Genetics, these tracks are MATHEMATICS (Perez § Montagnier L., 2021).