Cover Letter
Dear Editors,
Is Human Genome really a blueprint? This proposition is one of the most fundamental propositions in life-science. Watson-Click’s double helix is very beautiful. Therefore life-scientists might have been imprinted that Human Genome must be a blueprint because of the beauty of DNA double helix. I logically proved that Human genome is not a blueprint but just a storage of genes. Next, I logically solved the second proposition that human oocytes play a major role for an instruction to construct human bodies. I surveyed Database in which almost all gene expressed in human oocytes. As a reslt, about 20,000 genes expressed in human oocytes. That means that human oocytes express almost all genes to prepare for development of human bodies. I convinced that such experiments which support my theoretical solutions will be piled up from now on.
By the way, my IQ is 220. It is third position all over the world. Some people say that my IQ is 300. I submitted my last paper to Nature, but you rejected my paper. It was a big mistake. If you make second mistake or cannot understand my paper, that means you are all foolish! The journal Nature does not need to exist for human beings in this world. Do not repeat the same mistake. My paper is the extraordinary important for human beings. My paper is tremendously precious in these 100 years. That’s it! Thank you.
Best regards,
Koichi Itoh M.D.,Ph.D
Theoretical analysis indicates Genome is not a blueprint and oocytes have the instruction.
Koichi Itoh1
1: The Institute for Theoretical Molecular Biology
21-13 Rokurokuso-cho, Ashiya, Hyogo, JAPAN, 659-0011
TEL: +81-797-35-6368
FAX: +81-797-35-6368
e-mail: koichiitoh@yahoo.co.jp
Corresponding author: Koichi Itoh
The Institute for Theoretical Molecular Biology
21-13 Rokurokuso-cho, Ashiya, Hyogo, JAPAN, 659-0011
TEL: +81-797-35-6368
FAX: +81-797-35-6368
e-mail: koichiitoh@yahoo.co.jp
Abstract
Genome has been thought to be a blueprint, but what type of the blueprint has been a mystery. I have been thought that Genome is not a blueprint. Genome is storage of genes. An assembly instruction exists in oocytes. After fertilization, zygotes express genes according to the instruction. I get this result from the survey of Databases. Oocytes express several types of genes for blastula development and tissue differentiation such as Zinc finger proteins, Homeobox proteins, Pou homeobox proteins, Forkhead box proteins, High-mobility group proteins, Sex determination proteins, WNT and PAX. This result indicates that oocytes have the instruction. Finally, I foresee that once organogenesis begins tissue differentiation proceeds autonomously and human bodies are built.
After Human Genome Project was over and human genome sequence was determined, I expected that a blueprint existed in the genome. However I could not find any traces of the blueprint. 1) If Genome is a blueprint, it must have the regularity in the sequence. But there is no regularity. For example, within Genome, there are a lot of psudogenes. 2) In glycolysis pathway enzymes, hexokinase1 is located in 10q22, glucose-6-phospate isomerase is located in 19q13.1, phosphofructokinase, liver type is located in 21q22.3, phosphofructokinase, muscle type is located in 12q13.3, phosphofructokinase, platelet type is located in 10p15.3-p15.2, aldolase is located in 16p11.2, triosephosphate isomerase is located in 12p13, glyceraldehydes-3-phosphate dehydorogenase is located in 12p13.31-p13.1, phosphoglycerate kinase is located in 6p21.1-p12, phosphoglycerate mutase is located in 10q25.3, enolase 1 is located in 1pter-p36.13, enolase 2 is located in 12p13, enolase 3 is located in 17pter-p12, pyruvate kinase , liver and red blood cell type is located in 1q21 and pyruvate kinase muscle type is located in 15q22. A lot of examples like this can be easily found in other pathways. In glycolysis, important genes for enzymes are not located in the near portion on Genome. These 2 examples are enough for show that Genome is not a blueprint. I have been thinking that the instruction exists in oocytes. Unfortunately, at that time, methods for massive gene expression profiling and Databases were premature and I could not get enough data to answer the question. But now owing to the spread of microarray analysis and large scale expression profilings, I can easily get the data we want and Databases pile up enormous data.
Database survey
In 2006, Kocabas et al. reported the gene expression profile of human oocytes (Kocabas, A. M. et al.. 2006). In that profile, I paid attention for genes for transcription. I thought that among those genes, genes for instruction existed. I surveyed those genes in NCBI (National Center for Biotechnology) Databases. I found genes for１）Zinc finger proteins are large and diverse group of proteins in which the DNA-binding region contains projections (“fingers”) with Cys and/or His residues folding around zinc atom. Some examples are GATA factors important in the development of the blood and the gut, Kruppel in the early Drosophila embryo, Krrox20 in the rhombomeres of the hindbrain. 2) Pou homeobox proteins are related to pituitary development and neural fate. 3) Homeobox proteins have a special role in the control of anteroposterior pattern in animals. 4) High-mobility group and Sex determination are related sex determination. 5) Forkhead box are related to head development and liver formation. 6) PAX proteins are related neural specification and eye development (Slack, J.M.W 2006, Gilbert, S.F 2006, Alberts, B. et al. 2008, Schoenwolf, G..C. et al. 2009, Wolpert, L. et al. 2007, Moody, S.A, 2007). LHX5 is related to control of differentiation and development of the forebrain. TBX3 plays a role in the anterior/posterior axis. TBX5 plays a role for heart development and specification of limb identity. TCF15 plays a role for transcriptional regulation of patterning of the mesoderm (Table1). These genes are essential for blastula development and tissue differentiation. And genes for DNA maintenance and remodeling, cell cycle, transcription factors or transcription factor subunits are also essential for the expression of genes for metabolism, cell growth, and cytoskeleton. Genes for Oct3/4, Sox2, Klf4 and c-Myc can be found in http://www.crl.msu.edu/Supp%20WEB/Kocabas%20et%20al%20Supp.%20Web%20Index.htm. These four are essential for the generation of iPS cells (Takahashi, K. et al. 2007). I can indicate that the number of genes related in development is very large.
Discussion
Here I indicate that after fertilization, oocytes express genes for blastula development and tissue differentiation. I show the evidence that Genome is not the blueprint and oocytes have the instruction from the theoretical point of view. Kocabas et.al reported only up-regulated genes, that is why all essential genes for blastula development and tissue differentiation were not included in their lists. However, in the near future, experimental biologists will find all essential genes for blastula development and tissue differentiation. I surveyed Pathways for development in KEGG (Kyoto Encyclopedia of Genes and Genomes; http://www.genome.ad.jp/kegg/) and Transpath: The Pathway Database; http://www.transpath.de/), but I could not find any pathways for development. From now on, pathways for blastula development and tissue differentiation will be elucidated. Finally, I foresee that once organogenesis begins tissue differentiation proceeds autonomously and human bodies are built.
Reference
Alberts, B. et al. (2008). Molecular Biology of the Cell, Fifth edition (Garland Science)
Gilbert, S.F. Developmental Biology, eighth edition, (2006) (Sinauer Association Inc.)
Kocabas, A. M. et al.. The transcriptome of human oocytes. Proc. Natl Acad. Sci. USA 103 (2006) 14027-14032
Moody, S.A. (2007) Principles of Developmental Genetics (Academic Press)
Schoenwolf, G..C. et al. (2009). Larsen’s Human Embryology, Fourth edition, (Churchill Livingstone)
Slack, J.M.W. Essential Developmental Biology, second edition, (2006) (Blackwell Publishing)
Takahashi, K. et al.. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131 (2007) 861-72
Wolpert, L. et al. (2007). Principles of Development, Third edition, (Oxford University Press)
Table1. Up-regulated genes in human Oocytes
Unigene Symbol Gene name Group
Hs.37706
ZCCHC8 Zinc finger, CCHC domain containing 8 Zinc finger
Hs.523710
ZDHHC18 Zinc finger, DHHC-type containing 18
Hs.27239
ZDHHC5 Zinc finger, DHHC-type containing 5
Hs.592065
ZDHHC7 Zinc finger, DHHC-type containing 7
Hs.612084
ZHX1 Zinc fingers and homeoboxes 1
Hs.507355
ZNF10 Zinc finger protein 10
Hs.479874
ZNF136 Zinc finger protein 136
Hs.592591
ZNF148 Zinc finger protein 148
N.D. ZNF161 N.D.
Hs.155204
ZNF174 Zinc finger protein 174
Hs.172979
ZNF177 Zinc finger protein 177
Hs.112556
ZNF202 Zinc finger protein 202
Hs.530988
ZNF237 zinc finger protein 237 isoform 1
Hs.59757
ZNF281 Zinc finger protein 281
Hs.484324
ZNF354A Zinc finger protein 354A
Hs.659797
ZNF558 Zinc finger protein 558
Hs.655107
ZNF559 Zinc finger protein 559
Hs.13323
ZNF574 Zinc finger protein 574
Hs.709730
ZNF586 Zinc finger protein 586
Hs.388024
ZNF76 Zinc finger protein 76 (expressed in testis)
Hs.38004
ZNF77 Zinc finger protein 77
Hs.37138
ZNF85 Zinc finger protein 85
Hs.388927
YY1 YY1 transcription factor
Hs.518249
ZNF9 CCHC-type zinc finger, nucleic acid binding protein
Hs.493649
POU2F1 POU class 2 homeobox 1 Pou homeobox
Hs.182505
POU3F2 POU class 3 homeobox 2
Hs.654522
POU4F1 POU class 4 homeobox 1
Hs.249184
POU5F1 POU class 5 homeobox 1
Hs.67397
HOXA1 Homeobox A1 Homeobox
Hs.592172
HOXA13 Homeobox A13
Hs.660918
HOXA7 Homeobox A7
Hs.83465
HOXD1 Homeobox D1
Hs.152414
HOXD13 Homeobox D13
Hs.714377
HMG20A High-mobility group 20A High-mobility group
Hs.406534
HMG20B High-mobility group 20B
Hs.588815
HMG2L1 High-mobility group protein 2-like 1
Hs.518805
HMGA1 High mobility group AT-hook 1
Hs.434953
HMGB2 High-mobility group box 2
Hs.555947
LEF1 Lymphoid enhancer-binding factor 1
Hs.236774
HMGN4 High mobility group nucleosomal binding domain 4
Hs.201671
SOX13 SRY (sex determining region Y)-box 13 Sex determination
Hs.95582
SOX15 SRY (sex determining region Y)-box 15
Hs.529462
SOX30 SRY (sex determining region Y)-box 30
Hs.657542
SOX5 SRY (sex determining region Y)-box 5
Hs.546573
FOXD3 Forkhead box D3 Forkhead box
Hs.289292
FOXL2 Forkhead box L2
Hs.239
FOXM1 Forkhead box M1
Hs.370666
FOXO1A Forkhead box O1
FOX3A Forkhead box 3A
Hs.29764
WNT6 wingless-type, member 6 WNT
Hs.443881
PAXIP1 PAX interacting protein 1 paired box (PAX) gene
Hs.654389
CUTL1 Cut-like homeobox 1 homeodomein family of DNA binding protein
Hs.162032
HBP1 HMG-box transcription factor 1 HMG-box transcription factor 1
Hs.302029
LHX5 LIM homeobox 5 control of differentiation and development of the forebrain
Hs.129895
TBX3 T-box 3 play a role in the anterior/posterior axis
Hs.381715
TBX5 T-box 5 heart development and specification of limb identity.
Hs.437
TCF15 Transcription factor 15 (basic helix-loop-helix) transcriptional regulation of patterning of the mesoderm
Hs.33102
TFAP2B Transcription factor AP-2 beta developmentally regulated activator
Hs.696032
PPARD Peroxisome proliferator-activated receptor delta nuclear hormone receptor
Hs.655020
MXD4 MAX dimerization protein 4 regulation of cell growth in differentiating tissues
Hs.517948
DHX30 DEAH (Asp-Glu-Ala-His) box polypeptide 30 putative RNA helicases
Hs.191518
DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9
Hs.397465
HIPK2 homeodomain interacting protein kinase 2 serine/threonine nuclear kinase
Hs.471991
MTF1 Metal-regulatory transcription factor 1 Metal-regulatory transcription factor
Hs.483616
RNF14 Ring finger protein 14 ubiquitination
Hs.561815
STAU2 Staufen, RNA binding protein, homolog 2 RNA binding protein
Hs.285354
MAX MYC associated factor X cell proliferation, differentiation and apoptosis
Hs.638121
CRK V-crk sarcoma virus CT10 oncogene homolog signal transduction
Hs.437075
CREB5 CAMP responsive element binding protein 5 CRE (cAMP response element)-binding protein
Hs.654952
POLR2J Polymerase (RNA) II polypeptide J, 13.3kDa RNA polymerase II subunit
Hs.567494
YBX2 Y box binding protein 2 Y box family of nucleic acid-binding proteins
Hs.385998
WDHD1 WD repeat and HMG-box DNA binding protein 1 signal transduction/DNA maintenance and remodeling
Hs.26516
ASF1B ASF1 anti-silencing function 1 homolog B DNA maintenance and remodeling
Hs.162233
CHD4 Chromodomain helicase DNA binding protein 4
Hs.202672
DNMT1 DNA (cytosine-5-)-methyltransferase 1
Hs.713611
DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta
Hs.368322
CDH8 chromodomain helicase DNA binding protein 8
Hs.144287
HEY2 hairy/enhancer-of-split related with YRPW motif 2
Hs.368971
NCOA6 Nuclear receptor coactivator 6
Hs.589489
SMARCA5 SWI/SNF related, matrix associated, member 5
Hs.558463
MSX2 Spen homolog, transcriptional regulator (Drosophila)
Hs.184298
CDK7 Cyclin-dependent kinase 7 Cell cycle
Hs.436975
CLOCK circadian locomoter output cycles kaput protein
Hs.79353
TFDP1 Transcription factor Dp-1
Hs.348418
DR1 down-regulator of transcription 1 transcription factor OR transcription factor subunit
Hs.654393
E2F1 E2F transcription factor 1
Hs.591015
ELK3 ELK3, ETS-domain protein (SRF accessory protein 2)
Hs.25647
FOS V-fos FBJ murine osteosarcoma viral oncogene homolog
Hs.654350
GABPB2 GA binding protein transcription factor, beta subunit 2
Hs.406157
HSF2BP heat shock transcription factor 2 binding protein
Hs.534074
NFATC1 Nuclear factor of activated T-cells,calcineurin-dependent 1
Hs.632209
NFATC3 Nuclear factor of activated T-cells,calcineurin-dependent 3
Hs.631886
REL V-rel reticuloendotheliosis viral oncogene homolog
Hs.514276
SP2 Sp2 transcription factor
Hs.443258
SREBF2 Sterol regulatory element binding transcription factor 2
Hs.153088
TAF1A TATA box binding protein (TBP)-associated factor
Hs.122752
TAF2 TATA box binding protein (TBP)-associated factor
Hs.18857
TAF4 TATA box binding protein-associated factor
Hs.590872
TBP TATA box binding protein
Hs.486507
TBPL1 TBP-like 1
Hs.26837
TRIM33 Tripartite motif-containing 33
Hs.460988
CBFB Core-binding factor, beta subunit
Hs.555985
NARG1 NMDA receptor regulated 1 unknown
Hs.440219
UBN1 Ubinuclein 1
Hs.573153
TCF7 Transcription factor 7 (T-cell specific, HMG-box)
N.D. TCFL1 N.D.
Hs.12229
KLF11 Kruppel-like factor 11
Hs.428027
PBX3 Pre B-cell leukemia homeobox 3
Hs.92236
MLL4 Myeloid/lymphoid or mixed-lineage leukemia 4
Hs.90753
HTATIP2 HIV-1 Tat interactive protein 2, 30kDa
Hs.528641
SIRT7 Sirtuin (silent mating type information regulation 2 homolog) 7
Hs.271940
ELF4 E74-like factor 4 (ets domain transcription factor)
Hs.463045
GCN5L2 GCN5 general control of amino-acid synthesis 5-like 2 (yeast)
Hs.530539
NFRKB Nuclear factor related to kappaB binding protein
Hs.127950
BRD1 Bromodomain containing 1
Hs.286145
MED21 mediator complex subunit 21
N.D. SNARCB1 N.D.
N.D. SMRCC2 N.D.
N.D. not detected in NCBI database.
manuscript-original
Theoretical analysis indicates human genome is not a blueprint but a storage of genes, and human oocytes have an instruction.
Koichi Itoh
The Institute for Theoretical Molecular Biology
21-13, Rokurokuso-cho, Ashiya, Hyogo, JAPAN 659-0011
TEL: +81-797-35-6368 FAX: +81-797-35-6368
http://www.i-tmb.com/
E-mail: koichiitoh@yahoo.co.jp
Corresponding author: Koichi Itoh
The Institute for Theoretical Molecular Biology
21-13, Rokurokuso-cho, Ashiya, Hyogo, JAPAN 659-0011
TEL: +81-797-35-6368 FAX: +81-797-35-6368
E-mail: koichiitoh@yahoo.co.jp
http://www.i-tmb.com/
Key words: Blueprint, Human Genome, oocytes, gene expression profiles
Abstract
Is Human Genome really a blueprint? If it is not a blueprint, how are human bodies constructed? Firstly, this paper solves this proposition. I indicate 9 examples of important biological pathways and factors among house-keeping gene products and proved that human genome is not a blueprint. Genes of 9 examples are scattered at random in Human Genome in one-dimension. If the Human Genome is the blueprint, 9 important exceptions are not acceptable. That is why Human Genome is not a blueprint but a storage of genes. Secondly, I proved that human oocytes have an instruction for development and differentiation. In this case, I used opened public database for expression profiles of human oocytes. I discovered the number of genes expressed in human oocytes is about 20,000. That means human oocytes have the instruction for human body planning. Here I show that human genome is not a blueprint but a storage of genes, and human oocytes have the instructions.
1. Introduction
Human Genome has been thought to be a blueprint, but what type of the blueprint has been a mystery. Human Genome project was over in 2003, and 15 years are already passed, but even the number of human genes still unknown. Analysis of human genomes has been continuously done, but the discussion which Human Genome is a blueprint has not been done. Far from that, any traces of a blueprint are not found in Human Genome. This must be one of evidence that Human Genome is not a blueprint. The Watson-Click’s DNA double helix is very beautiful. Hence, we life-scientists might have been imprinted that Human Genome is a blueprint. If we hypothesize that Human Genome is a blueprint, what types of absurdity do emerge? And if Human Genome is not a blueprint, what must be needed to construct human bodies? To solve these propositions are the aim of this document1.
2. Materials and Methods
Table I was made from NCBI database OMIM (https://www.ncbi.nlm.nih.gov/omim/) and a Biochemistry Text book2. Supplemental Supplemental Table I was made from NCBI gene expression data of genes expressed in human oocytes. (https://www.ncbi.nlm.nih.gov/).
Results and Discussion
Proposition 1. Human genome is not a blueprint but a storage of genes. At first the definition of a blueprint must be determined. According to dictionaries, a blueprint for something is a plan or set of proposals that shows how it is expected to work. I scrutinized loci of genes for 9 important biological pathways and factors, and those loci are scattered all over Human Genome at random (Table I). I think that a blueprint must have the rule such as regularity, periodism, harmony, some types of patterns, or beauty which a blueprint itself has. But there do not exist such things. The loci of genes for 9 pathways and factors are scattered all over Human Genome at random in one-dimension. There are no reports that scattered genes in one-dimensional construct clusters in three-dimensional. Is it necessary that Human Genome make clusters in three dimensional in nuclei? Proteins make complexes and work in cytoplasm or are secreted from cells. Human Genome do not need to make clusters in three- dimensional in nuclei. It is enough to be a storage of genes in one-dimension. If genes make clusters in three dimensional, there must exist thousands or more clusters in a nucleus. It is not logical because Human Genome must easily tangle. In mathematics, sometimes one opposite example is enough for proof. But biology has many exceptions. However, genes in Table I are biologically important genes, and if a human genome is a blueprint, 9 exceptions must not be acceptable. I think that 9 exceptions are enough evidence. I already surveyed more than 20 pathways and I had the same results. Therefore, I logically prove that a human genome is not a blueprint. Human Genome is just a storage of genes.
Proposition 2. Human oocytes have the instructions. Before fertilization, human oocytes express genes. If a Human Genome is storage of genes, mRNAs which are important for development and differentiation must be expressed in human oocytes and translated into proteins before fertilization begins. Therefore, I surveyed the database and I find about 20,000 genes are expressed in human oocytes. In general, many sample data must be necessary for comparison of gene expression levels for statistical analysis. But in this case, I do not need to compare gene expression levels. Because the importance is what types of genes are expressed in human oocytes. As a result, almost all genes are expressed in human oocytes. That means human oocytes have the instruction to build human bodies If human oocytes do not have the simple instruction, where is the instruction? I already indicate that a human genome is not a blueprint. Hence, it is logical that human oocytes have the simple instruction because a human body begins to be built from only one cell, a fertilized egg. If other cells except for human oocytes give proteins or mRNAs from outside of human oocytes, stromal cells might be candidates for the cells having the simple instruction. But it is not realistic that those cells play major roles of development and differentiation of fertilized eggs. In case of In Vitro Fertilization (IVF), fertilized eggs develop and differentiate from only one cell. Therefore, I logically proved that human oocytes have the simple instruction. Hence, I think that Human Genome begins to exist as just a storage of genes. And human oocytes express essential genes for development and differentiation as the simple instruction. After fertilization, a fertilized egg differentiates according to micro-environment surround the fertilized egg. From now on, a lot of evidence will be piled up to support my hypothesis. Finally, I foresee that once organogenesis begins, tissue differentiation proceeds autonomously and human bodies are built. Here I show that Human Genome is not a blueprint but a storage of genes, and Human oocytes have the instruction.