Expression of evolutionarily novel genes in tumors

Kozlov, Andrei P.

doi:10.1186/s13027-016-0077-6

Cited by 22 publications

(39 citation statements)

References 201 publications

(256 reference statements)

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“…This prediction was verified in a number of papers from our laboratory [6, 8 -17]. We have described several evolutionarily young or novel genes with tumorpredominant or tumor-specific expression, and even the evolutionary novelty of the class of genescancer/testis genes -which consists of evolutionary young and novel genes expressed predominantly in tumors (reviewered in [6]). We suggested to call such genes TSEEN genes, i.e.…”

Section: Introductionsupporting

confidence: 53%

Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently

Makashov¹,

Malov

Kozlov³

2018

Preprint

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Abbreviations BMC -Biomedical CenterBMC GSTSE -Biomedical Center globally subtracted, tumor-specifically expressed BMC GSTSE-X non-coding sequences -Biomedical Center globally subtracted, tumor-specifically expressed non-coding sequences located on X chromosome CDD -computer-assisted differential display CT antigen gene -canser/testis antigen gene TSEEN genes -tumor specifically expressed, evolutionarily novel genes Ma -million years ago PPOD -Princeton Protein Orthology DatabaseCT-X antigen genes -CT antigen genes located on X chromosome Abstract Earlier we showed that human genome contains many evolutionarily young or novel genes with tumor-specific or tumor-predominant expression. We suggested to call them TSEEN genes, i.e. Tumor Specifically Expressed, Evolutionarily New genes. In this paper we performed a study of the evolutionary ages of different classes of human genes, using homology searches in genomes of different taxa in human lineage. We discovered that different classes of human genes have different evolutionary ages and confirmed the existence of TSEEN gene classes. On the other hand, we found that oncogenes, tumor-suppressor genes and differentiation genes are among the oldest gene classes in humans and their evolution occurs concurrently. These findings confirm predictions made by our hypothesis of the possible evolutionary role of hereditary tumors.

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Section: Introductionsupporting

confidence: 53%

Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently

Makashov¹,

Malov

Kozlov³

2018

Preprint

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“…The innovative role of reverse transcribed cDNAs is further enhanced by the well-documented phenomenon of “trans-splicing”, which involves the joining of sequences from two distinct transcripts [ 368 , 369 , 370 , 371 , 372 , 373 , 374 , 375 , 376 , 377 , 378 , 379 ]. Genome insertion of cDNA reverse-transcribed from a trans-spliced RNA molecule generates a novel chimeric domain coding sequence [ 379 , 380 ].…”

Section: Genome Writing By Natural Genetic Engineering—protein Evomentioning

confidence: 99%

Living Organisms Author Their Read-Write Genomes in Evolution

Shapiro

2017

Biology

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Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

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“…Interestingly, all AI267901-like tumor-specific ESTs are mapped on this non-conserved Eutheria -specific region of the gene. This links OTP-AS1 gene to so-called TSEEN (tumor-specifically expressed, evolutionary novel) genes described by the authors in previous papers [14, 15, 16, reviewed in 17].…”

Section: Discussionmentioning

confidence: 81%

A new cancer-testis long noncoding RNA, the OTP-AS1 RNA

De²,

Ll³

et al. 2018

Preprint

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14Orthopedia homeobox (OTP) gene encodes a homeodomain-containing transcription 15 factor involved in brain development. OTP is mapped to human chromosome 5q14.1. Earlier we 16 described transcription in the second intron of this gene in wide variety of tumors, but among 17 normal tissues only in testis. In GeneBank these transcripts are presented by several 300-400 18 nucleotides long AI267901-like ESTs. 19 We assumed that AI267901-like ESTs belong to longer transcript(s). We used the Rapid 20 Amplification of cDNA Ends (RACE) approach and other methods to find the full-length 21 transcript. The found transcript was 2436 nucleotides long polyadenylated sequence in antisense 22 48 (tumor-specifically expressed, evolutionary novel) genes described by the authors in previous 49 papers. 50 51 131 samples of endometrial adenocarcinoma (156, 270), meningiomas (45, 63); and in all lymphoma 132 samples (31, 67, 82, 92, 102, 94, 113) (Fig 8b). Weak signals corresponding to the studied 157 chromosome and consists of 3 exons and 2 introns.

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Expression of evolutionarily novel genes in tumors

Cited by 22 publications

References 201 publications

Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently

Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently

Living Organisms Author Their Read-Write Genomes in Evolution

A new cancer-testis long noncoding RNA, the OTP-AS1 RNA

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