Coding sequences of functioning human genes derived entirely from mobile element sequences

Britten, Roy J.

doi:10.1073/pnas.0406985101

Cited by 47 publications

(42 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In general, the amino acid sequence relationships are weak but significant. The average relationships show larger divergence than observed for the six genes previously identified that showed relatively precise relationships over most of their length (5). Because of the length of Table 3, the cases of genes with multiple transcript variants (tv) have been reduced to a single example.…”

Section: Comparison Of Three Methods Of Detecting Te Sequences In Humanmentioning

confidence: 99%

“…The test is whether amino acid sequence similarities to human proteins are found. It turns out that these probes are more effective in finding TE sequence relationships to coding sequences than the previously used DNA sequence methods (1)(2)(3)(4)(5). The amino acid sequence probes identify about six times as many as the DNA sequence searches, and the regions of sequence similarity are much longer.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Transposable elements have contributed to thousands of human proteins

Britten

2006

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

This is a report of many distant but significant protein sequence relationships between human proteins and transposable elements (TEs). The libraries of human repeated sequences contain the DNA sequences of many TEs. These were translated in all reading frames, ignoring stop codons, and were used as amino acid sequence probes to search with BLASTP for similar sequences in a library of 25,193 human proteins. The probes show regions of significant amino acid sequence similarity to 1,950 different human genes, with an expectation of <10 ؊3 . In comparison with previous REPEATMASKER (Institute for Systems Biology, Seattle) studies, these probes detect many more TE sequences in more human coding sequences with greater length than previous work using DNA sequences. If the criterion is opened, very many matches are found occurring on 4,653 different genes after correction for the number seen with random amino acid sequence probes. The processes that led to these extensive sets of sequence relationships between TEs and coding sequences of human genes have been a major source of variation and novel genes during evolution. This paper lists the number of sequence similarities seen by amino acid sequence comparison, which is surely an underestimate of the actual number of significant relationships. It appears that many of these are the result of past events of duplication of genes or gene regions, rather than a direct result of TE insertion. This report of observable relationships leaves to the future the functional implications as well as the detection of the events of TE insertion.sequence similarity ͉ mobile elements ͉ genes ͉ repeated sequences T he contribution of transposable elements (TEs) to eukaryotic genomes has been much studied and will not be reviewed here. I use the phrase TE to refer to any of the known repeated sequences, not including short tandem repeats and simple sequences. The presumption is that most TEs are the product of past insertions of active TE family members into the genomes of many eukaryote ancestors. No uncertainty in meaning results for the minority for which this may not have been demonstrated. Usage does not imply that the elements are currently active and transposable.This article describes measurements of the relationships of TE sequences to human coding sequences, which probably represent much of the contribution TEs have made to the coding sequences of human proteins. The logic underlying this approach is that among the human ''repeated sequences,'' there are many sequences that are related to TEs but are mostly incomplete and damaged, and the original ORFs of the once active TE cannot be recognized in many cases. Therefore, I have simply taken as probes the translation in each of the possible reading frames, ignoring stop codons, to make a set of six probes for each of the repeated sequences. The sequences available may well have undergone various mutations, including frame-shift events, and these will have broken up and limited the length of the TE probes. The relationship of the pr...

show abstract

Section: Comparison Of Three Methods Of Detecting Te Sequences In Humanmentioning

confidence: 99%

mentioning

confidence: 99%

Transposable elements have contributed to thousands of human proteins

Britten

2006

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Despite (or because of) their selfish nature, transposable elements have had a considerable impact on the evolution of their host genomes; for example, as a result of insertional mutagenesis or by promoting genomic rearrangements (12,13). In this study, we investigated another process by which mobile elements can impact their host genomes, often referred to as ''molecular domestication,'' whereby their coding sequences are recruited to serve a cellular function in their host genomes (4)(5)(6)(7)(8)(9). Specifically, we reconstructed the evolutionary steps leading to the birth of SETMAR, a new chimeric primate gene located on human chromosome 3p26 (14).…”

mentioning

confidence: 99%

“…A much less understood, yet ostensibly recurrent, source of genetic innovation is the recycling of coding material from selfish mobile genetic elements (4)(5)(6)(7)(8)(9). Mobile or transposable elements are ''jumping genes,'' pieces of DNA that can move and replicate within the genomes of virtually all living organisms (10).…”

mentioning

confidence: 99%

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

Cordaux

Udit

Batzer

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

226

264

View full text Add to dashboard Cite

The emergence of new genes and functions is of central importance to the evolution of species. The contribution of various types of duplications to genetic innovation has been extensively investigated. Less understood is the creation of new genes by recycling of coding material from selfish mobile genetic elements. To investigate this process, we reconstructed the evolutionary history of SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of a mobile element. We show that the transposase gene was recruited as part of SETMAR 40 -58 million years ago, after the insertion of an Hsmar1 transposon downstream of a preexisting SET gene, followed by the de novo exonization of previously noncoding sequence and the creation of a new intron. The original structure of the fusion gene is conserved in all anthropoid lineages, but only the N-terminal half of the transposase is evolving under strong purifying selection. In vitro assays show that this region contains a DNA-binding domain that has preserved its ancestral binding specificity for a 19-bp motif located within the terminal-inverted repeats of Hsmar1 transposons and their derivatives. The presence of these transposons in the human genome constitutes a potential reservoir of Ϸ1,500 perfect or nearly perfect SETMAR-binding sites. Our results not only provide insight into the conditions required for a successful gene fusion, but they also suggest a mechanism by which the circuitry underlying complex regulatory networks may be rapidly established.transposable elements ͉ gene fusion ͉ molecular domestication ͉ DNA binding ͉ regulatory network

show abstract

“…Lo que resulta desconcertante ---- es que cuando en los artículos sobre su actividad genética se ha planteado la disyuntiva de si los elementos móviles provienen de virus o es a la inversa, ambas alternativas se contemplan como probables 72 , sin definirse por ninguna como si el significado de la una y la otra no fueran abismalmente distintos. Pero si asumimos lo que parece evidente, es decir, que en un sentido genéri-co, los transposones deriven de virus y los retrotransposones de retrovirus, la contribución de los virus a la construcción de los genomas ha sido, por fuerza, la absolutamente mayoritaria 73 . Repitamos los cálculos: Si hemos de creer los resultados de la secuenciación de la fracción codificante de proteínas, que constituye el 1,5% del total del Genoma humano, además de 223 genes identificados como de origen bacteriano (aunque posiblemente sean más), hasta el 50% de sus secuencias están formadas por elementos móviles, por encima del 10% son virus endógenos y «Mucho del restante ADN único debe también ser derivado de copias de antiguos elementos transponibles que han divergido demasiado para ser reconocibles como tales» 74 .…”

Section: Sobre La «Integración De Sistemas Complejos»unclassified

En busca de la biología. Reflexiones sobre la evolución

Sandín

2009

Asclepio

View full text Add to dashboard Cite

RESUMENDespués de 150 años de concebir y tratar a la Naturaleza en términos de competencia, costebeneficio, explotación de recursos, estrategias…, hemos conseguido que ésta entre en «recesión». Este alejamiento de la realidad, de los fenómenos naturales, ha puesto en grave peligro el futuro de la Humanidad sobre nuestro planeta y hace necesaria, incluso urgente, la búsqueda de una concepción de la Biología basada en conceptos y vocabulario científicos que nos vuelva a conectar con la Naturaleza antes de que sea demasiado tarde.PALABRAS CLAVE: Evolución. Gen. Mercado. Información genética. Sistemas. IN SEARCH OF BIOLOGY. REFLECTIONS ON EVOLUTION ABSTRACTAfter 150 years conceiving and dealing with Nature in terms of competence, costs-benefits, exploitation of resources, strategies…, we have managed to make it enter into a «recession». This estrangement from reality and from natural phenomena, has seriously jeopardized the future of mankind on our planet and makes it necessary, even urgent, the search for a conception of biology based on scientific concepts and vocabulary that re-connects us with Nature before it is too late.KEY WORDS: Evolution. Gene. Market. Genetic information. Systems.La naturaleza debe ser obligada a servir, reducida a la obediencia y esclavizada… para extraer, bajo tortura, todos sus secretos.Francis Bacon (1561Bacon ( -1626 EN GUERRA CONTRA LA NATURALEZA Si intentamos encontrar una palabra que describa la relación de las sociedades autodenominadas «avanzadas» con la Naturaleza, esta sería 'miedo'. Y

show abstract

Coding sequences of functioning human genes derived entirely from mobile element sequences

Cited by 47 publications

References 30 publications

Transposable elements have contributed to thousands of human proteins

Transposable elements have contributed to thousands of human proteins

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

En busca de la biología. Reflexiones sobre la evolución

Contact Info

Product

Resources

About