New insight into transcription of human endogenous retroviral elements

New Biotechnology

Volumn 30, Issue 3, 2013, Pages 314-318

  Pačes, Jan ^a   Huang, Yao Ting ^b   Pačes, Václav ^a   Rídl, Jakub ^a   Chang, Chung Ming ^c  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

^b NATIONAL CHUNG CHENG UNIVERSITY   (Taiwan)

^c CHANG GUNG UNIVERSITY COLLEGE OF MEDICINE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOIMMUNE DISEASE; HIGH-THROUGHPUT; HUMAN ENDOGENOUS; MENTAL DISORDERS; NUCLEOTIDE SEQUENCES; RNA SEQUENCING;

BIOINFORMATICS; DNA SEQUENCES; GENES; RNA;

TRANSCRIPTION;

GENOMIC DNA; LONG UNTRANSLATED RNA; SPACER DNA;

ARTICLE; BIOINFORMATICS; BIPOLAR DISORDER; DNA METHYLATION; DNA SEQUENCE; ENDOGENOUS RETROVIRUS; GENE DELETION; GENE INSERTION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HOMOLOGOUS RECOMBINATION; HUMAN; HUMAN ENDOGENOUS RETROVIRAL ELEMENT; HUMAN GENOME; INTRON; LONG TERMINAL REPEAT; NEOPLASM; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA TRANSCRIPTION; SCHIZOPHRENIA; SEQUENCE ALIGNMENT; TRANSPOSON; VIRUS TRANSCRIPTION;

DNA TRANSPOSABLE ELEMENTS; ENDOGENOUS RETROVIRUSES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; ORGAN SPECIFICITY; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC;

HUMAN ENDOGENOUS RETROVIRUS H; HUMAN ENDOGENOUS RETROVIRUS W;

EID: 84878115704     PISSN: 18716784     EISSN: 18764347     Source Type: Journal    
DOI: 10.1016/j.nbt.2012.11.009     Document Type: Article

References (34)

1. Paces J., Pavlícek A., Zika R., Kapitonov V., Jurka J., Paces V. HERVd: the Human Endogenous RetroViruses Database: update. Nucleic Acids Research 2004, 32:50. (database issue).
2. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
3. Lower R., Lower J., Kurth R. The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:5177-5184.
4. Blikstad V., Benachenhou F., Sperber G.O., Blomberg J. Evolution of human endogenous retroviral sequences: a conceptual account. Cellular and Molecular Life Sciences 2008, 65:3348-3365.
5. Jern P., Sperber G.O., Blomberg J. Definition and variation of human endogenous retrovirus H. Virology 2004, 327:93-110.
6. Kovalskaya E., Buzdin A., Gogvadze E., Vinogradova T., Sverdlov E. Functional human endogenous retroviral LTR transcription start sites are located between the R and U5 regions. Virology 2006, 346:373-378.
7. Schön U., Seifarth W., Baust C., Hohenadl C., Erfle V., Leib-Mosch C., et al. Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats. Virology 2001, 279:280-291.
8. Stoye J.P. Endogenous retroviruses: still active after all these years?. Current Biology 2001, 11:R914-R916.
9. Lettini A.A., Guidoboni M., Fonsatti E., Anzalone L., Cortini E., Maio M., et al. Epigenetic remodelling of DNA in cancer. Histology and Histopathology 2007, 22:1413-1424.
10. Moyes D., Griffiths D.J., Venables P.J. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends in Genetics 2007, 23:326-333.
11. Urnovitz H.B., Murphy W.H. Human endogenous retroviruses: nature, occurrence, and clinical implications in human disease. Clinical Microbiology Reviews 1996, 9:72-99.
12. Lower R. The pathogenic potential of endogenous retroviruses: facts and fantasies. Trends in Microbiology 1999, 7:350-356.
13. Kuyl van der A.C. HIV infection and HERV expression: a review. Retrovirology 2012, 9:6-20.
14. Diem O., Schaffner M., Seifarth W., Leib-Mosch C. Influence of antipsychotic drugs on Human Endogenous Retrovirus (HERV) transcription in brain cells. PLoS ONE 2012, 7:1-8.
15. Liang Q., Ding J., Xu R., Xu Z., Zheng S. The novel human endogenous retrovirus-related gene, psiTPTE22-HERV, is silenced by DNA methylation in cancers. International Journal of Cancer 2010, 127:1833-1843.
16. Lerat E., Semon M. Influence of the transposable element neighborhood on human gene expression in normal and tumor tissue. Gene 2007, 396:303-311.
17. Yi J.M., Kim H.M., Kim H.S. Expression of the human endogenous retrovirus HERV-W family in various human tissues and cancer cells. Journal of General Virology 2004, 85:1203-1210.
18. Indik S., Gunzburg W.H., Kulich P., Salmons B., Rouault F. Rapid spread of mouse mammary tumor virus in cultured human breast cells. Retrovirology 2007, 4:73.
19. Kapitonov V.V., Jurka J. The long terminal repeat of an endogenous retrovirus induces alternative splicing and encodes an additional carboxy-terminal sequence in the human leptin receptor. Journal of Molecular Evolution 1999, 48:248-251.
20. Jern P., Coffin J.M. Effects of retroviruses on host genome function. Annual Review of Genetics 2008, 42:709-732.
21. Ahn K., Kim H.S. Structural and quantitative expression analyses of HERV gene family in human tissues. Molecules and Cells 2009, 28:99-103.
22. Okahara G., Matsubara S., Oda T., Sugimoto J., Jinno Y., Kanaya F., et al. Expression analyses of human endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Genomics 2004, 84:982-990.
23. Yi J.M., Kim H.M., Kim H.S. Human endogenous retrovirus HERV-H family in human tissues and cancer cells: expression, identification, and phylogeny. Cancer Letters 2006, 231:228-239.
24. Ansorge W.J. Next-generation DNA sequencing techniques. New Biotechnology 2009, 25:195-203.
25. Schuster S.C. Next-generation sequencing transforms today's biology. Nature Methods 2008, 5:16-18.
26. Li L., Akagi K., Hu Y., Trivett A.L., Hlynialuk C.J.W., Swing D.A., et al. Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome Research 2012, 22:870-884.
27. Mercer T.R., Dinger M.E., Mattick J.S. Long non-coding RNAs: insights into functions. Nature Reviews Genetics 2009, 10:155-159.
28. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10:R25.
29. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
30. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
31. Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-515.
32. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 2008, 5:621-628.
33. Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z., et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 2010, 20:265-272.
34. Koren S., Schatz M.C., Walenz B.P., Martin J., Howard J.T., Ganapathy G., et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 2012, 30:693-700.