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HERV Structure

RnaseH. MA. CA. NC. PR. RT. IN. SU. TM. pro. gag. pol. env. pro. 1. gag. pol. env. 2. U5. R. U5. U3. R. U3. gag. env. 3. transcription. NC. MA. CA. TM. SU. promoter. R. U5. U3. Type 1 transcript. Enhancer. HRE. promoter. Poly A signal. TGTTAT. AATAAA.

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HERV Structure

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  1. RnaseH MA CA NC PR RT IN SU TM pro gag pol env pro 1 gag pol env 2 U5 R U5 U3 R U3 gag env 3 transcription NC MA CA TM SU promoter R U5 U3 Type 1 transcript Enhancer HRE promoter Poly A signal TGTTAT AATAAA GTGCTAAG TGTTAT Type 2 transcript LTR Type 3 transcript Type 4 transcript PR pro RT IN pol HERV Structure SD SA R U5 R U3 U5 U3 3’ LTR 5’ LTR PBS PPT transcription regulatory elements cellular gene promoter U3 - unique to the 3’ end of viral genome R - direct repats present at both ends of viral genome U5 - unique to the 5’ end of viral genome (RNA) • pro(protease) - cleaves gag-pol and env • pol(polymerase) * RT (reverse transcriptase) - synthesizes DNA * IN (intergrase) - intergrates provirus DNA into genome • gag(group specific antigen) * MA (Matrix) - located between nucleocapsid and viral envelope * CA (capsid) - major structural component * NC (nucleocapsid) - packaging the dimer of RNA • env(envelope) * SU (surface protein) - spikes on virion that interact with host * TM (transmembrane) - mediates virus-host fusion

  2. Expressed Sequence Tags Single pass sequences of cDNA clones from different libraries High error rate (>1%) mainly frameshifts and insertions/deletions Redundant sampling of 5’ and 3’ ends Large number in public databases EST Data cDNA 3’ ESTs 5’ ESTs EST lengths vary due to varyingpolymerase activity

  3. The human ESTs were classified 37 tissues by cDNA library information of CGAP

  4. HESAS (HERV Expression and Structure Analysis System)

  5. Digital expression profiles of human endogenous retroviral families in normal and cancerous tissues Cancer Immunity, Vol. 4, p. 2 (11 February 2004) Yves Stauffer1, Gregory Theiler1, Peter Sperisen2, Yuri Lebedev3, and C. Victor Jongeneel1 1Ludwig Institute for Cancer Research, Office of Information Technology, Epalinges, Switzerland2Swiss Institute of Bioinformatics, Epalinges, Switzerland3Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Russia Kim Tae Hyung March 20, 2004

  6. Mapping of HERV proviral sequences to the human genome

  7. EST-based expression profiles of different HERV families

  8. The four expression ontologies are used to annotate cDNA clone libraries

  9. Clustering HERV proviruses according to their expression patterns Sbit=[lambdaS-(ln K)]/(ln 2) Bit score >= 36 P-value <= 0.01 d=1-[n11/(n11+n10+n01)] average-linkage agglomerative hierarchical clustering

  10. Comparison of the expression levels of different HERV families in normal and cancerous tissues

  11. HERV-K proviruses expressed in tissues in which other members of the family are not usually expressed

  12. HERV expression analysis by massively parallel signature sequencing (MPSS)

  13. Hs2_22340 Testis 1 357 6,663 BG723219 291 517 5163 5376 Hs6_7456 1 357 5955 BQ365460 203 360 1067 1387 Placenta AU140527 107 360 1067 1181 2305 2783 AU158537 5347 5880 AU158629 5470 5880 BF991666 2906 3332 Hs6_7456 5955 1 357 Lung BF881300, BF881993 3709 3870 4958 5336 BF882289, BF882291 4710 5109 BF881990, BF881991 3724 3862 Hs1_33153 1 357 6150 BM668904, BM669312, BM717273, BM705982, BM670153 5164 6079 860 408 AA197054 Eye Hs5_23289 1 357 6719 BQ189230 2841 5335 2714 5194 Analysis of ESTs matching retroviral open reading frames 37 tissues HERV-K : 66% (63/95) most ESTs matched either pol or env partial ORFs HERV-W : 67% (66/98) 66/66 (100%) HERV-E : 75% (27/36) HERV-H : 41% (74/157) 43/74 (58%) >150 aa >450 nt

  14. Analysis of ESTs matching retroviral open reading frames HERV-K : 66% (63/95) most ESTs matched either pol or env partial ORFs HERV-W : 67% (66/98)  66/66 (100%) HERV-E : 75% (27/36) HERV-H : 41% (74/157)  43/74 (58%) >150 aa >450 nt

  15. HERV ORF prediction

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