Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing

RNA

Volumn 17, Issue 4, 2011, Pages 665-674

  Miller, Heather B ^a   Robinson, Timothy J ^a   Gordân, Raluca ^b,c   Hartemink, Alexander J ^b   Garcia Blanco, Mariano A ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Duke University   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Alternative RNA processing; Exon array; RNA splicing; Tat SF1; Transcription

Indexed keywords

CELL PROTEIN; INSULIN; NUCLEIC ACID; TAT SPECIFIC FACTOR 1; UNCLASSIFIED DRUG;

ARTICLE; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; CELL CYCLE; CONTROLLED STUDY; EXON; GENE IDENTIFICATION; GENE TARGETING; HEALTH SURVEY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; MICROARRAY ANALYSIS; NUCLEIC ACID METABOLISM; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; RNA INTERFERENCE; RNA PROCESSING; RNA SPLICING; RNA TRANSCRIPTION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; CELL CYCLE; CELL LINE; DNA; EXONS; HIV-1; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79952996322     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2462011     Document Type: Article

References (55)

1. Abdueva D, Wing MR, Schaub B, Triche TJ. 2007. Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays. PLoS ONE 2: e913. doi: 10.1371/journal.pone.0000913.
2. Aoufouchi S, Flatter E, Dahan A, Faili A, Bertocci B, Storck S, Delbos F, Cocea L, Gupta N, Weill JC, et al. 2000. Two novel human and mouse DNA polymerases of the polX family. Nucleic Acids Res 28: 3684-3693.
3. Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. 2008. Gene expression and isoform variation analysis using Affymetrix exon arrays. BMC Genomics 9: 529 doi: 10.1186-1471-2164-9-529.
4. Bentley D. 2002. The mRNA assembly line: transcription and processing machines in the same factory. Curr Opin Cell Biol 14: 336-342. (Pubitemid 34626972)
5. Bentley DL. 2005. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 17: 251-256. (Pubitemid 40719913)
6. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ. 2008. Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: 921-926. (Pubitemid 351263756)
7. Chang JT, Nevins JR. 2006. GATHER: a systems approach to interpreting genomic signatures. Bioinformatics 22: 2926-2933. (Pubitemid 44811565)
8. Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H. 2009. DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation. Genes Dev 23: 2765-2777.
9. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, Wang H, Williams A, Blume JE. 2007. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol 8: R64. doi: 10.1186-gb-2007-8-4-r64.
10. Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210. (Pubitemid 34679544)
11. Fong YW, Zhou Q. 2000. Relief of two built-in autoinhibitory mechanisms in P-TEFb is required for assembly of a multicomponent transcription elongation complex at the human immunodeficiency virus type 1 promoter. Mol Cell Biol 20: 5897-5907. (Pubitemid 30613039)
12. Fong YW, Zhou Q. 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929-933. (Pubitemid 34024746)
13. French PJ, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent MJ, Luider TM, Kros JM, van der Spek P, Sillevis Smitt PA. 2007. Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res 67: 5635-5642. (Pubitemid 46984994)
14. Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, et al. 2006. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 7: 325. doi: 10.1186/1471-2164-7-325.
15. Goldstrohm AC, Greenleaf AL, Garcia-Blanco MA. 2001. Co-transcriptional splicing of pre-messenger RNAs: considerations for the mechanism of alternative splicing. Gene 277: 31-47. (Pubitemid 32973194)
16. Gurtan AM, D'Andrea AD. 2006. Dedicated to the core: understanding the Fanconi anemia complex. DNA Repair (Amst) 5: 1119-1125. (Pubitemid 44291606)
17. Hirose Y, Manley JL. 2000. RNA polymerase II and the integration of nuclear events. Genes Dev 14: 1415-1429. (Pubitemid 30421835)
18. Hung LH, Heiner M, Hui J, Schreiner S, Benes V, Bindereif A. 2008. Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis. RNA 14: 284-296. (Pubitemid 351171589)
19. Johnson NL, Kotz S, Kemp AW. 1992. Univariate discrete distributions, 2nd ed. Wiley, New York.
20. Kameoka S, Duque P, Konarska MM. 2004. p54(nrb) associates with the 5′ splice site within large transcription/splicing complexes. EMBO J 23: 1782-1791. (Pubitemid 38649641)
21. Kim JB, Yamaguchi Y, Wada T, Handa H, Sharp PA. 1999. Tat-SF1 protein associates with RAP30 and human SPT5 proteins. Mol Cell Biol 19: 5960-5968. (Pubitemid 29399301)
22. Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G. 2004. Multiple links between transcription and splicing. RNA 10: 1489-1498. (Pubitemid 39288183)
23. Laajala E, Aittokallio T, Lahesmaa R, Elo LL. 2009. Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol 10: R77. doi: 10- 1186/gb-2009-10-7-r77.
24. Levitus M, Joenje H, de Winter JP. 2006. The Fanconi anemia pathway of genomic maintenance. Cell Oncol 28: 3-29. (Pubitemid 43673124)
25. Li XY, Green MR. 1998. The HIV-1 Tat cellular coactivator Tat-SF1 is a general transcription elongation factor. Genes Dev 12: 2992-2996. (Pubitemid 28469301)
26. Maniatis T, Reed R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506. (Pubitemid 34288845)
27. McKee AE, Neretti N, Carvalho LE, Meyer CA, Fox EA, Brodsky AS, Silver PA. 2007. Exon expression profiling reveals stimulusmediated exon use in neural cells. Genome Biol 8: R159. doi: 10- 1186/gb-2007-8-8-r159.
28. Miller HB, Saunders KO, Tomaras GD, Garcia-Blanco MA. 2009. Tat- SF1 is not required for Tat transactivation but does regulate the relative levels of unspliced and spliced HIV-1 RNAs. PLoS ONE 4: e5710. doi: 10.1371/journal.pone. 0005710.
29. Montgomery DC. 2006. Design and analysis of experiments, 5th ed. Wiley and Sons, Hoboken, NJ.
30. Moore MJ, Silver PA. 2008. Global analysis of mRNA splicing. RNA 14: 197-203. (Pubitemid 351171579)
31. Neugebauer KM. 2002. On the importance of being co-transcriptional. J Cell Sci 115: 3865-3871. (Pubitemid 35256487)
32. Oberdoerffer S, Moita LF, Neems D, Freitas RP, Hacohen N, Rao A. 2008. Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science 321: 686-691.
33. Orphanides G, Reinberg D. 2002. A unified theory of gene expression. Cell 108: 439-451. (Pubitemid 34260870)
34. Pandit S, Wang D, Fu XD. 2008. Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 20: 260-265.
35. Parada CA, Roeder RG. 1999. A novel RNA polymerase II-containing complex potentiates Tat-enhanced HIV-1 transcription. EMBO J 18: 3688-3701. (Pubitemid 29308848)
36. Patel KJ, Joenje H. 2007. Fanconi anemia and DNA replication repair. DNA Repair (Amst) 6: 885-890. (Pubitemid 46880469)
37. Pfaff l MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45. doi: 10.1093/nar/29.9.e45.
38. Pfaff l MW, Horgan GW, Dempfle L. 2002. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30: e36. doi: 10.1093/nar/30.9.e36.
39. Proudfoot NJ, Furger A, Dye MJ. 2002. Integrating mRNA processing with transcription. Cell 108: 501-512. (Pubitemid 34260875)
40. Robinson MD, Speed TP. 2007. A comparison of Affymetrix gene expression arrays. BMC Bioinformatics 8: 449. doi: 10.1186/1471-2105-8-449.
41. Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL. 2010. SplicerAV: a tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics 11: 108. doi: 10.1186/1471-2105-11-108
42. Sanchez-Alvarez M, Goldstrohm AC, Garcia-Blanco MA, Sune C. 2006. Human transcription elongation factor CA150 localizes to splicing factor-rich nuclear speckles and assembles transcription and splicing components into complexes through its amino and carboxyl regions. Mol Cell Biol 26: 4998-5014. (Pubitemid 43955814)
43. Smith MJ, Kulkarni S, Pawson T. 2004. FF domains of CA150 bind transcription and splicing factors through multiple weak interactions. Mol Cell Biol 24: 9274-9285. (Pubitemid 39391666)
44. Sun J, Li R. 2009. Human negative elongation factor activates transcription and regulates alternative transcription initiation. J Biol Chem 285: 6443-6452.
45. Tan S, Aso T, Conaway RC, Conaway JW. 1994. Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II. J Biol Chem 269: 25684-25691. (Pubitemid 24336264)
46. Tan S, Conaway RC, Conaway JW. 1995. Dissection of transcription factor TFIIF functional domains required for initiation and elongation. Proc Natl Acad Sci 92: 6042-6046.
47. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74.
48. Wang W. 2007. Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. Nat Rev Genet 8: 735-748. (Pubitemid 47429206)
49. Warzecha CC, Shen S, Xing Y, Carstens RP. 2009. The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol 6: 546-562.
50. Wu-Baer F, Lane WS, Gaynor RB. 1998. Role of the human homolog of the yeast transcription factor SPT5 in HIV-1 Tat-activation. J Mol Biol 277: 179-197. (Pubitemid 28174961)
51. Xing Y, Stoilov P, KapurK,Han A, JiangH, Shen S, Black DL,WongWH. 2008. MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14: 1470-1479.
52. Yan D, Perriman R, Igel H, Howe KJ, Neville M, Ares M Jr. 1998. CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif. Mol Cell Biol 18: 5000-5009. (Pubitemid 28388083)
53. Zhou Q, Sharp PA. 1995. Novel mechanism and factor for regulation by HIV-1 Tat. EMBO J 14: 321-328.
54. Zhou Q, Sharp PA. 1996. Tat-SF1: cofactor for stimulation of transcriptional elongation by HIV-1 Tat. Science 274: 605-610. (Pubitemid 26360439)
55. Zhou Q, Chen D, Pierstorff E, Luo K. 1998. Transcription elongation factor P-TEFb mediates Tat activation of HIV-1 transcription at multiple stages. EMBO J 17: 3681-3691. (Pubitemid 28327386)