Transcriptional pausing at +62 of the HIV-1 nascent RNA modulates formation of the TAR RNA structure.
A strong transcriptional pause delays human RNA polymerase II three nt after the last potentially paired base in HIV-1 TAR, the RNA structure that binds the transactivator protein Tat. We report here that the HIV-1 pause depends in part on an alternative RNA structure (the HIV-1 pause hairpin) that competes with formation of TAR. By probing the nascent RNA structure in halted transcription complexes, we found that the transcript folds as the pause hairpin before and at the pause, and rearranges to TAR concurrent with or just after escape from the pause. The pause signal triggers a 2 nt reverse translocation by RNA polymerase that may block the active site and be counteracted by formation of TAR. Thus, the HIV-1 pause site modulates nascent RNA rearrangement from a structure that favors pausing to one that both recruits Tat and promotes escape from the pause.
Palangat
M
M
Department of Bacteriology, University of Wisconsin-Madison 53706, USA.
Meier
T I
TI
Keene
R G
RG
Landick
R
R
D001483:Base Sequence; D001665:Binding Sites; D011756:Diphosphates / Q000494:pharmacology; D015967:Gene Expression Regulation, Viral; D006160:Guanosine Triphosphate / Q000235:genetics / Q000378:metabolism; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D009363:Neoplasm Proteins / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics; D012319:RNA Polymerase II / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012107:Research Design; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000378:metabolism / Q000494:pharmacology; D035165:Transcription Factors, General; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics; D035602:Transcriptional Elongation Factors
D011756:Diphosphates; D009363:Neoplasm Proteins; D009692:Nucleic Acid Heteroduplexes; D012367:RNA, Viral; D014157:Transcription Factors; D035165:Transcription Factors, General; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D006160:Guanosine Triphosphate; D012319:RNA Polymerase II