A transcription bubble is a localized region of separated DNA strands within a transcription complex, exposing a template for RNA synthesis. During bacterial initiation, promoter binding and DNA opening produce an RNA-polymerase complex positioned to initiate the transcript [1]. Regulatory proteins can alter promoter recognition and the transitions leading to productive initiation [2]. In an elongating complex, the template strand enters the polymerase active site, where the growing RNA forms a short hybrid with DNA before emerging from the enzyme [3][4]. The displaced nontemplate strand follows a separate path. Structural elements of RNA polymerase coordinate the two bubble boundaries, with downstream strand separation and upstream strand reannealing accompanying progression of the transcription complex along the DNA [5].
- RNA polymerase
- DNA strand separation
- open promoter complex
- RNA–DNA hybrid
RNA Research and Splicing·Molecular Biology·Biochemistry, Genetics and Molecular Biology·Life Sciences
References
- Douglas F. Browning; Stephen J. W. Busby; The Regulation of Bacterial Transcription Initiation. Nat. Rev. Microbiol. 2004, 2, 57-65, 10.1038/nrmicro787.
- Douglas F. Browning; Stephen J. W. Busby; Local and Global Regulation of Transcription Initiation in Bacteria. Nat. Rev. Microbiol. 2016, 14, 638-650, 10.1038/nrmicro.2016.103.
- Christopher O. Barnes; Monica Calero; Indranil Malik; Brian W. Graham; Henrik Spahr; Guowu Lin; Aina E. Cohen; Ian S. Brown; Qiangmin Zhang; Filippo Pullara; et al. Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol. Cell 2015, 59, 258-269, 10.1016/j.molcel.2015.06.034.
- Patrick Cramer; Organization and Regulation of Gene Transcription. Nature 2019, 573, 45-54, 10.1038/s41586-019-1517-4.
- Andreas U. Mueller; James Chen; Mengyu Wu; Courtney Chiu; B. Tracy Nixon; Elizabeth A. Campbell; Seth A. Darst; A General Mechanism for Transcription Bubble Nucleation in Bacteria. Proc. Natl. Acad. Sci. 2023, 120, e2220874120, 10.1073/pnas.2220874120.