RNA Polymerase II Pause Prepares Promoters for Upcoming Transcription during Drosophila Development

According to previous studies, during Drosophila embryogenesis, the recruitment of RNA polymerase II precedes active gene transcription. This work is aimed at exploring whether this mechanism is used during Drosophila metamorphosis. In addition, the composition of the RNA polymerase II paused complexes associated with promoters at different developmental stages are described in detail. For this purpose, we performed ChIP-Seq analysis using antibodies for various modifications of RNA polymerase II (total, Pol II CTD Ser5P, and Pol II CTD Ser2P) as well as for subunits of the NELF, DSIF, and PAF complexes and Brd4/Fs(1)h that control transcription elongation. We found that during metamorphosis, similar to mid-embryogenesis, the promoters were bound by RNA polymerase II in the paused state, preparing for activation at later stages of development. During mid-embryogenesis, RNA polymerase II in a pause state was phosphorylated at Ser5 and Ser2 of Pol II CTD and bound the NELF, DSIF, and PAF complexes, but not Brd4/Fs(1)h. During metamorphosis, the paused RNA polymerase II complex included Brd4/Fs(1)h in addition to NELF, DSIF, and PAF. The RNA polymerase II in this complex was phosphorylated at Ser5 of Pol II CTD, but not at Ser2. These results indicate that, during mid-embryogenesis, RNA polymerase II stalls in the post-pause state, being phosphorylated at Ser2 of Pol II CTD (after the stage of p-TEFb action). During metamorphosis, the pause mechanism is closer to classical promoter-proximal pausing and is characterized by a low level of Pol II CTD Ser2P.

Automated summary

This study investigated the recruitment and pausing mechanism of RNA polymerase II during Drosophila metamorphosis. The results indicate that, similar to mid-embryogenesis, promoters are bound by paused RNA polymerase II during metamorphosis, preparing for activation in later developmental stages.