Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.涉及RNA聚合酶II（RNA polymerase II）的基因表达，受mRNA合成与降解的协同互作调控，在此串扰过程中，mRNA降解机器与转录机器分别对转录进程及mRNA稳定性产生调控作用。Rpb4以及可能存在的二聚体Rpb4/7，是RNA聚合酶II调控上述进程的核心组分。本研究阐明了Rpb4参与介导的、调控mRNA印记与稳定性的转录后分子机制。我们通过RNA免疫沉淀测序（RIP-Seq）开展了全基因组范围内Rpb4与mRNA结合关联的分析，证实其靶向了超过1400种转录本的庞大群体。其中一类mRNA同时也是RNA结合蛋白Puf3的靶标。我们证实Rpb4与Puf3可在物理、遗传及功能层面发生相互作用，并共同调控一类共有mRNA的稳定性以及可能的印记过程。此外，Rpb4与Puf3和mRNA的结合依赖彼此。我们还首次证实，Puf3可通过Rpb4依赖的方式与染色质结合。本研究数据同时表明，Rpb4或许是RNA聚合酶II的关键组分，可与RNA结合蛋白（RBPs）协同协作，调控mRNA合成、印记与稳定性。