RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

Abstract

words)Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4∆ mutant. In contrast to the other looping-defective mutants, rpb4∆ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4∆ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4∆ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.[14]. Besides activators and TFIIB, TFIIH and Mediator complex also play a critical role in gene loop formation by directly interacting with the CF1 and CPF 3'-end processing/termination factors [12,16]. It is generally believed that RNAPII is not directly involved in formation of gene loops, but is a rather passive player in the process. Since gene looping is a transcription-dependent process, it has been presumed that all mutations that affect transcription will also alter gene looping. Accordingly, gene looping was completely abolished in the rpb1-1 mutant [17].The structure of RNAPII is highly conserved among eukaryotes. In all eukaryotes from yeast to humans, RNAPII is composed of 12 subunits. Only Saccharomyces cerevisiae RNAPII exists in a 10-subunit core and a dissociable subcomplex formed by Rpb4 and Rpb7 [18,19].The 12 subunits of RNAPII have been implicated in different functions during the process of transcription. The two largest subunits, Rpb1 and Rpb2, are required for binding to the DNA template. Rpb1 contains a groove for the entry of deoxyribonucleotides. Rpb7 has two RNA binding domains and plays a pivotal role in mRNA decay [20]. Rpb9 has been implicated in start-site selection, but is dispensable for assembly of the 10-subunit enzyme (Hull et al., 1995). While the two largest subunits, Rpb1 and Rpb2, have well-established roles in the initiation of transcription, a few published reports suggest that some of the RNAPII subunits function in the termination of transcription. The CTD of the largest subunit Rpb1 consists of multiple repeats of the heptapeptide sequence (YSPTSPS). The phosphorylation of Ser2 of the CTD is critical for the recruitment of 3'-end processing factors and for termination of transcription [21,22]. In the crystal structure, the Rpb3/Rpb11 heterodimer lies in close proximity of the RNA exit channel [...

AFF4 regulates osteogenic differentiation of human dental follicle cells

“…RNA Pol II can accelerate translation by the enzymatic machinery to transcribe protein-coding genes into mRNA. 29 Transcriptional elongation is a vital step during gene transcription, and the SEC has a positive regulatory effect on this process. 22 For the initial induction stage of transcription, an external stimulus is required.…”

RNA polimerasa II: transcribiendo y regulando

“…Más recientemente, nuestros estudios han permitido esclarecer el papel de la RNAPII en la formación de los bucles génicos (11). En un gran número de genes transcripcionalmente activos, el promotor y terminador de los mismos se yuxtaponen para formar una estructura dinámica denominada "gene loop".…”

“…Sin embargo, nuestro trabajo ha demostrado que esto es erróneo y que la RNAPII juega un papel directo en la formación de los bucles génicos vía Rpb4 al mediar la interacción directa entre dos factores esenciales de este proceso, TFIIB, un GFT, y Ssu72, fosfatasa del CTD y además componente del factor de corte y poliadenilación CPF (15,16). Nuestro trabajo demuestra claramente que Rpb4 desempeña un papel fundamental, no sólo al mediar la interacción de TFIIB y Ssu72 entre sí, sino también con la RNAPII durante la formación de bucles génicos, promoviendo así la transferencia de la misma desde las regiones terminadoras a los promotores para reiniciar la transcripción (Figura C, (11).…”

Boosting detection of low abundance proteins in thermal proteome profiling experiments by addition of an isobaric trigger channel to TMT multiplexes

“…Ssu72 is an integral component of CPF and its function is required for proper termination and 3'-end processing of RNAs [59][60][61][62][63] . Additionally, its interactions with TFIIB have shown to be critical for the formation of gene loops, which regulate gene expression by linking transcription termination and initiation factors [64][65][66][67] . Much of the characterization of Ssu72 has been accomplished through studies using the ssu72-2 mutant yeast strain 41,59,65,68 .…”

“…Additionally, its interactions with TFIIB have shown to be critical for the formation of gene loops, which regulate gene expression by linking transcription termination and initiation factors [64][65][66][67] . Much of the characterization of Ssu72 has been accomplished through studies using the ssu72-2 mutant yeast strain 41,59,65,68 . The ssu72-2 TS mutant contains a single mutation, R129A, that confers temperature sensitivity at 37°C.…”