Yeast PAF1 complex counters the pol III accumulation and replication stress on the tRNA genes

Pratibha Bhalla,Kuljeet Singh Sandhu,Ashutosh Shukla,Dipti Vinayak Vernekar,Aneeshkumar Gopalakrishnan Arimbasseri,Purnima Bhargava

doi:10.1038/s41598-019-49316-5

Abstract

The RNA polymerase (pol) III transcribes mostly short, house-keeping genes, which produce stable, non-coding RNAs. The tRNAs genes, highly transcribed by pol III in vivo are known replication fork barriers. One of the transcription factors, the PAF1C (RNA polymerase II associated factor 1 complex) is reported to associate with pol I and pol II and influence their transcription. We found low level PAF1C occupancy on the yeast pol III-transcribed genes, which is not correlated with nucleosome positions, pol III occupancy and transcription. PAF1C interacts with the pol III transcription complex and causes pol III loss from the genes under replication stress. Genotoxin exposure causes pol III but not Paf1 loss from the genes. In comparison, Paf1 deletion leads to increased occupancy of pol III, γ-H2A and DNA pol2 in gene-specific manner. Paf1 restricts the accumulation of pol III by influencing the pol III pause on the genes, which reduces the pol III barrier to the replication fork progression.

Highlights

Eukaryotic transcription is accomplished by three multi-subunit RNA polymerase enzymes; pol I, pol II and pol III
These results show that influences of Paf[1] and HU on the replication stress on the tRNA genes are opposite and Paf[1] plays a damage-preventive role on the tRNA genes during the replication fork progression
This study shows a protective role of Paf[1] on pol III-transcribed genes, which are naturally occurring sites of the replication fork stalling in the normally cycling cells

Summary

Introduction

Eukaryotic transcription is accomplished by three multi-subunit RNA polymerase (pol) enzymes; pol I, pol II and pol III. It does not affect the low level nucleosomes near the pol III-transcribed genes, which carry very low levels of active state H3K4 and H3K36 histone methylation marks It restricts pol III occupancy levels on the genes, as pol III levels increase several fold on all the tested genes in the paf1∆ cells. This pol III accumulation represents its stalling as the mature tRNA levels show only a small increase in the paf1∆ cells These results suggest an inhibitory influence of Paf[1] on pol III-transcribed genes, which may serve to protect these highly transcribed, known replication fork pause sites[10,11] against the DNA damage

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Results

Conclusion