Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability

Abstract

DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication–transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication–transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome stability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

“…Multiple pathways ranging from RNA processing and transcriptional termination to specific helicases that remove DNA-RNA hybrids (Brambati et al 2015) facilitate replication fork progression and promote genome stability. A recent report identified RNAPII itself as a dual-function factor that can block the progression of replication forks and favor replication restart, albeit by an unknown mechanism (Felipe-Abrio et al 2015).…”

“…For instance, tRNA genes are transiently silenced by Maf1 to promote the passage of replication forks during normal S phase in eukaryotic cells (Nguyen et al 2010). In addition, both bacteria and eukaryotes express specific DNA helicases such as Sen1/ Senataxin or Aquarius, which remove proteins and/or RNA-DNA hybrids that hinder replication fork progression (Brambati et al 2015). Under stress, additional mechanisms deal with transcription-replication interference.…”

The Causes and Consequences of Topological Stress during DNA Replication

“…RNA transcription complexes could act as both sterical and topological blocks to DNA unwinding by replication. Other recent reviews have extensively discussed how transcription could impede unwinding DNA either through direct collision, or through the generation of non-B form structures and R loops [28,29]. In this review we will focus on how topological stress induced by transcription can disrupt DNA unwinding.…”

Transcription activity contributes to the firing of non-constitutive origins in Trypanosoma brucei

“…To measure natural R-loop foci, we used a specific antibody (S9.6) that recognizes DNA:RNA hybrids (41). R-loops are triple-stranded nucleic acid structures composed of a DNA:RNA hybrid and a single-stranded DNA (ssDNA), and their generation is related to various factors, among them replication-transcription collisions (8,42,43). Similar to γH2A, T. brucei shows natural levels of R-loops represented by green fluorescent foci throughout the S and G2 phases, which become rare during mitosis and cytokinesis ( Figure 5D and F).…”