TY - JOUR
T1 - Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites
AU - Promonet, Alexy
AU - Padioleau, Ismaël
AU - Liu, Yaqun
AU - Sanz, Lionel
AU - Biernacka, Anna
AU - Schmitz, Anne Lyne
AU - Skrzypczak, Magdalena
AU - Sarrazin, Amélie
AU - Mettling, Clément
AU - Rowicka, Maga
AU - Ginalski, Krzysztof
AU - Chedin, Frédéric
AU - Chen, Chun Long
AU - Lin, Yea Lih
AU - Pasero, Philippe
N1 - Funding Information:
We thank Benjamin Pardo and Vincent Vanoosthuyse for critical comments on the manuscript. We thank the imaging facility MRI, member of the national infrastructure France-BioImaging supported by the French National Research Agency (ANR-10-INBS-04, «Investments for the future»). A.P. thanks the Ligue Nationale contre le Cancer for fellowship. Work in the PP lab is supported by grants from the Agence Nationale pour la Recherche (ANR), Institut National du Cancer (INCa), SIRIC Montpellier Cancer (INCa Inserm DGOS 12553) the Ligue Nationale Contre le Cancer (équipe labellisée), and the Fondation MSDAvenir. Work of CC lab is supported by the Curie YPI program, the ATIP-Avenir program from CNRS and Plan Cancer, the Agence Nationale pour la Recherche (ANR) and Institut National du Cancer (INCa). Work in the FC lab is supported by the National Institutes of Health (GM120607). Funding to K.G. and M.S. was provided by Foundation for Polish Science (TEAM) and Polish National Science Centre (2015/17/D/NZ2/03711). Work in the MR lab was supported by the NIH grant R01GM112131.
PY - 2020/12/1
Y1 - 2020/12/1
N2 - R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, here, we map RNA:DNA hybrids, replication stress markers and DNA double-strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR is only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also accumulate at TTS, leading to persistent checkpoint activation, spreading of γ-H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.
AB - R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, here, we map RNA:DNA hybrids, replication stress markers and DNA double-strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR is only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also accumulate at TTS, leading to persistent checkpoint activation, spreading of γ-H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.
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U2 - 10.1038/s41467-020-17858-2
DO - 10.1038/s41467-020-17858-2
M3 - Article
C2 - 32769985
AN - SCOPUS:85089185115
VL - 11
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 3940
ER -