The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses
Open accessAbstract
Summary Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states.
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Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Causes and consequences of replication stress
Zeman, M. K., & Cimprich, K. A. (2014) · Nature Cell Biology · doi:10.1038/ncb2897 · Cited by 2,079
Self-citationOncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints
Bartkova, J., Rezaei, N., Liontos, M., Karakaidos, P., Kletsas, D., Issaeva, N., Vassiliou, L.-V. F., Kolettas, E., Niforou, K., Zoumpourlis, V. C., et al. (2006) · Nature · doi:10.1038/nature05268 · Cited by 1,986
ATR: an essential regulator of genome integrity
Cimprich, K. A., & Cortez, D. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2450 · Cited by 1,798
Self-citationDNA Damage Sensing by the ATM and ATR Kinases
Marechal, A., & Zou, L. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012716 · Cited by 1,514
Byun, T. S., Pacek, M., Yee, M.-C., Walter, J. C., & Cimprich, K. A. (2005) · Genes & Development · doi:10.1101/gad.1301205 · Cited by 767
Self-citationReplication fork stalling at natural impediments
Mirkin, E. V., & Mirkin, S. M. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00030-06 · Cited by 482
Cited by
Mechanisms of Oncogene-Induced Replication Stress: Jigsaw Falling into Place
Kotsantis, P., Petermann, E., & Boulton, S. J. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1461 · Cited by 416
The DNA damage response to transcription stress
Lans, H., Hoeijmakers, J. H. J., Vermeulen, W., & Marteijn, J. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0169-4 · Cited by 321
Zatreanu, D., Han, Z., Mitter, R., Tumini, E., Williams, H., Gregersen, L., Dirac-Svejstrup, A. B., Roma, S., Stewart, A., Aguilera, A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.037 · Cited by 124
Wang, M., Wei, P.-C., Lim, C. K., Gallina, I. S., Marshall, S., Marchetto, M. C., Alt, F. W., & Gage, F. H. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2019.12.013 · Cited by 105
Treating ARID1A mutated cancers by harnessing synthetic lethality and DNA damage response
Mandal, J., Mandal, P., Wang, T.-L., & Shih, I.-M. (2022) · Journal of Biomedical Science · doi:10.1186/s12929-022-00856-5 · Cited by 84
Metadata
- Authors
- Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T., & Cimprich, K. A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2017-08
- Volume
- 170
- Issue
- 4
- Pages
- 774-786.e19
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2743954317
- Cited by
- 646
- References
- 10
- FWCI
- 18.25
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T., & Cimprich, K. A. (2017). Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell. https://doi.org/10.1016/j.cell.2017.07.043
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