The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria
Open accessAbstract
During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5'-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes.
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
Coupling mRNA processing with transcription in time and space
Bentley, D. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3662 · Cited by 828
Nascent transcript sequencing visualizes transcription at nucleotide resolution
Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823
Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity
Hiller, B., Achleitner, M., Glage, S., Naumann, R., Behrendt, R., & Roers, A. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20120876 · Cited by 245
Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells
Gudipati, R. K., Xu, Z., Lebreton, A., Séraphin, B., Steinmetz, L. M., Jacquier, A., & Libri, D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.018 · Cited by 236
Scholes, D. T., Banerjee, M., Bowen, B., & Curcio, M. J. (2001) · Genetics · doi:10.1093/genetics/159.4.1449 · Cited by 235
Baller, J. A., Gao, J., Stamenova, R., Curcio, M. J., & Voytas, D. F. (2012) · Genome Research · doi:10.1101/gr.129585.111 · Cited by 61
Ruhanen, H., Ushakov, K., & Yasukawa, T. (2011) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2011.08.008 · Cited by 41
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A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation
Conn, V. M., Hugouvieux, V., Nayak, A., Conos, S. A., Capovilla, G., Cildir, G., Jourdain, A., Tergaonkar, V., Schmid, M., Zubieta, C., et al. (2017) · Nature Plants · doi:10.1038/nplants.2017.53 · Cited by 584
Chen, L., Chen, J.-Y., Zhang, X., Gu, Y., Xiao, R., Shao, C., Tang, P., Qian, H., Luo, D., Li, H., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.008 · Cited by 375
Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1
Nguyen, H. D., Yadav, T., Giri, S., Saez, B., Graubert, T. A., & Zou, L. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.01.029 · Cited by 267
Metadata
- Authors
- El Hage, A., Webb, S., Kerr, A., & Tollervey, D.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-10-30
- Volume
- 10
- Issue
- 10
- Pages
- e1004716
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2134885583
- Cited by
- 203
- References
- 9
- FWCI
- 5.96
- Type
- journal article
- Language
- en
- Open access
- gold
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