{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T20:22:42Z","timestamp":1791490962285,"version":"4.3.4"},"reference-count":69,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2018,8,10]],"date-time":"2018-08-10T00:00:00Z","timestamp":1533859200000},"content-version":"vor","delay-in-days":374,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T00:00:00Z","timestamp":1501545600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB1243492"],"award-info":[{"award-number":["MCB1243492"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI116669"],"award-info":[{"award-number":["AI116669"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI108698"],"award-info":[{"award-number":["AI108698"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DP2GM110773"],"award-info":[{"award-number":["DP2GM110773"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell"],"published-print":{"date-parts":[[2017,8]]},"DOI":"10.1016\/j.cell.2017.07.044","type":"journal-article","created":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T14:16:34Z","timestamp":1502374594000},"page":"787-799.e18","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":267,"title":["Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis"],"prefix":"10.1016","volume":"170","author":[{"given":"Kevin S.","family":"Lang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley N.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher N.","family":"Merrikh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Ragheb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Tabakh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex J.","family":"Pollock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua J.","family":"Woodward","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia E.","family":"Dreifus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Houra","family":"Merrikh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cell.2017.07.044_bib1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.molcel.2012.04.009","article-title":"R loops: from transcription byproducts to threats to genome stability","volume":"46","author":"Aguilera","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.cell.2017.07.044_bib2","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1099\/mic.0.022277-0","article-title":"lmo1273, a novel gene involved in Listeria monocytogenes virulence","volume":"155","author":"Bigot","year":"2009","journal-title":"Microbiology"},{"key":"10.1016\/j.cell.2017.07.044_bib3","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/emboj.2009.308","article-title":"The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in\u00a0vivo","volume":"29","author":"Boubakri","year":"2010","journal-title":"EMBO J."},{"key":"10.1016\/j.cell.2017.07.044_bib4","doi-asserted-by":"crossref","first-page":"5809","DOI":"10.1093\/nar\/gkm613","article-title":"The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates","volume":"35","author":"Boul\u00e9","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2017.07.044_bib5","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1128\/jb.115.3.1063-1070.1973","article-title":"Phenotypes of pleiotropic-negative sporulation mutants of Bacillus subtilis","volume":"115","author":"Brehm","year":"1973","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib6","doi-asserted-by":"crossref","first-page":"5335","DOI":"10.1128\/JB.05490-11","article-title":"Osmotically controlled synthesis of the compatible solute proline is critical for cellular defense of Bacillus subtilis against high osmolarity","volume":"193","author":"Brill","year":"2011","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib7","doi-asserted-by":"crossref","first-page":"e1000449","DOI":"10.1371\/journal.ppat.1000449","article-title":"In\u00a0vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection","volume":"5","author":"Camejo","year":"2009","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cell.2017.07.044_bib8","doi-asserted-by":"crossref","first-page":"2948","DOI":"10.1128\/JB.187.9.2948-2956.2005","article-title":"Bacillus subtilis paraquat resistance is directed by sigmaM, an extracytoplasmic function sigma factor, and is conferred by YqjL and BcrC","volume":"187","author":"Cao","year":"2005","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib9","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3390\/genes8010033","article-title":"Replication fork protection factors controlling R-loop bypass and suppression","volume":"8","author":"Chang","year":"2017","journal-title":"Genes (Basel)"},{"key":"10.1016\/j.cell.2017.07.044_bib10","doi-asserted-by":"crossref","first-page":"5889","DOI":"10.1074\/jbc.M115.688648","article-title":"Yeast helicase Pif1 unwinds RNA:DNA hybrids with higher processivity than DNA:DNA duplexes","volume":"291","author":"Chib","year":"2016","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cell.2017.07.044_bib11","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.jmb.2005.11.017","article-title":"Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus","volume":"356","author":"Chon","year":"2006","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib12","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ceb.2015.04.008","article-title":"The yin and yang of R-loop biology","volume":"34","author":"Costantino","year":"2015","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib13","series-title":"Molecular Biological Methods for Bacillus","author":"Cutting","year":"1990"},{"key":"10.1016\/j.cell.2017.07.044_bib14","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1016\/S0021-9258(17)42136-3","article-title":"Hypernegative supercoiling of the DNA template during transcription elongation in\u00a0vitro","volume":"269","author":"Drolet","year":"1994","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cell.2017.07.044_bib15","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.cell.2011.07.034","article-title":"Linking RNA polymerase backtracking to genome instability in E.\u00a0coli","volume":"146","author":"Dutta","year":"2011","journal-title":"Cell"},{"key":"10.1016\/j.cell.2017.07.044_bib16","doi-asserted-by":"crossref","first-page":"7681","DOI":"10.1128\/JB.01053-07","article-title":"gerT, a newly discovered germination gene under the control of the sporulation transcription factor sigmaK in Bacillus subtilis","volume":"189","author":"Ferguson","year":"2007","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib17","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0076-6879(05)09012-9","article-title":"Methods for determining spontaneous mutation rates","volume":"409","author":"Foster","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.cell.2017.07.044_bib18","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1126\/science.1455232","article-title":"Consequences of replication fork movement through transcription units in\u00a0vivo","volume":"258","author":"French","year":"1992","journal-title":"Science"},{"key":"10.1016\/j.cell.2017.07.044_bib19","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/0076-6879(95)62048-6","article-title":"Analysis of replication intermediates by two-dimensional agarose gel electrophoresis","volume":"262","author":"Friedman","year":"1995","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.cell.2017.07.044_bib20","doi-asserted-by":"crossref","first-page":"8575","DOI":"10.1128\/JB.00653-07","article-title":"Reassessment of the in\u00a0vivo functions of DNA polymerase I and RNase H in bacterial cell growth","volume":"189","author":"Fukushima","year":"2007","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib21","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1101\/gad.17010011","article-title":"R-loop-mediated genomic instability is caused by impairment of replication fork progression","volume":"25","author":"Gan","year":"2011","journal-title":"Genes Dev."},{"key":"10.1016\/j.cell.2017.07.044_bib22","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/B978-0-12-387665-2.00002-X","article-title":"Transcription-coupled DNA repair in prokaryotes","volume":"110","author":"Ganesan","year":"2012","journal-title":"Prog. Mol. Biol. Transl. Sci."},{"key":"10.1016\/j.cell.2017.07.044_bib23","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nrm.2016.88","article-title":"Transcription-replication conflicts: how they occur and how they are resolved","volume":"17","author":"Garc\u00eda-Muse","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib24","doi-asserted-by":"crossref","first-page":"e1005674","DOI":"10.1371\/journal.pgen.1005674","article-title":"The Fanconi anemia pathway protects genome integrity from R-loops","volume":"11","author":"Garc\u00eda-Rubio","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib25","doi-asserted-by":"crossref","first-page":"6223","DOI":"10.1128\/JB.06023-11","article-title":"Bacillus subtilis \u03c3(V) confers\u00a0lysozyme resistance by activation of two cell wall modification pathways, peptidoglycan O-acetylation and D-alanylation of teichoic acids","volume":"193","author":"Guariglia-Oropeza","year":"2011","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib26","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/S0014-5793(02)03503-2","article-title":"Cleavage of a DNA-RNA-DNA\/DNA chimeric substrate containing a single ribonucleotide at the DNA-RNA junction with prokaryotic RNases HII","volume":"531","author":"Haruki","year":"2002","journal-title":"FEBS Lett."},{"key":"10.1016\/j.cell.2017.07.044_bib27","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.1128\/JB.181.7.2118-2123.1999","article-title":"Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168","volume":"181","author":"Itaya","year":"1999","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib28","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.jmb.2012.06.024","article-title":"Tuning in to Interference: R-Loops and Cascade Complexes in CRISPR Immunity","volume":"422","author":"Ivan\u010di\u0107-Ba\u0107e","year":"2012","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib29","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nsmb.2019","article-title":"Structural basis for CRISPR RNA-guided DNA recognition by Cascade","volume":"18","author":"Jore","year":"2011","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib30","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2148-7-128","article-title":"Evolution of ribonuclease H\u00a0genes in prokaryotes to avoid inheritance of redundant genes","volume":"7","author":"Kochiwa","year":"2007","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib31","first-page":"212","article-title":"Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription","volume":"61","author":"Kogoma","year":"1997","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.cell.2017.07.044_bib32","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2017.07.044_bib33","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2017.07.044_bib34","doi-asserted-by":"crossref","first-page":"65","DOI":"10.2174\/138920212799034767","article-title":"Interference between DNA replication and transcription as a cause of genomic instability","volume":"13","author":"Lin","year":"2012","journal-title":"Curr. Genomics"},{"key":"10.1016\/j.cell.2017.07.044_bib35","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1126\/science.7855590","article-title":"Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex","volume":"267","author":"Liu","year":"1995","journal-title":"Science"},{"key":"10.1016\/j.cell.2017.07.044_bib36","doi-asserted-by":"crossref","first-page":"25033","DOI":"10.1074\/jbc.274.35.25033","article-title":"PriA-directed assembly of a primosome on D loop DNA","volume":"274","author":"Liu","year":"1999","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cell.2017.07.044_bib37","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/mmi.12440","article-title":"Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics","volume":"91","author":"Maduike","year":"2014","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2017.07.044_bib38","doi-asserted-by":"crossref","first-page":"16654","DOI":"10.1074\/jbc.274.23.16654","article-title":"Relaxation of Transcription-induced Negative Supercoiling Is an Essential Function of Escherichia coli DNA Topoisomerase I","volume":"274","author":"Masse","year":"1999","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cell.2017.07.044_bib39","doi-asserted-by":"crossref","first-page":"4430","DOI":"10.1073\/pnas.86.12.4430","article-title":"Escherichia coli DNA helicase II (uvrD gene product) catalyzes the unwinding of DNA.RNA hybrids in\u00a0vitro","volume":"86","author":"Matson","year":"1989","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2017.07.044_bib40","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.tim.2017.01.008","article-title":"Spatial and temporal control of evolution through replication-transcription conflicts","volume":"25","author":"Merrikh","year":"2017","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.cell.2017.07.044_bib41","doi-asserted-by":"crossref","first-page":"e1005289","DOI":"10.1371\/journal.pgen.1005289","article-title":"The B. subtilis accessory helicase PcrA facilitates DNA replication through transcription units","volume":"11","author":"Merrikh","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib42","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/nature09758","article-title":"Co-directional replication-transcription conflicts lead to replication restart","volume":"470","author":"Merrikh","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.cell.2017.07.044_bib43","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1128\/jb.169.6.2650-2658.1987","article-title":"Mode of initiation of constitutive stable DNA replication in RNase H-defective mutants of Escherichia coli K-12","volume":"169","author":"von Meyenburg","year":"1987","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib44","series-title":"Experiments in Molecular Genetics","author":"Miller","year":"1972"},{"key":"10.1016\/j.cell.2017.07.044_bib45","doi-asserted-by":"crossref","first-page":"E1096","DOI":"10.1073\/pnas.1416651112","article-title":"An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis","volume":"112","author":"Million-Weaver","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2017.07.044_bib46","doi-asserted-by":"crossref","first-page":"2374","DOI":"10.1128\/JB.00237-15","article-title":"Replication restart after replication-transcription conflicts requires recA in Bacillus subtilis","volume":"197","author":"Million-Weaver","year":"2015","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cell.2017.07.044_bib47","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1128\/MCB.25.3.888-895.2005","article-title":"Mechanisms of transcription-replication collisions in bacteria","volume":"25","author":"Mirkin","year":"2005","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.cell.2017.07.044_bib48","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1099\/mic.0.26665-0","article-title":"Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress","volume":"150","author":"Mostertz","year":"2004","journal-title":"Microbiology"},{"key":"10.1016\/j.cell.2017.07.044_bib49","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1126\/science.1206848","article-title":"Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis","volume":"335","author":"Nicolas","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.cell.2017.07.044_bib50","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/S1389-1723(99)80168-6","article-title":"Molecular diversities of RNases H","volume":"88","author":"Ohtani","year":"1999","journal-title":"J.\u00a0Biosci. Bioeng."},{"key":"10.1016\/j.cell.2017.07.044_bib51","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1021\/bi982207z","article-title":"Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families","volume":"38","author":"Ohtani","year":"1999","journal-title":"Biochemistry"},{"key":"10.1016\/j.cell.2017.07.044_bib52","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/nature11989","article-title":"Accelerated gene evolution through replication-transcription conflicts","volume":"495","author":"Paul","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.cell.2017.07.044_bib53","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/nature07527","article-title":"The replisome uses mRNA as a primer after colliding with RNA polymerase","volume":"456","author":"Pomerantz","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.cell.2017.07.044_bib54","doi-asserted-by":"crossref","first-page":"W187","DOI":"10.1093\/nar\/gku365","article-title":"deepTools: a flexible platform for exploring deep-sequencing data","volume":"42","author":"Ram\u00edrez","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2017.07.044_bib55","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/ng1209","article-title":"Essentiality, not expressiveness, drives gene-strand bias in bacteria","volume":"34","author":"Rocha","year":"2003","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib56","doi-asserted-by":"crossref","first-page":"6570","DOI":"10.1093\/nar\/gkg859","article-title":"Gene essentiality determines chromosome organisation in bacteria","volume":"31","author":"Rocha","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2017.07.044_bib57","doi-asserted-by":"crossref","first-page":"e1004001","DOI":"10.1371\/journal.pgen.1004001","article-title":"Base pairing interaction between 5\u2032- and 3\u2032-UTRs controls icaR mRNA translation in Staphylococcus aureus","volume":"9","author":"Ruiz de los Mozos","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib58","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1016\/j.celrep.2015.01.067","article-title":"Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection","volume":"10","author":"Rutkauskas","year":"2015","journal-title":"Cell Rep"},{"key":"10.1016\/j.cell.2017.07.044_bib59","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nrg3961","article-title":"R loops: new modulators of genome dynamics and function","volume":"16","author":"Santos-Pereira","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib60","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1016\/j.micinf.2007.05.007","article-title":"The PrfA virulence regulon","volume":"9","author":"Scortti","year":"2007","journal-title":"Microbes Infect."},{"key":"10.1016\/j.cell.2017.07.044_bib61","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1101\/gad.242990.114","article-title":"A double-edged sword: R\u00a0loops as threats to genome integrity and powerful regulators of gene expression","volume":"28","author":"Skourti-Stathaki","year":"2014","journal-title":"Genes Dev."},{"key":"10.1016\/j.cell.2017.07.044_bib62","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1111\/j.1365-2958.2009.06999.x","article-title":"Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in\u00a0vivo","volume":"75","author":"Smits","year":"2010","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2017.07.044_bib63","doi-asserted-by":"crossref","first-page":"e1000810","DOI":"10.1371\/journal.pgen.1000810","article-title":"Co-orientation of replication and transcription preserves genome integrity","volume":"6","author":"Srivatsan","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.cell.2017.07.044_bib64","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1016\/j.cell.2014.07.046","article-title":"The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function","volume":"158","author":"Sureka","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.cell.2017.07.044_bib65","doi-asserted-by":"crossref","first-page":"2294","DOI":"10.1073\/pnas.73.7.2294","article-title":"Hybridization of RNA to double-stranded DNA: formation of R-loops","volume":"73","author":"Thomas","year":"1976","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.cell.2017.07.044_bib66","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1101\/gad.280834.116","article-title":"S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation","volume":"30","author":"Wahba","year":"2016","journal-title":"Genes Dev."},{"key":"10.1016\/j.cell.2017.07.044_bib67","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/0092-8674(88)90163-8","article-title":"Transcription generates positively and negatively supercoiled domains in the template","volume":"53","author":"Wu","year":"1988","journal-title":"Cell"},{"key":"10.1016\/j.cell.2017.07.044_bib68","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1016\/j.molcel.2014.02.005","article-title":"DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest","volume":"53","author":"Zhang","year":"2014","journal-title":"Mol. Cell"},{"key":"10.1016\/j.cell.2017.07.044_bib69","doi-asserted-by":"crossref","first-page":"16431","DOI":"10.1038\/srep16431","article-title":"Essentiality drives the orientation bias of bacterial genes in a continuous manner","volume":"5","author":"Zheng","year":"2015","journal-title":"Sci. Rep."}],"container-title":["Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867417308802?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867417308802?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T15:10:25Z","timestamp":1777475425000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0092867417308802"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8]]},"references-count":69,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,8]]}},"alternative-id":["S0092867417308802"],"URL":"https:\/\/doi.org\/10.1016\/j.cell.2017.07.044","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.728371135.793536354","asserted-by":"object"}]},"ISSN":["0092-8674"],"issn-type":[{"value":"0092-8674","type":"print"}],"subject":[],"published":{"date-parts":[[2017,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis","name":"articletitle","label":"Article Title"},{"value":"Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cell.2017.07.044","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"https:\/\/doi.org\/10.1016\/j.cell.2017.07.043","name":"associatedlink","label":"CrossRef DOI link to the associated document"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2017 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}