{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T20:14:22Z","timestamp":1791404062919,"version":"4.3.3"},"reference-count":38,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2015,8,25]],"date-time":"2015-08-25T00:00:00Z","timestamp":1440460800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2015,9,1]],"date-time":"2015-09-01T00:00:00Z","timestamp":1441065600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2015,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Repeated extragenic palindromes (\n            <jats:italic>REP<\/jats:italic>\n            s) in the enterobacterial genomes are usually composed of individual palindromic units separated by linker sequences. A total of 355 annotated\n            <jats:italic>REP<\/jats:italic>\n            s are distributed along the\n            <jats:named-content content-type=\"genus-species\">Escherichia coli<\/jats:named-content>\n            genome. RNA sequence (RNAseq) analysis showed that almost 80% of the\n            <jats:italic>REP<\/jats:italic>\n            s in\n            <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n            are transcribed. The DNA sequence of\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            showed that it is a cluster of six repeats, each with two palindromic units capable of forming cruciform structures in supercoiled DNA. Here, we report that components of the\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            element and at least one of its RNA products play a role in bacterial nucleoid DNA condensation. These RNA not only are present in the purified nucleoid but bind to the bacterial nucleoid-associated HU protein as revealed by RNA IP followed by microarray analysis (RIP-Chip) assays. Deletion of\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (TEM), and expression of one of the\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            RNAs, nucleoid-associated noncoding RNA 4 (naRNA4), from a plasmid restored the wild-type condensed structure. Independently, chromosome conformation capture (3C) analysis demonstrated physical connections among various\n            <jats:italic>REP<\/jats:italic>\n            elements around the chromosome. These connections are dependent in some way upon the presence of HU and the\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            element; deletion of HU genes and\/or the\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            element removed the connections. Finally, naRNA4 together with HU condensed DNA\n            <jats:italic>in vitro<\/jats:italic>\n            by connecting\n            <jats:italic>\n              REP\n              <jats:sub>325<\/jats:sub>\n            <\/jats:italic>\n            or other DNA sequences that contain cruciform structures in a pairwise manner as observed by atomic force microscopy (AFM). On the basis of our results, we propose molecular models to explain connections of remote cruciform structures mediated by HU and naRNA4.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Nucleoid organization in bacteria is being studied extensively, and several models have been proposed. However, the molecular nature of the structural organization is not well understood. Here we characterized the role of a novel nucleoid-associated noncoding RNA, naRNA4, in nucleoid structures both\n            <jats:italic>in vivo<\/jats:italic>\n            and\n            <jats:italic>in vitro<\/jats:italic>\n            . We propose models to explain how naRNA4 together with nucleoid-associated protein HU connects remote DNA elements for nucleoid condensation. We present the first evidence of a noncoding RNA together with a nucleoid-associated protein directly condensing nucleoid DNA.\n          <\/jats:p>","DOI":"10.1128\/mbio.00998-15","type":"journal-article","created":{"date-parts":[[2015,8,26]],"date-time":"2015-08-26T00:43:45Z","timestamp":1440549825000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":30,"title":["A New Noncoding RNA Arranges Bacterial Chromosome Organization"],"prefix":"10.1128","volume":"6","author":[{"given":"Zhong","family":"Qian","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirjana","family":"Macvanin","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilios K.","family":"Dimitriadis","sequence":"additional","affiliation":[{"name":"Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ximiao","family":"He","sequence":"additional","affiliation":[{"name":"Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Zhurkin","sequence":"additional","affiliation":[{"name":"Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sankar","family":"Adhya","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, National Cancer 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