[{"publication":"BMC Genomics","article_type":"original","volume":19,"title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","month":"12","quality_controlled":"1","publication_identifier":{"issn":["1471-2164"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12864-018-5245-1"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        19","article_number":"965","date_created":"2020-08-15T11:02:08Z","citation":{"ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>","short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., &#38; Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>, vol. 19, 965, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>.","ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965.","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” <i>BMC Genomics</i>, vol. 19. Springer Nature, 2018.","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>."},"oa_version":"Published Version","publication_status":"published","date_published":"2018-12-27T00:00:00Z","day":"27","abstract":[{"lang":"eng","text":"Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei."}],"author":[{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga"},{"last_name":"Moroz","full_name":"Moroz, Elena V.","first_name":"Elena V."},{"last_name":"Davydov","first_name":"Iakov I.","full_name":"Davydov, Iakov I."},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"oa":1,"_id":"8262","status":"public","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5245-1","publisher":"Springer Nature","date_updated":"2023-02-23T13:28:52Z","year":"2018"},{"abstract":[{"lang":"eng","text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function."}],"day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","status":"public","date_updated":"2023-09-13T09:10:47Z","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"5712","date_created":"2018-12-17T14:52:57Z","checksum":"a56516e734dab589dc7f3e1915973b4d","date_updated":"2020-07-14T12:45:23Z","file_name":"2018_BMCGenomics_Higareda.pdf","file_size":4629784}],"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","external_id":{"isi":["000450976700002"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9807"},{"status":"public","id":"9808","relation":"research_data"}]},"publication":"BMC Genomics","has_accepted_license":"1","scopus_import":"1","issue":"1","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>.","ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>"},"date_published":"2018-11-03T00:00:00Z","_id":"20","oa":1,"author":[{"last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan","first_name":"Juan"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"first_name":"Maude","full_name":"Giroud, Maude","last_name":"Giroud"},{"orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"first_name":"Marcel","full_name":"Scheideler, Marcel","last_name":"Scheideler"}],"type":"journal_article","year":"2018","publisher":"BioMed Central","doi":"10.1186/s12864-018-5173-0","language":[{"iso":"eng"}],"volume":19,"article_type":"original","isi":1,"publist_id":"8035","publication_identifier":{"issn":["1471-2164"]},"quality_controlled":"1","month":"11","intvolume":"        19","file_date_updated":"2020-07-14T12:45:23Z","ddc":["570"],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","department":[{"_id":"SiHi"}],"date_created":"2018-12-11T11:44:12Z"}]