Prevalence of transcription promoters within archaeal operons and coding sequences

Koide, Tie; Reiss, David J.; Bare, J. Christopher; Pang, Wyming Lee; Facciotti, Marc T.; Schmid, Amy K.; Pan, Min; Marzolf, Bruz; Van, Phu T.; Lo, Fang‐Yin; Pratap, Abhishek; Deutsch, Eric W.; Peterson, Amelia; Martin, Dan; Baliga, Nitin S.

doi:10.1038/msb.2009.42

Prevalence of transcription promoters within archaeal operons and coding sequences

Journal Article · Thu Jan 01 00:00:00 EST 2009 · Molecular Systems Biology

DOI:https://doi.org/10.1038/msb.2009.42· OSTI ID:1623794

Koide, Tie ^[1]; Reiss, David J. ^[2]; Bare, J. Christopher ^[2]; Pang, Wyming Lee ^[2]; Facciotti, Marc T. ^[3]; Schmid, Amy K. ^[2]; Pan, Min ^[2]; Marzolf, Bruz ^[2]; Van, Phu T. ^[2]; Lo, Fang‐Yin ^[2]; Pratap, Abhishek ^[2]; Deutsch, Eric W. ^[2]; Peterson, Amelia ^[4]; Martin, Dan ^[5]; Baliga, Nitin S. ^[5]

Inst. for Systems Biology, Seattle, WA (United States); DOE/OSTI
Inst. for Systems Biology, Seattle, WA (United States)
Inst. for Systems Biology, Seattle, WA (United States); Univ. of California, Davis, CA (United States). UC Davis Genome Center. Dept. of Biomedical Engineering
Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Divisions of Human Biology and Clinical Research
Inst. for Systems Biology, Seattle, WA (United States); Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Divisions of Human Biology and Clinical Research

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of B64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein–DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 30 ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes—events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.

View Accepted Manuscript (DOE)

Research Organization:: Institute for Systems Biology, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-07ER64327

OSTI ID:: 1623794

Journal Information:: Molecular Systems Biology, Journal Name: Molecular Systems Biology Journal Issue: 1 Vol. 5; ISSN 1744-4292

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (65)

Chromatin and Regulation Reeve, John N.; Sandman, Kathleen Archaea: Evolution, Physiology, and Molecular Biology https://doi.org/10.1002/9780470750865.ch13	book	December 2006
Regulation of gvp genes encoding gas vesicle proteins in halophilic Archaea Scheuch, Sandra; Marschaus, Larissa; Sartorius-Neef, Simone Archives of Microbiology, Vol. 190, Issue 3 https://doi.org/10.1007/s00203-008-0362-x	journal	April 2008
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell Bonneau, Richard; Facciotti, Marc T.; Reiss, David J. Cell, Vol. 131, Issue 7 https://doi.org/10.1016/j.cell.2007.10.053	journal	December 2007
Establishment of an mRNA Gradient Depends on the Promoter: An Investigation of Polarity in Gene Expression Lee, Hee Jung; Jeon, Heung Jin; Ji, Sang Chun Journal of Molecular Biology, Vol. 378, Issue 2 https://doi.org/10.1016/j.jmb.2008.02.067	journal	April 2008
The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting Reppas, Nikos B.; Wade, Joseph T.; Church, George M. Molecular Cell, Vol. 24, Issue 5 https://doi.org/10.1016/j.molcel.2006.10.030	journal	December 2006
Structural evolution of multisubunit RNA polymerases Werner, Finn Trends in Microbiology, Vol. 16, Issue 6 https://doi.org/10.1016/j.tim.2008.03.008	journal	June 2008
Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1 Pfeiffer, F.; Schuster, S. C.; Broicher, A. Genomics, Vol. 91, Issue 4 https://doi.org/10.1016/j.ygeno.2008.01.001	journal	April 2008
An integrated systems approach for understanding cellular responses to gamma radiation Whitehead, Kenia; Kish, Adrienne; Pan, Min Molecular Systems Biology, Vol. 2, Issue 1 https://doi.org/10.1038/msb4100091	journal	January 2006
Regulation of gene expression by small non‐coding RNAs: a quantitative view Shimoni, Yishai; Friedlander, Gilgi; Hetzroni, Guy Molecular Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1038/msb4100181	journal	January 2007
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution Wilhelm, Brian T.; Marguerat, Samuel; Watt, Stephen Nature, Vol. 453, Issue 7199 https://doi.org/10.1038/nature07002	journal	May 2008
High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons McGrath, Patrick T.; Lee, Honglak; Zhang, Li Nature Biotechnology, Vol. 25, Issue 5 https://doi.org/10.1038/nbt1294	journal	April 2007
A high-resolution map of transcription in the yeast genome David, L.; Huber, W.; Granovskaia, M. Proceedings of the National Academy of Sciences, Vol. 103, Issue 14 https://doi.org/10.1073/pnas.0601091103	journal	March 2006
Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module Hebbeln, P.; Rodionov, D. A.; Alfandega, A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 8 https://doi.org/10.1073/pnas.0609905104	journal	February 2007
General transcription factor specified global gene regulation in archaea Facciotti, M. T.; Reiss, D. J.; Pan, M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 11 https://doi.org/10.1073/pnas.0611663104	journal	March 2007
Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus Tang, T. -H.; Bachellerie, J. -P.; Rozhdestvensky, T. Proceedings of the National Academy of Sciences, Vol. 99, Issue 11 https://doi.org/10.1073/pnas.112047299	journal	May 2002
Genome sequence of Halobacterium species NRC-1 Ng, W. V.; Kennedy, S. P.; Mahairas, G. G. Proceedings of the National Academy of Sciences, Vol. 97, Issue 22, p. 12176-12181 https://doi.org/10.1073/pnas.190337797	journal	October 2000
Orientation of the transcription preinitiation complex in Archaea Bell, S. D.; Kosa, P. L.; Sigler, P. B. Proceedings of the National Academy of Sciences, Vol. 96, Issue 24 https://doi.org/10.1073/pnas.96.24.13662	journal	November 1999
Transcriptional Regulation of SDHa Flavoprotein by Nuclear Respiratory Factor-1 Prevents Pseudo-hypoxia in Aerobic Cardiac Cells Piantadosi, Claude A.; Suliman, Hagir B. Journal of Biological Chemistry, Vol. 283, Issue 16 https://doi.org/10.1074/jbc.m709741200	journal	April 2008
New Problems in RNA Polymerase II Transcription Initiation: Matching the Diversity of Core Promoters with a Variety of Promoter Recognition Factors Muöller, Ferenc; Demé;ny, Màté; A.; Tora, Làszlò Journal of Biological Chemistry, Vol. 282, Issue 20 https://doi.org/10.1074/jbc.r700012200	journal	May 2007
The Subunit Structure and Dynamics of the 20S Proteasome in Chicken Skeletal Muscle Hayter, Julia R.; Doherty, Mary K.; Whitehead, Colin Molecular & Cellular Proteomics, Vol. 4, Issue 9 https://doi.org/10.1074/mcp.m400138-mcp200	journal	September 2005
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes Wang, C.; Ding, C.; Meraz, R. F. Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl441	journal	August 2006
Model-based deconvolution of genome-wide DNA binding Reiss, David J.; Facciotti, Marc T.; Baliga, Nitin S. Bioinformatics, Vol. 24, Issue 3 https://doi.org/10.1093/bioinformatics/btm592	journal	December 2007
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences Ward, Lucas D.; Bussemaker, Harmen J. Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn154	journal	July 2008
A novel method for accurate operon predictions in all sequenced prokaryotes Price, M. N. Nucleic Acids Research, Vol. 33, Issue 3 https://doi.org/10.1093/nar/gki232	journal	February 2005
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D Perocchi, Fabiana; Xu, Zhenyu; Clauder-Münster, Sandra Nucleic Acids Research, Vol. 35, Issue 19 https://doi.org/10.1093/nar/gkm683	journal	September 2007
Extensive low-affinity transcriptional interactions in the yeast genome Tanay, A. Genome Research, Vol. 16, Issue 8 https://doi.org/10.1101/gr.5113606	journal	June 2006
A systems view of haloarchaeal strategies to withstand stress from transition metals Kaur, A. Genome Research, Vol. 16, Issue 7 https://doi.org/10.1101/gr.5189606	journal	July 2006
Evolution and multilevel optimization of the genetic code Bollenbach, Tobias; Vetsigian, Kalin; Kishony, Roy Genome Research, Vol. 17, Issue 4 https://doi.org/10.1101/gr.6144007	journal	March 2007
The anatomy of microbial cell state transitions in response to oxygen Schmid, A. K.; Reiss, D. J.; Kaur, A. Genome Research, Vol. 17, Issue 10 https://doi.org/10.1101/gr.6728007	journal	September 2007
The mutL repair gene of Escherichia coli K-12 forms a superoperon with a gene encoding a new cell-wall amidase Tsui, Ho-Ching Tiffany; Zhao, Genshi; Feng, Gang Molecular Microbiology, Vol. 11, Issue 1 https://doi.org/10.1111/j.1365-2958.1994.tb00300.x	journal	January 1994
Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization Wade, Joseph T.; Struhl, Kevin; Busby, Stephen J. W. Molecular Microbiology, Vol. 65, Issue 1 https://doi.org/10.1111/j.1365-2958.2007.05781.x	journal	July 2007
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing Nagalakshmi, U.; Wang, Z.; Waern, K. Science, Vol. 320, Issue 5881 https://doi.org/10.1126/science.1158441	journal	June 2008
Genome-Wide Location and Function of DNA Binding Proteins Ren, B. Science, Vol. 290, Issue 5500 https://doi.org/10.1126/science.290.5500.2306	journal	December 2000
Suboperonic Regulatory Signals Adhya, Sankar Science's STKE, Vol. 2003, Issue 185 https://doi.org/10.1126/stke.2003.185.pe22	journal	June 2003
Essential Internal Promoter in the spoIIIA Locus of Bacillus subtilis Guillot, Chris; Moran, Charles P. Journal of Bacteriology, Vol. 189, Issue 20 https://doi.org/10.1128/jb.00915-07	journal	August 2007
Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor. Yang, C. F.; DasSarma, S. Journal of Bacteriology, Vol. 172, Issue 7 https://doi.org/10.1128/jb.172.7.4118-4121.1990	journal	January 1990
Saturation Mutagenesis of the TATA Box and Upstream Activator Sequence in the Haloarchaeal bop Gene Promoter Baliga, Nitin S.; DasSarma, Shiladitya Journal of Bacteriology, Vol. 181, Issue 8 https://doi.org/10.1128/jb.181.8.2513-2518.1999	journal	April 1999
An Abundance of rna Regulators Storz, Gisela; Altuvia, Shoshy; Wassarman, Karen M. Annual Review of Biochemistry, Vol. 74, Issue 1 https://doi.org/10.1146/annurev.biochem.74.082803.133136	journal	June 2005
Prediction of Genomic Functional Elements Jones, Steven J. M. Annual Review of Genomics and Human Genetics, Vol. 7, Issue 1 https://doi.org/10.1146/annurev.genom.7.080505.115745	journal	September 2006
Localization of TFIIB binding regions using serial analysis of chromatin occupancy Yochum, Gregory S.; Rajaraman, Veena; Cleland, Ryan BMC Molecular Biology, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2199-8-102	journal	January 2007
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles Faith, Jeremiah J.; Hayete, Boris; Thaden, Joshua T. PLoS Biology, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pbio.0050008	journal	January 2007
A semi-parametric approach for mixture models: Application to local false discovery rate estimation Robin, Stéphane; Bar-Hen, Avner; Daudin, Jean-Jacques Computational Statistics & Data Analysis, Vol. 51, Issue 12 https://doi.org/10.1016/j.csda.2007.02.028	journal	August 2007
Small non-coding RNAs in Archaea Dennis, Patrick P.; Omer, Arina Current Opinion in Microbiology, Vol. 8, Issue 6 https://doi.org/10.1016/j.mib.2005.10.013	journal	December 2005
Genome-Wide Occupancy Profile of Mediator and the Srb8-11 Module Reveals Interactions with Coding Regions Zhu, Xuefeng; Wirén, Marianna; Sinha, Indranil Molecular Cell, Vol. 22, Issue 2 https://doi.org/10.1016/j.molcel.2006.03.032	journal	April 2006
Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage Van, Phu T.; Schmid, Amy K.; King, Nichole L. Journal of Proteome Research, Vol. 7, Issue 9 https://doi.org/10.1021/pr800031f	journal	September 2008
The X-ray crystal structure of RNA polymerase from Archaea Hirata, Akira; Klein, Brianna J.; Murakami, Katsuhiko S. Nature, Vol. 451, Issue 7180 https://doi.org/10.1038/nature06530	journal	January 2008
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Robertson, Gordon; Hirst, Martin; Bainbridge, Matthew Nature Methods, Vol. 4, Issue 8 https://doi.org/10.1038/nmeth1068	journal	June 2007
Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?. MicroCorrespondence Baliga, Nitin S.; Goo, Young Ah; Ng, Wailap Victor Molecular Microbiology, Vol. 36, Issue 5 https://doi.org/10.1046/j.1365-2958.2000.01916.x	journal	June 2000
In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum: Shine-Dalgarno sequences of halophilic archea Sartorius-Neef, Simone; Pfeifer, Felicitas Molecular Microbiology, Vol. 51, Issue 2 https://doi.org/10.1046/j.1365-2958.2003.03858.x	journal	January 2004
Model-based analysis of tiling-arrays for ChIP-chip Johnson, W. E.; Li, W.; Meyer, C. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 33 https://doi.org/10.1073/pnas.0601180103	journal	August 2006
Transcriptional Regulation of SDHa Flavoprotein by Nuclear Respiratory Factor-1 Prevents Pseudo-hypoxia in Aerobic Cardiac Cells Piantadosi, Claude A.; Suliman, Hagir B. Journal of Biological Chemistry, Vol. 283, Issue 16 https://doi.org/10.1074/jbc.M709741200	journal	April 2008
New Problems in RNA Polymerase II Transcription Initiation: Matching the Diversity of Core Promoters with a Variety of Promoter Recognition Factors Muöller, Ferenc; Demé;ny, Màté; A.; Tora, Làszlò Journal of Biological Chemistry, Vol. 282, Issue 20 https://doi.org/10.1074/jbc.R700012200	journal	May 2007
The Subunit Structure and Dynamics of the 20S Proteasome in Chicken Skeletal Muscle Hayter, Julia R.; Doherty, Mary K.; Whitehead, Colin Molecular & Cellular Proteomics, Vol. 4, Issue 9 https://doi.org/10.1074/mcp.M400138-MCP200	journal	September 2005
The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions Shimada, Tomohiro; Ishihama, Akira; Busby, Stephen J. W. Nucleic Acids Research, Vol. 36, Issue 12 https://doi.org/10.1093/nar/gkn339	journal	May 2008
Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1 Baliga, N. S. Genome Research, Vol. 14, Issue 6 https://doi.org/10.1101/gr.1993504	journal	May 2004
The genetic code is nearly optimal for allowing additional information within protein-coding sequences Itzkovitz, S.; Alon, U. Genome Research, Vol. 17, Issue 4 https://doi.org/10.1101/gr.5987307	journal	March 2007
Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus: ncRNAs in S. solfataricus Tang, Thean-Hock; Polacek, Norbert; Zywicki, Marek Molecular Microbiology, Vol. 55, Issue 2 https://doi.org/10.1111/j.1365-2958.2004.04428.x	journal	December 2004
Transcriptional Regulatory Networks in Saccharomyces cerevisiae Lee, T. I. Science, Vol. 298, Issue 5594 https://doi.org/10.1126/science.1075090	journal	October 2002
Analysis of Proteasome-Dependent Proteolysis in Haloferax volcanii Cells, Using Short-Lived Green Fluorescent Proteins Reuter, Christopher J.; Maupin-Furlow, Julie A. Applied and Environmental Microbiology, Vol. 70, Issue 12 https://doi.org/10.1128/AEM.70.12.7530-7538.2004	journal	December 2004
Essential Internal Promoter in the spoIIIA Locus of Bacillus subtilis Guillot, Chris; Moran, Charles P. Journal of Bacteriology, Vol. 189, Issue 20 https://doi.org/10.1128/JB.00915-07	journal	August 2007
Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor. Yang, C. F.; DasSarma, S. Journal of Bacteriology, Vol. 172, Issue 7 https://doi.org/10.1128/JB.172.7.4118-4121.1990	journal	January 1990
Saturation Mutagenesis of the TATA Box and Upstream Activator Sequence in the Haloarchaeal bop Gene Promoter Baliga, Nitin S.; DasSarma, Shiladitya Journal of Bacteriology, Vol. 181, Issue 8 https://doi.org/10.1128/JB.181.8.2513-2518.1999	journal	April 1999
Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster. Ruepp, A.; Soppa, J. Journal of bacteriology, Vol. 178, Issue 16 https://doi.org/10.1128/jb.178.16.4942-4947.1996	journal	January 1996
Experimental Characterization of Cis-Acting Elements Important for Translation and Transcription in Halophilic Archaea Brenneis, Mariam; Hering, Oliver; Lange, Christian PLoS Genetics, Vol. 3, Issue 12 https://doi.org/10.1371/journal.pgen.0030229	journal	December 2007
Experimental characterization of cis-acting elements important for translation and transcription in halophilic Archaea Brenneis, Mariam; Hering, Oliver; Lange, Christian PLoS Genetics, Vol. preprint, Issue 2007 https://doi.org/10.1371/journal.pgen.0030229.eor	journal	January 2005

Cited By (41)

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea Gomes-Filho, José Vicente; Zaramela, Livia Soares; Italiani, Valéria Cristina da Silva RNA Biology, Vol. 12, Issue 5 https://doi.org/10.1080/15476286.2015.1019998	journal	March 2015
Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea Ten-Caten, Felipe; Vêncio, Ricardo Z. N.; Lorenzetti, Alan Péricles R. RNA Biology https://doi.org/10.1080/15476286.2018.1509661	journal	September 2018
Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis Maruyama, Hugo; Shin, Minsang; Oda, Toshiyuki Molecular Biology of the Cell, Vol. 22, Issue 3 https://doi.org/10.1091/mbc.e10-08-0668	journal	February 2011
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons Muro, Enrique M.; Mah, Nancy; Moreno-Hagelsieb, Gabriel Nucleic Acids Research, Vol. 39, Issue 5 https://doi.org/10.1093/nar/gkq1067	journal	November 2010
Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon Schmid, Amy K.; Pan, Min; Sharma, Kriti Nucleic Acids Research, Vol. 39, Issue 7 https://doi.org/10.1093/nar/gkq1211	journal	November 2010
Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea Todor, H.; Sharma, K.; Pittman, A. M. C. Nucleic Acids Research, Vol. 41, Issue 18 https://doi.org/10.1093/nar/gkt659	journal	July 2013
Copy number variation is associated with gene expression change in archaea Dulmage, Keely A.; Darnell, Cynthia L.; Vreugdenhil, Angie Microbial Genomics, Vol. 4, Issue 9 https://doi.org/10.1099/mgen.0.000210	journal	September 2018
Conservation of Transcription Start Sites within Genes across a Bacterial Genus Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M. mBio, Vol. 5, Issue 4 https://doi.org/10.1128/mbio.01398-14	journal	July 2014
Integration and visualization of systems biology data in context of the genome Bare, J. Christopher; Koide, Tie; Reiss, David J. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-382	journal	January 2010
Transcriptome dynamics-based operon prediction in prokaryotes Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-145	journal	May 2014
The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon Sharma, Kriti; Gillum, Nicholas; Boyd, J. Lomax BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-351	journal	July 2012
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain Campanaro, Stefano; De Pascale, Fabio; Telatin, Andrea BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-567	journal	January 2012
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling Li, Shan; Dong, Xia; Su, Zhengchang BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-520	journal	January 2013
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis Jäger, Dominik; Förstner, Konrad U.; Sharma, Cynthia M. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-684	journal	January 2014
Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays Yu, Wen-Han; Høvik, Hedda; Olsen, Ingar BMC Molecular Biology, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2199-12-3	journal	January 2011
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Rajeev, Lara; Luning, Eric G.; Dehal, Paramvir S. Genome Biology, Vol. 12, Issue 10 https://doi.org/10.1186/gb-2011-12-10-r99	journal	January 2011
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq) Babski, Julia; Haas, Karina A.; Näther-Schindler, Daniela BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2920-y	journal	August 2016
Evolution of context dependent regulation by expansion of feast/famine regulatory proteins Plaisier, Christopher L.; Lo, Fang-Yin; Ashworth, Justin BMC Systems Biology, Vol. 8, Issue 1 https://doi.org/10.1186/s12918-014-0122-2	journal	November 2014
Genome-Wide Identification of Transcriptional Start Sites in the Plant Pathogen Pseudomonas syringae pv. tomato str. DC3000 Filiatrault, Melanie J.; Stodghill, Paul V.; Myers, Christopher R. PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0029335	journal	December 2011
Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms Geng, Jianing; Chiu, Cheng-Hsun; Tang, Petrus PLoS ONE, Vol. 7, Issue 4 https://doi.org/10.1371/journal.pone.0034769	journal	April 2012
The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature Wurtzel, Omri; Yoder-Himes, Deborah R.; Han, Kook PLoS Pathogens, Vol. 8, Issue 9 https://doi.org/10.1371/journal.ppat.1002945	journal	September 2012
Mechanism for microbial population collapse in a fluctuating resource environment Turkarslan, Serdar; Raman, Arjun V.; Thompson, Anne W. Molecular Systems Biology, Vol. 13, Issue 3 https://doi.org/10.15252/msb.20167058	journal	March 2017
RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H Kranz, Angela; Busche, Tobias; Vogel, Alexander RWTH Aachen University https://doi.org/10.18154/rwth-2019-01481	text	January 2018
The Dawning Era of Comprehensive Transcriptome Analysis in Cellular Microbiology Aikawa, Chihiro; Maruyama, Fumito; Nakagawa, Ichiro Frontiers in Microbiology, Vol. 1 https://doi.org/10.3389/fmicb.2010.00118	journal	January 2010
Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus Hausner, Winfried; Reichelt, Robert Martin; Gindner, Antonia Universität Regensburg https://doi.org/10.5283/epub.33537	text	January 2016
Current Challenges in Bacterial Transcriptomics Cho, Suhyung; Cho, Yoobok; Lee, Sooin Genomics & Informatics, Vol. 11, Issue 2 https://doi.org/10.5808/gi.2013.11.2.76	journal	January 2013
Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea Dar, Daniel; Prasse, Daniela; Schmitz, Ruth A. Nature Microbiology, Vol. 1, Issue 10 https://doi.org/10.1038/nmicrobiol.2016.143	journal	August 2016
Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity Sorek, Rotem; Cossart, Pascale Nature Reviews Genetics, Vol. 11, Issue 1 https://doi.org/10.1038/nrg2695	journal	November 2009
Identification of RNA 3´ ends and termination sites in Haloferax volcanii Berkemer, Sarah J.; Maier, Lisa-Katharina; Amman, Fabian RNA Biology, Vol. 17, Issue 5 https://doi.org/10.1080/15476286.2020.1723328	journal	February 2020
Next-generation sequencing technologies and their impact on microbial genomics Forde, B. M.; O'Toole, P. W. Briefings in Functional Genomics, Vol. 12, Issue 5 https://doi.org/10.1093/bfgp/els062	journal	January 2013
Identification of RNA 3’ ends and termination sites in Haloferax volcanii Berkemer, Sarah J.; Maier, Lisa-Katharina; Amman, Fabian RNA Biology https://doi.org/10.1101/748780	posted_content	January 2019
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes Lomsadze, Alexandre; Gemayel, Karl; Tang, Shiyuyun Genome Research, Vol. 28, Issue 7 https://doi.org/10.1101/gr.230615.117	journal	May 2018
Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii: Transcriptional profiling in a psychrophilic archaeon Campanaro, S.; Williams, T. J.; Burg, D. W. Environmental Microbiology, Vol. 13, Issue 8 https://doi.org/10.1111/j.1462-2920.2010.02367.x	journal	November 2010
Transcriptome Complexity in a Genome-Reduced Bacterium Güell, Marc; van Noort, Vera; Yus, Eva Science, Vol. 326, Issue 5957 https://doi.org/10.1126/science.1176951	journal	November 2009
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli Mao, Xizeng; Ma, Qin; Liu, Bingqiang BMC Bioinformatics, Vol. 16, Issue 1 https://doi.org/10.1186/s12859-015-0805-8	journal	November 2015
Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus Reichelt, Robert; Gindner, Antonia; Thomm, Michael BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-015-2360-0	journal	January 2016
RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H Kranz, Angela; Busche, Tobias; Vogel, Alexander BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-017-4415-x	journal	January 2018
Coordinated regulation of acid resistance in Escherichia coli Aquino, Patricia; Honda, Brent; Jaini, Suma BMC Systems Biology, Vol. 11, Issue 1 https://doi.org/10.1186/s12918-016-0376-y	journal	January 2017
Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq Laass, Sebastian; Monzon, Vivian A.; Kliemt, Jana PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0215986	journal	April 2019
A system‐level model for the microbial regulatory genome Brooks, Aaron N.; Reiss, David J.; Allard, Antoine Molecular Systems Biology, Vol. 10, Issue 7 https://doi.org/10.15252/msb.20145160	journal	July 2014
The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1 de Almeida, João Paulo Pereira; Vêncio, Ricardo Z. N.; Lorenzetti, Alan P. R. Genes, Vol. 10, Issue 4 https://doi.org/10.3390/genes10040280	journal	April 2019

Similar Records

Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction

Journal Article · Wed Sep 24 20:00:00 EDT 2014 · PLoS ONE · OSTI ID:1797294

A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

Journal Article · Tue Nov 30 23:00:00 EST 2004 · Nucleic Acids Research · OSTI ID:859714

A system-level model for the microbial regulatory genome

Journal Article · Mon Jun 30 20:00:00 EDT 2014 · Molecular Systems Biology · OSTI ID:1627935

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
ChIP–chip
archaea
chromatin & transcription
functional genomics
non-coding RNA
tiling array
transcription

Prevalence of transcription promoters within archaeal operons and coding sequences

Citation Formats

References (65)

Cited By (41)

Similar Records

Related Subjects