[{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"117","date_published":"2020-10-13T00:00:00Z","doi":"10.15479/AT:ISTA:8653","date_created":"2020-10-13T13:02:33Z","has_accepted_license":"1","year":"2020","day":"13","author":[{"last_name":"Tomanek","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"}],"article_processing_charge":"No","title":"The evolution of gene expression by copy number and point mutations","citation":{"ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"7652","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"c01d9f59794b4b70528f37637c17ad02","file_id":"8666","creator":"itomanek","file_size":25131884,"date_updated":"2021-10-20T22:30:03Z","file_name":"Thesis_ITomanek_final_201016.docx","date_created":"2020-10-16T12:14:21Z"},{"date_updated":"2021-10-20T22:30:03Z","file_size":15405675,"creator":"itomanek","date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","file_id":"8667","embargo":"2021-10-19"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"_id":"8653","file_date_updated":"2021-10-20T22:30:03Z","department":[{"_id":"CaGu"}],"supervisor":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:22:42Z","ddc":["576"]},{"date_created":"2019-11-13T09:07:31Z","contributor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","contributor_type":"project_leader"}],"doi":"10.15479/AT:ISTA:7016","date_published":"2019-11-13T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7652","status":"public"}]},"year":"2019","has_accepted_license":"1","day":"13","file":[{"file_name":"D8_S35_R2_001.fastq","title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","file_size":2456192500,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_id":"7017","checksum":"72441055043eda4cbf1398a422e2c118","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified.","relation":"main_file","access_level":"open_access"},{"description":"Illumina whole genome sequence data for Locus 1 - ancestral.","content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","file_id":"7018","date_updated":"2020-07-14T12:47:47Z","file_size":2833452234,"creator":"itomanek","date_created":"2019-11-13T08:52:59Z","title":"Locus1_ancestral","file_name":"IT028_S11_R2_001.fastq"},{"creator":"itomanek","file_size":2878017264,"date_updated":"2020-07-14T12:47:47Z","file_name":"D8-DOG1_S47_R2_001.fastq","date_created":"2019-11-13T08:54:10Z","title":"Locus1_amplified_DOG","relation":"main_file","access_level":"open_access","description":"Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection.","content_type":"application/octet-stream","file_id":"7019","checksum":"5b227708ff478ca06e3f0448a4efdc2f"},{"date_updated":"2020-07-14T12:47:47Z","file_size":2180826995,"creator":"itomanek","title":"Locus2_amplified","date_created":"2019-11-13T08:54:27Z","file_name":"D4_S71_R2_001.fastq","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 2 - amplified.","access_level":"open_access","relation":"main_file","checksum":"d9550a4c044116075fa83f8f2ea31d6f","file_id":"7020"},{"description":"Illumina whole genome sequence data for Locus 2 - ancestral.","content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"466ceb302c020ac013007a879fcde69d","file_id":"7021","date_updated":"2020-07-14T12:47:47Z","file_size":2108826444,"creator":"itomanek","date_created":"2019-11-13T08:55:58Z","title":"Locus2_ancestral","file_name":"IT030_S23_R2_001.fastq"},{"content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection.","access_level":"open_access","relation":"main_file","file_id":"7092","checksum":"8aeb1da771713c7baa5a847eff889604","date_updated":"2020-07-14T12:47:47Z","file_size":3144330494,"creator":"itomanek","date_created":"2019-11-21T12:31:01Z","title":"Locus2_amplified_DOG","file_name":"D4-DOG1_S83_R2_001.fastq"},{"checksum":"bf7d4b053f14af4655fb5574209fdb2d","file_id":"7273","description":"Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette.","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2020-01-14T11:22:27Z","title":"DNA sequence of the chromosomal reporter gene cassette","file_name":"galK_dual_reporter_cassette.gb.zip","date_updated":"2020-07-14T12:47:47Z","file_size":4179,"creator":"itomanek"},{"file_id":"7335","checksum":"5e91cee2eff6f4a7cde456c6fb07c2ff","content_type":"text/plain","access_level":"open_access","relation":"main_file","title":"Read_me_sequence_data","date_created":"2020-01-15T14:15:55Z","file_name":"Readme_7016.txt","date_updated":"2020-07-14T12:47:47Z","file_size":435,"creator":"dernst"},{"checksum":"5e6745dcfb9c1b11dd935ac3ee45fe33","file_id":"7351","description":"FACS data associated with Fig. 2c - see read_me_FACS","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2020-01-22T15:44:16Z","title":"FACS data","file_name":"FACS_data.xlsx.zip","date_updated":"2020-07-14T12:47:47Z","file_size":3765861,"creator":"itomanek"},{"content_type":"text/rtf","access_level":"open_access","relation":"main_file","file_id":"7352","checksum":"a85caf092ae4b17668f70af2d93fad00","date_updated":"2020-07-14T12:47:47Z","file_size":4996,"creator":"itomanek","date_created":"2020-01-22T15:44:16Z","file_name":"read_me_FACS.rtf"},{"date_created":"2020-01-22T15:44:16Z","file_name":"read_me_microfluidics.rtf","date_updated":"2020-07-14T12:47:47Z","file_size":868,"creator":"itomanek","file_id":"7353","checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","content_type":"text/rtf","access_level":"open_access","relation":"main_file"},{"creator":"itomanek","file_size":8141727,"date_updated":"2020-07-14T12:47:47Z","file_name":"microfuidics_data.zip","title":"microfluidics data","date_created":"2020-01-22T15:44:17Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","description":"microfluidics time trace data - see read_me_microfluidics","checksum":"69c5dc5ca5c069a138183c934acc1778","file_id":"7354"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"11","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","last_name":"Tomanek","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X"}],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:47Z","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","date_updated":"2024-02-21T12:45:25Z","citation":{"chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","short":"I. Tomanek, (2019).","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"type":"research_data","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"status":"public","_id":"7016"}]