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We began analyzing https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r45, but it redirected us to https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r45. The analysis below is for the second page.

Title[redir]:
Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsisambient temperature response | Genome Biology | Full Text
Description:
Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance.

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Keywords {🔍}

transcription, genes, temperature, rates, rate, decay, rna, figure, pubmed, article, gene, mrna, google, scholar, data, transcript, analysis, show, arabidopsis, labeling, file, cas, ambient, temperatures, additional, central, levels, abundance, synthesis, plant, response, samples, plants, haz, higher, authors, expression, distribution, passive, chromatin, role, high, hours, calculated, halflives, factors, low, total, hkme, nature,

Topics {✒️}

springer nature article sidaway-lee figures 2a sharing protocols ca2 + −responsive cis elements author information authors basic helix-loop-helix multiple atp-dependent steps extended time-series analysis pdf 400 kb authors scientific editing decay rates genome-wide latest sequence files privacy choices/manage cookies high temperature-mediated adaptations temperature-dependent transcriptional effects ambient temperature sensing authors’ original file bmc pre-existing transcript remaining gene body h2a discussion term-based analysis showed half-lives half-lives 1186/gb-2014-15-3-r45 share circadian binding sites encoding ribosomal proteins arabidopsis information resource temperature-regulated transcription factors steven penfield higher transcription/decay rates abbreviations 4su 1474-760x contact heat shock elements multiple chromatin marks conclusions background full size image friedel cc quantitative pcr step false discovery rate transcription factor activities slower decay rate multiple transcription factors detectable 4su-labeled rna separated pre-existing rna aba response element transcription rate q10s arabidopsisambient temperature response transcriptome-wide analysis

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