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DNA:cytoplasm ratio defines an upper limit to cell size [RNA-seq]

ABSTRACT: Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important is not understood. Here we show that growing beyond a certain size has wide-ranging effects on cell physiology. Large cells are defective in gene induction, cell cycle progression and cell signaling. We further show that these defects are caused by the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. Finally, we determine why nucleic acid and protein biosynthesis do not scale with cell volume beyond a certain critical size. DNA becomes limiting. We conclude that the correct DNA to cytoplasm ratio is vital for many perhaps all cellular functions and that the range where this ratio supports optimal cell function is remarkably narrow.

ORGANISM(S): Candida albicans Saccharomyces cerevisiae

PROVIDER: GSE110704 | GEO | 2019/02/07

REPOSITORIES: GEO

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Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (âI_xxxxxxâ is corresponding to EST clones); Column B: Genbank accession no. Column C: Description; Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA; Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h); Column F: Average value of expression levels in polysomal fraction in the absence of PMA; Column G: Average value of expression levels in polysomal fraction in the presence of PMA; Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-); Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+); Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-); Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-); Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1; Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1; Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1; Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1; ; Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (âI_xxxxxxâ is corresponding to EST clones); Column B: Genbank accession no. Column C: Description; Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA; Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA; Column F: Average value of expression levels in polysomal fraction in the absence of PMA; Column G: Average value of expression levels in polysomal fraction in the presence of PMA; Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-); Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+); Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-); Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-)

Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h) Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1 Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1 Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1 Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1 Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Keywords = phorbol ester Keywords = macrophage Keywords = polysome Keywords = post-transcriptional regulation Keywords: parallel sample

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DNA:cytoplasm ratio defines an upper limit to cell size [RNA-seq]

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