Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume

被引:0
|
作者
Qirun Wang
Jie Lin
机构
[1] Peking University,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies
[2] Peking University,Peking
来源
Nature Communications | / 12卷
关键词
D O I
暂无
中图分类号
学科分类号
摘要
While most genes’ expression levels are proportional to cell volumes, some genes exhibit nonlinear scaling between their expression levels and cell volume. Therefore, their mRNA and protein concentrations change as the cell volume increases, which often have crucial biological functions such as cell-cycle regulation. However, the biophysical mechanism underlying the nonlinear scaling between gene expression and cell volume is still unclear. In this work, we show that the nonlinear scaling is a direct consequence of the heterogeneous recruitment abilities of promoters to RNA polymerases based on a gene expression model at the whole-cell level. Those genes with weaker (stronger) recruitment abilities than the average ability spontaneously exhibit superlinear (sublinear) scaling with cell volume. Analysis of the promoter sequences and the nonlinear scaling of Saccharomyces cerevisiae’s mRNA levels shows that motifs associated with transcription regulation are indeed enriched in genes exhibiting nonlinear scaling, in concert with our model.
引用
收藏
相关论文
共 50 条
  • [21] Development- and tissue-specific expression of the RpoT gene family of Arabidopsis encoding mitochondrial and plastid RNA polymerases
    Emanuel, C
    von Groll, U
    Müller, M
    Börner, T
    Weihe, A
    PLANTA, 2006, 223 (05) : 998 - 1009
  • [22] Cell-centered nonlinear finite-volume methods for the heterogeneous anisotropic diffusion problem
    Terekhov, Kirill M.
    Mallison, Bradley T.
    Tchelepi, Hamdi A.
    JOURNAL OF COMPUTATIONAL PHYSICS, 2017, 330 : 245 - 267
  • [23] cDNA expression array reveals heterogeneous gene expression profiles in three glioblastoma cell lines
    Rhee, CH
    Hess, K
    Jabbur, J
    Ruiz, M
    Yang, Y
    Chen, S
    Chenchik, A
    Fuller, GN
    Zhang, W
    ONCOGENE, 1999, 18 (17) : 2711 - 2717
  • [24] cDNA expression array reveals heterogeneous gene expression profiles in three glioblastoma cell lines
    Chang Hun Rhee
    Kenneth Hess
    James Jabbur
    Maribelis Ruiz
    Yu Yang
    Stephen Chen
    Alex Chenchik
    Gregory N Fuller
    Wei Zhang
    Oncogene, 1999, 18 : 2711 - 2717
  • [25] The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma
    Khoshnoud, Mahmoud R.
    He, Qimin
    Sylvan, Maria
    Khoshnoud, Aida
    Ivarsson, Madleen
    Fornander, Tommy
    Bergh, Jonas
    Frisell, Jan
    Rutqvist, Lars-Erik
    Skog, Sven
    INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, 2010, 26 : S38 - S38
  • [26] The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma
    Khoshnoud, Reza
    He, Qimin
    Sylvan, Maria
    Khoshnoud, Aida
    Ivarsson, Madleen
    Fornander, Tommy
    Bergh, Jonas
    Frisell, Jan
    Rutqvist, Lars-Erik
    Skog, Sven
    INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, 2010, 25 (05) : 735 - 741
  • [27] SAVER: gene expression recovery for single-cell RNA sequencing
    Mo Huang
    Jingshu Wang
    Eduardo Torre
    Hannah Dueck
    Sydney Shaffer
    Roberto Bonasio
    John I. Murray
    Arjun Raj
    Mingyao Li
    Nancy R. Zhang
    Nature Methods, 2018, 15 : 539 - 542
  • [28] Gene expression distribution deconvolution in single-cell RNA sequencing
    Wang, Jingshu
    Huang, Mo
    Torre, Eduardo
    Dueck, Hannah
    Shaffer, Sydney
    Murray, John
    Raj, Arjun
    Li, Mingyao
    Zhang, Nancy R.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (28) : E6437 - E6446
  • [29] SAVER: gene expression recovery for single-cell RNA sequencing
    Huang, Mo
    Wang, Jingshu
    Torre, Eduardo
    Dueck, Hannah
    Shaffer, Sydney
    Bonasio, Roberto
    Murray, John I.
    Raj, Arjun
    Li, Mingyao
    Zhang, Nancy R.
    NATURE METHODS, 2018, 15 (07) : 539 - +
  • [30] MicroRNA-Offset RNA Alters Gene Expression and Cell Proliferation
    Zhao, Jin
    Schnitzler, Gavin R.
    Iyer, Lakshmanan K.
    Aronovitz, Mark J.
    Baur, Wendy E.
    Karas, Richard H.
    PLOS ONE, 2016, 11 (06):