Cell cycle control

Papers @ Stanford 2016-present

J Makela, A Papagiannakis, W Lin, MC Lanz, S Glenn, M Swaffer, GK Marinov, JM Skotheim & C Jacobs-Wagner, “Genome concentration limits cell growth and modulates proteome composition in Escherichia coli”https://doi.org/10.7554/eLife.97465.1 eLife (2024).

MC Lanz, S Zhang, MP Swaffer, I Ziv, L Hernández Götz, F McCarty, DF Jarosz, JE Elias & JM Skotheim, “Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells” bioRxiv doi:https://doi.org/10.1101/2023.10.16.562558 to appear in Nature Structural and Molecular Biology (2024).

J Xiao, JJ Turner, M Kõivomägi & JM Skotheim, “Whi5 hypo- and hyper-phosphorylation dynamics control cell cycle entry and progression” https://doi.org/10.1016/j.cub.2024.04.052 Current Biology (2024).

MP Swaffer, GK Marinov, H Zheng, AW Jones, J Greenwood, A Kundaje, AP Snijders, WJ Greenleaf, R Reyes-Lamothe & JM Skotheim, “RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size” 186 (24), 5254-5268. Cell (2023). 

MC Lanz, L Valenzuela, JE Elias & JM Skotheim, “Cell size contributes to single-cell proteome variation” https://doi.org/10.1021/acs.jproteome.3c00441 J. Proteome Res. (2023).

F Proulx-Giraldeau, JM Skotheim & P Francois, “Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures” bioRxiv doi: https://doi.org/10.1101/2022.04.12.488093 eLife (2022).

E Zatulovskiy, MC Lanz, S Zhang, F McCarthy, JE Elias & JM Skotheim. “Delineation of proteome changes driven by cell size and growth rate” Frontiers in Cell and Developmental Biology;10:980721. DOI: 10.3389/fcell.2022.980721 (2022).

S Xie, M Swaffer & JM Skotheim, “Eukaryotic Cell Size Control and Its Relation to Biosynthesis and Senescence”, Annu. Rev. Cell Dev. Biol. 38:7.1-7.29 (2022)

S Zhang, E Zatulovskiy, J Arand, J Sage & JM Skotheim, “The cell cycle inhibitor RB is diluted in G1 and contributes to controlling cell size in the mouse liver” bioRxiv doi: https://doi.org/10.1101/2022.06.08.495371 to appear in Frontiers in Cell and Developmental Biology

MC Lanz*, E Zatulovskiy*, MP Swaffer, L Zhang, S Zhang, DS You, G Marinov, P McAlpine, JE Elias & JM Skotheim “Increasing cell size remodels the proteome and promotes senescence” bioRxiv doi: https://doi.org/10.1101/2021.07.29.454227 to appear in Molecular Cell

F Proulx-Giraldeau, JM Skotheim & P Francois, “Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures” bioRxiv doi: https://doi.org/10.1101/2022.04.12.488093

KM Schmoller*, MC Lanz*, J Kim, M Koivomagi, Y Qu, C Tang, IV Kukhtevich, R Schneider, F Rudolf, DF Moreno, M Aldea, R Lucena, D Kellogg, JM Skotheim, “Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1”, Molecular Biology of the Cell 33:lt1, 1–9 (2022).

S Pu, S Schor, V Nicolaescu, M Koivomagi, P Cassonnet, M Robinson, G Neveu, LI Prugar, DE Dorosky, J Brannan, A Yueh, JM Dye, C Demeret, JM Skotheim, Y Jacob, G Randall & S Einav, “BIKE regulates dengue virus infection via CLINT1 phosphorylation and is a host target for broad-spectrum antivirals” J. Biol. Chem. 298(6) 101956 (2022).

A Doan*, J Arand*, D Gong, AP Drainas, S Zhang, DM Walter, DM Feldser, H Vogel, LE Dow, JM Skotheim & J Sage, “RB depletion is required for the continuous growth of tumors initiated by loss of RB” PLoS Genetics 17(12): e1009941. https://doi.org/10.1371/journal.pgen.1009941 (2021).

MP Swaffer, D Chandler-Brown, M Langhinrichs, G Marinov, W Greenleaf, A Kundaje, KM Schmoller & JM Skotheim, “Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell”, Molecular Cell 81, 1–15 doi.org/10.1016/j.molcel.2021.10.007 (2021).

M Kõivomägi, MP Swaffer, JJ Turner & Jan M. Skotheim, “Localized phosphorylation of RNA Polymerase II by G1 cyclin-Cdk promotes cell cycle entry”, Science 374 (6565), 347-351 doi:10.1126/science.aba5186 (2021).

D Jukam, RR Kapoor, AF Straight*, JM Skotheim*, “The DNA-to-cytoplasm ratio broadly activates zygotic gene expression in Xenopus” Current Biology 31: 1–13 doi.org/10.1016/j.cub.2021.07.035 (2021).

SM Rubin, J Sage & JM Skotheim, “Integrating old and new paradigms for G1/S control”, Molecular Cell 80 (2) 183-192 doi: 10.1016/j.molcel.2020.08.020 (2020). 

E Zatulovskiy & JM Skotheim, “On the Molecular Mechanisms Regulating Animal Cell Size Homeostasis” Trends in Genetics 36, (5) 360-372 (2020).

Zatulovskiy, E., Zhang, S., Berensen, D., Topacio, B.R., Skotheim, J.M. “Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division” Science, 369 (6502), 466-471 (2020).

S Xie & JM Skotheim, “A G1 sizer mechanism coordinates growth and division in the mouse epidermis” Current Biology. doi:10.1016/j.cub.2019.12.062 (2020).

S Khondker, S Kajjo, D Chandler-Brown, JM Skotheim, A Rudner & Amy Ikui, “PP2ACdc55 dephosphorylates Pds1 to inhibit spindle elongation. Journal of Cell Science 133 (14), (2020).

Z Shipony, GK Marinov, MP Swaffer, NA Sinott-Armstrong, JM Skotheim, A Kundaje, WJ Greenleaf, “Long-range single-molecule mapping of chromatin accessibility in eukaryotes” Nature Methods doi: 10.1038/s41592-019-0730-2 Feb 10 (2020).

L Zhang, S Winkler, F Schlottmann, O Kohlbacher, JE Elias, JM Skotheim & JC Ewald, “Multiple layers of phospho-regulation coordinate metabolism and the cell cycle in budding yeast” Front. Cell Dev. Biol. 7:338. doi: 10.3389/fcell.2019.00338 (2019).

DF Berenson, E Zatulovskiy, S Xie & JM Skotheim, “Constitutive expression of a fluorescent protein reports the size of live human cells” Molecular Biology of the Cell 30:24 doi:10.1091/mbc.E19-03-0171 (2019). 

A Shariati, A Dominguez, M Wernig, LS Qi & JM Skotheim, “Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9” Molecular Cell 74, 622–633 doi:10.1016/j.molcel.2019.04. (2019).

BR Topacio, E Zatulovskiy, S Cristea, S Xie, CS Tambo, SM Rubin, J Sage, M Kõivomägi & JM Skotheim, “Cyclin D-Cdk4,6 drives cell cycle progression via the retinoblastoma protein’s C-terminal helix”, DOI:https://doi-org.stanford.idm.oclc.org/10.1016/j.molcel.2019.03.020 Molecular Cell (2019)

 JC Bell, D Jukam, NA Teran, VI Risca, OK Smith, WL Johnson, JM Skotheim, WJ Greenleaf & AF Straight, “Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts” eLife 7:e27024 (2018).

C Schwarz, A Johnson, M Koivomagi, E Zatulovskiy, C Kravitz, A Doncic & JM Skotheim, “A precise Cdk2 threshold determines passage through the restriction point” Molecular Cell, 69 (2), 253-264, e5 (2018).

D Chandler-Brown*, K Schmoller*, Y Winetraub & JM Skotheim, “The adder phenomenon emerges from independent control of pre- and post-Start phases of the budding yeast cell cycle”, Current Biology, Volume 27, Issue 18, 2774-2783.e3 (2017).

U Eser*, D Chandler-Brown*, F Ay, AF Straight, Z Duan, WS Noble, JM Skotheim, “Form and function of topologically associated domains in yeast” PNAS E3061–E3070, doi: 10.1073/pnas.1612256114 (2017).

O Atay & JM Skotheim, “Spatial and Temporal Signal Processing and Decision Making by MAPK Pathways”, DOI: 10.1083/jcb.201609124 Journal of Cell Biology (2017).

D Jukam, A Shariati & JM Skotheim, “Zygotic genome activation in vertebrates”, Developmental Cell 42, 316–332 (2017).

O Atay, A Doncic & JM Skotheim, “Switch-like transitions can modularize complex biological networks”, Cell Systems doi:10.1016/j.cels.2016.06.010 (2016).

B Treutlein, QY Lee, J Camp, M Mall, A Shariati, S Sim, N Neff, JM Skotheim, M Wernig, W Koh & S Quake, “Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq”, Nature, doi:10.1038/nature18323 (2016).

E Medina-Tovar, JJ Turner, JM Skotheim & NE Buchler, “Punctuated evolution of a complex ancestral cell cycle” eLife, DOI: 10.7554/eLife.09492.001 (2016).

J Ewald, A Kuehne, N Zamboni & JM Skotheim, “The yeast cyclin-dependent kinase routes carbon fluxes to fuel cell cycle progression” Molecular Cell 62, 532-45 (2016). 

Papers @ Stanford 2008-2015

A Doncic, O Atay, E Valk, A Grande, A Bush, G Vasen, A Colman-Lerner, M Loog & JM Skotheim, “Compartmentalization of a bistable switch enhances memory across a cellular transition” Cell 160, 1182-95 (2015).

E Zatulovskiy & JM Skotheim, 'Mitosis is swell' doi: 10.1083/jcb.201511007 JCB (2015) 

K Schmoller, JJ Turner, M Koivomagi & JM Skotheim, 'Dilution of the cell cycle inhibitor Whi5 controls budding yeast cell size' DOI: 10.1038/nature14908 Nature (2015).

AA Amodeo, D Jukam, AF Straight & JM Skotheim, 'Histone titration by DNA sets the threshold for the mid-blastula transition in Xenopus' www.pnas.org/cgi/doi/10.1073/pnas.1413990112, PNAS 2015.

EA Peroza, JC Ewald, G Parakkal, JM Skotheim, N Zamboni, 'A genetically encoded FRET sensor reveals in vivo trehalose-6-phosphate dynamics' Analytical Biochemistry doi:10.1016/j.ab.2014.12.019 (2015).

O Atay & JM Skotheim, 'Modularity and predictability in cell signaling and decision-making' MBoC 25, 3445-50 (2014).

M Koivomagi and JM Skotheim, 'Docking interactions: the cell cycle and beyond' Current Biology 24, R647-9 (2014).

 CA Anderson, U Eser, T Korndorf, ME Borsuk, JM Skotheim, AS Gladfelter, 'Nuclear repulsion enables division autonomy in a single cytoplasm' Current Biology 23, 1999-2010 (2013).

A Johnson & JM Skotheim, 'Start and the Restriction Point', Current Opinion in Cell Biology25, 717-723 (2013).

C Bertoli, JM Skotheim & RA de Bruin, ‘Transcriptional control of the G1-to-S transition’, Nature Rev. Mol. Cell Bio. 14, 518-28 (2013).

F Caval-Holme, JL Payne & JM Skotheim, “Physiological and cell biological limits on protist offspring size”  Evolution DOI: 10.1111/evo.12210 (2013).

A Doncic & JM Skotheim, “Feed-forward regulation ensures stability and rapid reversibility of a cellular state”,  Mol. Cell. 50, 1-13 (2013).

A Doncic, U Eser, O Atay & JM Skotheim, “An algorithm to automate yeast segmentation and tracking” PLoS ONE 8(3): e57970 (2013).  

U Eser, Ph.D. Thesis 2013, "Spatio-temporal regulation of cell cycle transcription" click to download.

A Doncic & JM Skotheim, “Cell cycle control: single-cell analysis”, Encyclopedia for Systems Biology, Dubitzky, W.; Wolkenhauer, O.; Yokota, H.; Cho, K.-H. (Eds.) (2013).

JM Skotheim, 'Cell growth and cell cycle control', MBoC 24, 678 (2013).

JL Payne, AB Jost, SC Wang & JM Skotheim, “A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction” Evolution 67, 816-27 (2013).

JL Payne, JR Groves, AB Jost, T Nguyen, S Myhre, TM Hills & JM Skotheim, “Late Paleozoic fusulinoidean gigantism driven by atmospheric hyperoxia” Evolution 66, 2929-39 (2012).

J Turner, J Ewald & JM Skotheim, "Cell size control in yeast" Current Biology, 22, R350-9 (2012).

FR Cross, N Buchler & JM Skotheim, “Evolution of networks and sequences in eukaryotic cell cycle control” Phil. Trans. Roy. Soc. B 366, 3532-3544 (2011).

A Doncic, M Falleur-Fettig & JM Skotheim, “Distinct interactions select and maintain a specific cell fate” Mol. Cell 43, 528–539 (2011).  Featured in Mol. Cell preview; Selected for faculty of 1000. 

U Eser, M Falleur-Fettig, A Johnson & JM Skotheim, “Commitment to a cellular transition precedes genome-wide transcriptional change” Mol. Cell 43, 515–527 (2011).   Featured in Mol. Cell preview; Selected for faculty of 1000

S DiTalia, H Wang, JM Skotheim, A Rosebrock, B Futcher & FR Cross, “Daughter-specific transcription factors regulate cell size control in budding yeast” PLoS Biology 7(10): e1000221 (2009). See Nature Reviews Genetics research highlight.

JM Skotheim, “To divide or not to divide”, Science 324, 476-7 (2009).

Papers @ Rockefeller University 2005-8

JM Skotheim, S DiTalia, ED Siggia & FR Cross, "Positive feedback of G1 cyclins ensures coherent cell cycle entry", Nature 454, 291-296 (2008). See Nature News and Views; Mol. Cell preview; Cell Leading Edge; Selected for Faculty of 1000.

S DiTalia, JM Skotheim, JM Bean, ED Siggia & FR Cross, "The effects of molecular noise and size control on variability in the budding yeast cell cycle", Nature 448, 947-951 (2007). Selected for faculty of 1000.

M Argentina, JM Skotheim & L Mahadevan, “Settling and swimming of flexible fluid-lubricated foils,” Phys. Rev. Lett. 99, 224503 (2007).

JM Skotheim & TW Secomb, "Red blood cells and other non-spherical capsules in shear flow: oscillatory motion and the tank-treading-to-tumbling transition", Phys Rev. Lett. 98, 078301 (2007).

Papers @ University of Cambridge 2001-2005

JM Skotheim & L Mahadevan, “Soft elastohydrodynamic contacts”, Phys. Fluids, 17, 092101 (2005). Awarded the François Frenkiel Award by the American Physical Society for significant contributions to the field of fluid mechanics by a young scientist.

S Manley, JM Skotheim, L Mahadevan & DA Weitz, “Gravitational collapse of colloidal gels,” Phys. Rev. Lett., 94, 218302 (2005).

JM Skotheim & L Mahadevan “Physical limits and design principles for plant and fungal movements,” Science, 308, 1308-1310 (2005). Featured on the cover; Selected for Faculty of 1000.

Y Forterre, JM Skotheim, J Dumais & L Mahadevan, “How the Venus flytrap snaps,” Nature, 433, 421-425 (2005). Selected for Faculty of 1000.

JM Skotheim & L Mahadevan, “Soft lubrication,” Phys. Rev. Lett. 92, 245509 (2004).

JM Skotheim & L Mahadevan, “Dynamics of poroelastic filaments,” Proc. R. Soc. London Ser. A 460, 1995-2020 (2004).

JM Skotheim, U Thiele & B Scheid, “On the instability of a falling film due to localized heating,” J. Fluid Mech., 475, 1-19, (2003).

Papers @ MIT

JM Skotheim & JWM Bush, “Evaporatively driven convection in a draining soap film,” Phys. Fluids, S1, Sept. (2000). Featured on the Cover.