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| Status |
Public on Mar 30, 2026 |
| Title |
Cell size-dependent mRNA transcription drives proteome remodeling [SLAM-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Increasing cell size drives proteomic changes that impact cell physiology. However, the molecular basis of size-dependent proteome remodeling has remained unclear. Here, we develop an inducible Cyclin D1 expression system in human cells to generate proliferating cells spanning over a two-fold size range. We use this system to make comprehensive genome-wide measurements of mRNA and protein concentrations and stability. We find that protein and mRNA turnover rates are weakly related to cell size, but that mRNA concentrations are strongly size-dependent. This establishes that transcriptional regulation is the basis of proteome remodeling. Live-cell imaging of nascent mRNAs using the MS2 system is used to measure how transcriptional dynamics change with cell size. Larger cells prolong transcriptional bursts and shorten inactive periods between bursts but maintain similar burst amplitudes to achieve transcriptional scaling. Together, our results show how transcription is modulated by cell size to remodel the proteome and alter cell physiology.
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| Overall design |
SLAM-seq profiling of CCND1 overexpression or knockdown hTERT-RPE-1 lines with induction by doxycycline at day 4. Cells are pulsed with 10uM thiouridine at day 4 for 24 hours, with the media refreshed every 3 hours. Chase is started by washing twice with PBS and applying growth media with 1mM uridine. Negative control of unlabelled samples are also provided. Note that time points are not uniform across replicates and samples as only high quality datasets were selected for downstream analysis and upload
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| Contributor(s) |
You D, Bohrer CH, Rumde PH, Sanidas I, Swaffer MP, Larson DR, Elias JE, Lanz MC, Skotheim JM |
| Citation(s) |
42275220 |
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| Submission date |
Mar 23, 2026 |
| Last update date |
Jul 01, 2026 |
| Contact name |
Dong Shin You |
| Organization name |
Stanford University
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| Street address |
327 Campus Drive
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| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL34281 |
Illumina NovaSeq X (Homo sapiens) |
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| Samples (34)
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| GSM9611293 |
hTERT-RPE1 cells, overexpression ccnd1, dox, no label, rep1 |
| GSM9611294 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 0, rep1 |
| GSM9611295 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 20, rep1 |
| GSM9611296 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 90, rep1 |
| GSM9611297 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 180, rep1 |
| GSM9611298 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 360, rep1 |
| GSM9611299 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 720, rep1 |
| GSM9611300 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 1440, rep1 |
| GSM9611301 |
hTERT-RPE1 cells, overexpression ccnd1, dox, no label, rep2 |
| GSM9611302 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 0, rep2 |
| GSM9611303 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 10, rep2 |
| GSM9611304 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 20, rep2 |
| GSM9611305 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 45, rep2 |
| GSM9611306 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 180, rep2 |
| GSM9611307 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 360, rep2 |
| GSM9611308 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 720, rep2 |
| GSM9611309 |
hTERT-RPE1 cells, overexpression ccnd1, dox, 1440, rep2 |
| GSM9611310 |
hTERT-RPE1 cells, knockdown ccnd1, dox, no label, rep1 |
| GSM9611311 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 0, rep1 |
| GSM9611312 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 45, rep1 |
| GSM9611313 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 180, rep1 |
| GSM9611314 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 360, rep1 |
| GSM9611315 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 720, rep1 |
| GSM9611316 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 1440, rep1 |
| GSM9611317 |
hTERT-RPE1 cells, knockdown ccnd1, dox, no label, rep2 |
| GSM9611318 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 0, rep2 |
| GSM9611319 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 10, rep2 |
| GSM9611320 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 20, rep2 |
| GSM9611321 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 45, rep2 |
| GSM9611322 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 90, rep2 |
| GSM9611323 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 180, rep2 |
| GSM9611324 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 360, rep2 |
| GSM9611325 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 720, rep2 |
| GSM9611326 |
hTERT-RPE1 cells, knockdown ccnd1, dox, 1440, rep2 |
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| Relations |
| BioProject |
PRJNA1441515 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE325723_RAW.tar |
53.7 Mb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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