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| Status |
Public on May 10, 2024 |
| Title |
Disentangling cell-intrinsic and extrinsic factors underlying gene expression evolution |
| Organism |
Mus musculus x Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Chimeras have played a foundational role in biology, for example by enabling the classification of developmental processes into those driven intrinsically by individual cells versus those driven extrinsically by their extracellular environment. Here, we extend this framework to decompose evolutionary divergence in gene expression and other quantitative traits into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to reciprocal rat-mouse chimeras, we found that the majority of gene expression divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level for both genes we tested, suggesting propagation through multiple regulatory levels. We also demonstrate that our framework is applicable to a cellular trait, neuronal differentiation, and estimated the intrinsic and extrinsic contributions to its divergence. Finally, we show that many imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens up new avenues to investigate the mechanistic basis of evolutionary divergence in gene expression and other quantitative traits in any multicellular organism.
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| Overall design |
We used interspecies rat-mouse and mouse-rat chimeras to study intrinsic and extrinsic mechanisms controlling gene expression. Mouse-rat (i.e. mouse cells injected into a rat blastocyst) chimeras and the wildtype rat samples were collected at embryonic day (E) 15.5 and rat-mouse chimeras and the wildtype mouse sample were collected at E13.5. Cells from connective tissue and forebrain were FACS sorted to enrich for TdTomato+ donor cells (i.e. cells injected into the blastocyst). Single cell RNA-sequencing was then performed using 10x v3.1 3’ chemistry and sequenced on a Novaseq X. Wildtype mouse and rat cells were pooled together and sequenced in one WT-Mouse_WT-Rat library. We use Mouse-Rat and MR as well as Rat-Mouse and RM interchangeably. Read 1 was trimmed in accordance with 10x recommendations. Each library was sequenced to a low depth initially and then libraries Mouse-Rat_2, Mouse-Rat_3, and Rat-Mouse_3 were not sequenced further. All other libraries were sequenced more deeply in a second round of sequencing and fastq files were concatenated together.
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| Contributor(s) |
Starr AL, Nishimura T, Nakauchi H, Fraser HB |
| Citation missing |
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| Submission date |
Apr 30, 2024 |
| Last update date |
May 10, 2024 |
| Contact name |
Hunter B. Fraser |
| E-mail(s) |
hbfraser@stanford.edu
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| Organization name |
Stanford University
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| Street address |
371 Jane Stanford Way
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94040 |
| Country |
USA |
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| Platforms (1) |
| GPL34201 |
Illumina NovaSeq 6000 (Mus musculus x Rattus norvegicus) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA1106395 |
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