Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.
Pluripotent stem cells retain the developmental timing of their species of origin in vitro, an observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature and machinery of the clock remain a mystery. We hypothesize that one possible component may lie in species-sp...
Saved in:
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-12-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007543&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850077319982481408 |
|---|---|
| author | Christopher Barry Matthew T Schmitz Cara Argus Jennifer M Bolin Mitchell D Probasco Ning Leng Bret M Duffin John Steill Scott Swanson Brian E McIntosh Ron Stewart Christina Kendziorski James A Thomson Rhonda Bacher |
| author_facet | Christopher Barry Matthew T Schmitz Cara Argus Jennifer M Bolin Mitchell D Probasco Ning Leng Bret M Duffin John Steill Scott Swanson Brian E McIntosh Ron Stewart Christina Kendziorski James A Thomson Rhonda Bacher |
| author_sort | Christopher Barry |
| collection | DOAJ |
| description | Pluripotent stem cells retain the developmental timing of their species of origin in vitro, an observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature and machinery of the clock remain a mystery. We hypothesize that one possible component may lie in species-specific differences in the kinetics of transcriptional responses to differentiation signals. Using a liquid-handling robot, mouse and human pluripotent stem cells were exposed to identical neural differentiation conditions and sampled for RNA-sequencing at high frequency, every 4 or 10 minutes, for the first 10 hours of differentiation to test for differences in transcriptomic response rates. The majority of initial transcriptional responses occurred within a rapid window in the first minutes of differentiation for both human and mouse stem cells. Despite similarly early onsets of gene expression changes, we observed shortened and condensed gene expression patterns in mouse pluripotent stem cells compared to protracted trends in human pluripotent stem cells. Moreover, the speed at which individual genes were upregulated, as measured by the slopes of gene expression changes over time, was significantly faster in mouse compared to human cells. These results suggest that downstream transcriptomic response kinetics to signaling cues are faster in mouse versus human cells, and may offer a partial account for the vast differences in developmental rates across species. |
| format | Article |
| id | doaj-art-14bcc2d6b0e84205bbe5dfa387cbcb92 |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2019-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-14bcc2d6b0e84205bbe5dfa387cbcb922025-08-20T02:45:50ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582019-12-011512e100754310.1371/journal.pcbi.1007543Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.Christopher BarryMatthew T SchmitzCara ArgusJennifer M BolinMitchell D ProbascoNing LengBret M DuffinJohn SteillScott SwansonBrian E McIntoshRon StewartChristina KendziorskiJames A ThomsonRhonda BacherPluripotent stem cells retain the developmental timing of their species of origin in vitro, an observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature and machinery of the clock remain a mystery. We hypothesize that one possible component may lie in species-specific differences in the kinetics of transcriptional responses to differentiation signals. Using a liquid-handling robot, mouse and human pluripotent stem cells were exposed to identical neural differentiation conditions and sampled for RNA-sequencing at high frequency, every 4 or 10 minutes, for the first 10 hours of differentiation to test for differences in transcriptomic response rates. The majority of initial transcriptional responses occurred within a rapid window in the first minutes of differentiation for both human and mouse stem cells. Despite similarly early onsets of gene expression changes, we observed shortened and condensed gene expression patterns in mouse pluripotent stem cells compared to protracted trends in human pluripotent stem cells. Moreover, the speed at which individual genes were upregulated, as measured by the slopes of gene expression changes over time, was significantly faster in mouse compared to human cells. These results suggest that downstream transcriptomic response kinetics to signaling cues are faster in mouse versus human cells, and may offer a partial account for the vast differences in developmental rates across species.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007543&type=printable |
| spellingShingle | Christopher Barry Matthew T Schmitz Cara Argus Jennifer M Bolin Mitchell D Probasco Ning Leng Bret M Duffin John Steill Scott Swanson Brian E McIntosh Ron Stewart Christina Kendziorski James A Thomson Rhonda Bacher Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. PLoS Computational Biology |
| title | Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. |
| title_full | Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. |
| title_fullStr | Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. |
| title_full_unstemmed | Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. |
| title_short | Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. |
| title_sort | automated minute scale rna seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007543&type=printable |
| work_keys_str_mv | AT christopherbarry automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT matthewtschmitz automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT caraargus automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT jennifermbolin automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT mitchelldprobasco automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT ningleng automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT bretmduffin automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT johnsteill automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT scottswanson automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT brianemcintosh automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT ronstewart automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT christinakendziorski automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT jamesathomson automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics AT rhondabacher automatedminutescalernaseqofpluripotentstemcelldifferentiationrevealsearlydivergenceofhumanandmousegeneexpressionkinetics |