Summary of Study ST001898
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001194. The data can be accessed directly via it's Project DOI: 10.21228/M8CD8G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001898 |
| Study Title | Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape |
| Study Summary | Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature. |
| Institute | Stanford University |
| Last Name | Contrepois |
| First Name | Kevin |
| Address | 300 Pasteur Dr |
| kcontrep@stanford.edu | |
| Phone | 6506664538 |
| Submit Date | 2021-08-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-12-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003083 | AN003084 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
| Column | Thermo Accucore (150 x 2.1mm,2.6um) | Thermo Accucore (150 x 2.1mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | MS count | MS count |
MS:
| MS ID: | MS002865 |
| Analysis ID: | AN003083 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC-MS peak extraction, alignment, quantification and annotation was performed using LipidSearch software version 4.2.21 (Thermo Fisher Scientific). Lipids were identified by matching the precursor ion mass to a database and the experimental MS/MS spectra to a spectral library containing theoretical fragmentation spectra. To reduce the risk of misidentification, MS/MS spectra from lipids of interest were validated as follows: 1) both positive and negative mode MS/MS spectra match the expected fragments, 2) the main lipid adduct forms detected in positive and negative modes agree with the lipid class identified, 3) the retention time is compatible with the lipid class identified and 4) the peak shape is acceptable. The fragmentation pattern of each lipid class was experimentally validated using lipid internal standards. Single-point internal standard calibrations were used to estimate absolute concentrations for 431 unique lipids belonging to 14 classes using one internal standard for each lipid class. Importantly, we ensured linearity within the range of detected endogenous lipids using serial dilutions of internal standards spanning 4 orders of magnitude. Subsequently, median normalization (excluding TG and DG) was employed on lipid molar concentrations to correct for differential quantity of starting material. The normalized lipid intensities were well correlated with protein abundances measured using BCA Protein Assay Kit (Pierce, cat# 23225) suggesting good sample quality. One development (diapause escape) sample had an unexpectedly low protein concentration and thus was discarded. Lipid molar concentrations for a given class were calculated by summing individual lipid species molar concentrations belonging to that class. Fatty acid composition analysis was performed in each lipid class. Fatty acid composition was calculated by taking the ratio of the sum molar concentration of a given fatty acid over the sum molar concentration across fatty acids found in the lipids of the class. Subsequently, saturated fatty acids (SFA), mono-unsaturated fatty acids (MUFA) and poly-unsaturated fatty acids (PUFA) were grouped together for comparative analysis. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002866 |
| Analysis ID: | AN003084 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC-MS peak extraction, alignment, quantification and annotation was performed using LipidSearch software version 4.2.21 (Thermo Fisher Scientific). Lipids were identified by matching the precursor ion mass to a database and the experimental MS/MS spectra to a spectral library containing theoretical fragmentation spectra. To reduce the risk of misidentification, MS/MS spectra from lipids of interest were validated as follows: 1) both positive and negative mode MS/MS spectra match the expected fragments, 2) the main lipid adduct forms detected in positive and negative modes agree with the lipid class identified, 3) the retention time is compatible with the lipid class identified and 4) the peak shape is acceptable. The fragmentation pattern of each lipid class was experimentally validated using lipid internal standards. Single-point internal standard calibrations were used to estimate absolute concentrations for 431 unique lipids belonging to 14 classes using one internal standard for each lipid class. Importantly, we ensured linearity within the range of detected endogenous lipids using serial dilutions of internal standards spanning 4 orders of magnitude. Subsequently, median normalization (excluding TG and DG) was employed on lipid molar concentrations to correct for differential quantity of starting material. The normalized lipid intensities were well correlated with protein abundances measured using BCA Protein Assay Kit (Pierce, cat# 23225) suggesting good sample quality. One development (diapause escape) sample had an unexpectedly low protein concentration and thus was discarded. Lipid molar concentrations for a given class were calculated by summing individual lipid species molar concentrations belonging to that class. Fatty acid composition analysis was performed in each lipid class. Fatty acid composition was calculated by taking the ratio of the sum molar concentration of a given fatty acid over the sum molar concentration across fatty acids found in the lipids of the class. Subsequently, saturated fatty acids (SFA), mono-unsaturated fatty acids (MUFA) and poly-unsaturated fatty acids (PUFA) were grouped together for comparative analysis. |
| Ion Mode: | NEGATIVE |
