DOI: 10.5061/dryad.2rbnzs80v
title: EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational inheritance of a predatory trait

description: Environmental influences on traits and associated transgenerational
 epigenetic inheritance have widespread implications, but remain
 controversial and underlying mechanisms poorly understood. We introduce
 long-term environmental induction experiments on alternative diets in
 Pristionchus pacificus, a nematode exhibiting mouth-form plasticity
 including predation, by propagating 110 isogenic lines for 101 generations
 with associated food-reversal experiments. We found dietary induction and
 subsequent transgenerational inheritance of the predatory morph and
 identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process.
 Ppa-ebax-1 mutants are transgenerational inheritance-defective and
 Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35.
 Deletions of a cluster of 44 identical miR-2235a copies resulted in
 precocious and extended transgenerational inheritance of the predatory
 morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs
 resulting in transgenerational inheritance, suggesting a role for
 target-directed miRNA degradation.
description: # EBAX-1/ZSWIM8 destabilizes clustered microRNAs resulting in
 transgenerational memory of a predatory trait ## General Information
 **Authors:** Shiela Pearl Quiobe, Ata Kalirad, Waltraud Röseler, Hanh
 Witte, Yinan Wang, Christian Rödelsperger and Ralf J. Sommer **Date of
 Data Collection:** 2020 - 2024 **Date of Upload to Dryad:** 25-2-2025 ##
 Description of Dataset This dataset provides all the experimental data, as
 well as, statistical analyses assoicated with the manuscript
 *EBAX-1/ZSWIM8 destabilizes clustered microRNAs resulting in
 transgenerational memory of a predatory trait*. ## Data Files and
 Structure ### Main Files | File Name | Description | | ------------------
 |
 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `figures.ipynb` | Jupyter notebook containing main and supplementary figures. | | `stat_model.ipynb` | Jupyter notebook illustrating the statistical model used to infer the probability of developing the wide-mouthed ‘eurystomatous’ (Eu) form based on the experimental data. | ### Archived Data The following folders are available as compressed `.zip` archives: #### `raw_data.zip` This archive contains raw experimental data files: ``` 📁 raw_data ├── 📄 DMSO_control.xlsx ├── 📄 F15_reversal.xlsx ├── 📄 F1Rev.xlsx ├── 📄 F25_reversal.xlsx ├── 📄 F2Rev.xlsx ├── 📄 F35_reversal.xlsx ├── 📄 F3Rev.xlsx ├── 📄 F45_reversal.xlsx ├── 📄 F4Rev.xlsx ├── 📄 F55_reversal.xlsx ├── 📄 F5Rev.xlsx ├── 📄 F65_reversal.xlsx ├── 📄 F75_reversal.xlsx ├── 📄 F85_reversal.xlsx ├── 📄 F95_reversal.xlsx ├── 📄 HSP90_F10Rev.xlsx ├── 📄 HSP90_F5Rev.xlsx ├── 📄 WT_F10Rev.xlsx ├── 📄 WT_F1Rev.xlsx ├── 📄 WT_F3Rev.xlsx ├── 📄 WT_F5rev.xlsx ├── 📄 control_LTEI.xlsx ├── 📄 ebax-tu1754-F10Rev.xlsx ├── 📄 ebax-tu1754-F5Rev.xlsx ├── 📄 ebax-tu1755-F5Rev.xlsx ├── 📄 ebax-tu1756-F5Rev.xlsx ├── 📄 kana_response.xlsx ├── 📁 miR_deletion │ ├── 📄 WT_F5Rev.xlsx ├── 📄 novo_LTEI.xlsx ├── 📄 novo_LTEI_2.xlsx ├── 📄 tuDf10_F1Rev.xlsx ├── 📄 tuDf10_F3Rev.xlsx ├── 📄 tuDf10_F5Rev.xlsx ├── 📄 tuDf11_F1Rev.xlsx ├── 📄 tuDf11_F3Rev.xlsx ├── 📄 tuDf11_F5Rev.xlsx ├── 📄 tuDf9_F1Rev.xlsx ├── 📄 tuDf9_F3Rev.xlsx ├── 📄 tuDf9_F5Rev.xlsx ``` | File Name | Description | | ------------------------- | -------------------------------------------------------------------------- | | `DMSO_control.xlsx` | Raw data for the DMSO (Dimethyl sulfoxide) control experiment. | | `F15_reversal.xlsx` | Raw data for F15 reversal experimental condition. | | `F1Rev.xlsx` | Raw data for F1 reversal experimental condition. | | `F25_reversal.xlsx` | Raw data for F25 reversal experimental condition. | | `F2Rev.xlsx` | Raw data for F2 reversal experimental condition. | | `F35_reversal.xlsx` | Raw data for F35 reversal experimental condition. | | `F3Rev.xlsx` | Raw data for F3 reversal experimental condition. | | `F45_reversal.xlsx` | Raw data for F45 reversal experimental condition. | | `F4Rev.xlsx` | Raw data for F4 reversal experimental condition. | | `F55_reversal.xlsx` | Raw data for F55 reversal experimental condition. | | `F5Rev.xlsx` | Raw data for F5 reversal experimental condition. | | `F65_reversal.xlsx` | Raw data for F65 reversal experimental condition. | | `F75_reversal.xlsx` | Raw data for F75 reversal experimental condition. | | `F85_reversal.xlsx` | Raw data for F85 reversal experimental condition. | | `F95_reversal.xlsx` | Raw data for F95 reversal experimental condition. | | `HSP90_F10Rev.xlsx` | Raw data for HSP90 F10 reversal experimental condition. | | `HSP90_F5Rev.xlsx` | Raw data for HSP90 F5 reversal experimental condition. | | `WT_F10Rev.xlsx` | Raw data for wild-type F10 reversal experimental condition. | | `WT_F1Rev.xlsx` | Raw data for wild-type F1 reversal experimental condition. | | `WT_F3Rev.xlsx` | Raw data for wild-type F3 reversal experimental condition. | | `WT_F5rev.xlsx` | Raw data for wild-type F5 reversal experimental condition. | | `control_LTEI.xlsx` | Raw data for control Long-term experimental induction (LTEI) experiment. | | `ebax-tu1754-F10Rev.xlsx` | Raw data for ebax-tu1754 F10 reversal experimental condition. | | `ebax-tu1754-F5Rev.xlsx` | Raw data for ebax-tu1754 F5 reversal experimental condition. | | `ebax-tu1755-F5Rev.xlsx` | Raw data for ebax-tu1755 F5 reversal experimental condition. | | `ebax-tu1756-F5Rev.xlsx` | Raw data for ebax-tu1756 F5 reversal experimental condition. | | `kana_response.xlsx` | Raw data for kana response experiment. | | `WT_F5Rev.xlsx` | Raw data for wild-type F5 reversal experiment (in miR deletion subfolder). | | `novo_LTEI.xlsx` | Raw data for *Novosphingobium* L76 LTEI experiment. | | `novo_LTEI_2.xlsx` | Additional data for *Novosphingobium* L76 LTEI experiment. | | `tuDf10_F1Rev.xlsx` | Raw data for tuDf10 F1 reversal experimental condition. | | `tuDf10_F3Rev.xlsx` | Raw data for tuDf10 F3 reversal experimental condition. | | `tuDf10_F5Rev.xlsx` | Raw data for tuDf10 F5 reversal experimental condition. | | `tuDf11_F1Rev.xlsx` | Raw data for tuDf11 F1 reversal experimental condition. | | `tuDf11_F3Rev.xlsx` | Raw data for tuDf11 F3 reversal experimental condition. | | `tuDf11_F5Rev.xlsx` | Raw data for tuDf11 F5 reversal experimental condition. | | `tuDf9_F1Rev.xlsx` | Raw data for tuDf9 F1 reversal experimental condition. | | `tuDf9_F3Rev.xlsx` | Raw data for tuDf9 F3 reversal experimental condition. | | `tuDf9_F5Rev.xlsx` | Raw data for tuDf9 F5 reversal experimental condition. | --- *Note*: `Reversal experimental condition` referes to the standard laboratory food source *E. coli* OP50. **Description of variables found in `raw_data.zip`:** | Column Header | Description | | ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Fi** | The number of adults (unless specified, out of 20) with the wide-mouthed ‘eurystomatous’ (Eu) form on generation **i** when grown on *Novosphingobium* L76. | | **Ri** | The number of Eu adults (unless specified, out of 20) on generation **i** when grown on the standard laboratory food source *E. coli* OP50. | | **FiRj** | The number of Eu adults (unless specified, out of 20) on generation **j** when grown on the standard laboratory food source *E. coli* OP50, after **i** generations on *Novosphingobium* L76. | | **P0** and **F0** | The number of Eu adults (unless specified, out of 20) of naïve *P. pacificus* cultures that were always grown on the standard laboratory food source *E. coli* OP50. | #### `stat_inf.zip` This archive contains statistical analyses objects generated by PyMC, saved in *pickle* format, and used in `figures.ipynb` to generate the figures from the manuscript: 📄 DMSO_control_inf.pickle 📄 HSP90_F10Rev_inf.pickle 📄 R15_HM.pickle 📄 R1_HM.pickle 📄 R25_HM.pickle 📄 R2_HM.pickle 📄 R35_HM.pickle 📄 R3_HM.pickle 📄 R45_HM.pickle 📄 R4_HM.pickle 📄 R55_HM.pickle 📄 R5_HM.pickle 📄 R65_HM.pickle 📄 R75_HM.pickle 📄 R85_HM.pickle 📄 R95_HM.pickle 📄 WT_F10Rev_inf.pickle 📄 WT_F1Rev_inf.pickle 📄 WT_F3Rev_inf.pickle 📄 WT_F5Rev_inf.pickle 📄 control_LTEI_HM_comp.pickle 📄 ebax_tu1754_F10Rev_inf.pickle 📄 ebax_tu1754_F5Rev_inf.pickle 📄 ebax_tu1755_F5Rev_inf.pickle 📄 ebax_tu1756_F5Rev_inf.pickle 📄 hsp90_F5Rev_inf.pickle 📄 kana_inf.pickle 📄 mir0_F3_inf.pickle 📄 mir0_F5_inf.pickle 📄 mir0_inf.pickle 📄 mir1_F3_inf.pickle 📄 mir1_F5_inf.pickle 📄 mir1_inf.pickle 📄 mir2_F3_inf.pickle 📄 mir2_F5_inf.pickle 📄 mir2_inf.pickle #### `miscellaneous.zip` This archive contains additional analysis files: ``` 📁 miscellaneous ├── 📁 stat_inf_obj │ ├── 📄 WT_F1Rev_inf │ ├── 📄 WT_F3Rev_inf │ ├── 📄 WT_F5Rev_inf │ ├── 📄 mir0_F3_inf │ ├── 📄 mir0_F5_inf │ ├── 📄 mir0_inf │ ├── 📄 mir1_F3_inf │ ├── 📄 mir1_F5_inf │ ├── 📄 mir1_inf │ ├── 📄 mir2_F3_inf │ ├── 📄 mir2_F5_inf │ ├── 📄 mir2_inf ``` ##### `stat_inf_obj` Subfolder This subfolder contains inference results for different conditions: | File Name | Description | | -------------- | -------------------------------------------- | | `WT_F1Rev_inf` | Inference results for wild-type F1 reversal. | | `WT_F3Rev_inf` | Inference results for wild-type F3 reversal. | | `WT_F5Rev_inf` | Inference results for wild-type F5 reversal. | | `mir0_F3_inf` | Inference results for mir0 F3. | | `mir0_F5_inf` | Inference results for mir0 F5. | | `mir0_inf` | General inference results for mir0. | | `mir1_F3_inf` | Inference results for mir1 F3. | | `mir1_F5_inf` | Inference results for mir1 F5. | | `mir1_inf` | General inference results for mir1. | | `mir2_F3_inf` | Inference results for mir2 F3. | | `mir2_F5_inf` | Inference results for mir2 F5. | | `mir2_inf` | General inference results for mir2. | ## Methodology **Data Collection Methods:** The description of experimental conditions under which that data in this repository were collected can be found in the manuscript. ## Usage Notes **How to Use the Data:** In order to recreate the figures, statistical analyses objects generated by PyMC should be loaded in Jupyter notebooks. The notebooks contain instruction to how the raw experimental data and statistical analyses objects should be loaded in order to recreate the main and supplementary figures. **Software Requirements:** The repository uses the following software and libraries: | Software/Library | Version | | ---------------- | ------- | | Python | 3.11.5 | | IPython | 8.27.0 | | matplotlib | 3.8.1 | | pandas | 2.2.2 | | seaborn | 0.13.2 | | scipy | 1.11.3 | | numpy | 1.25.2 | | pymc | 5.9.1 | | arviz | 0.19.0 |