Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors
- Howard Hughes Medical Institute, University of California, United States
Figures
Figure 1
Predicting disorder from the proteome.
(A) A summary of the workflow of the intrinsically disordered region (IDR) prediction algorithm. IUPred scores were computed for the entire proteome, and the output was parsed into scores for …
Figure 2
Intrinsically disordered region (IDR) imaging screen.
(A) Representative images from each Schneider-2 (S2) cell line in the imaging screen. Untransfected controls were transfected with the p8HCO methotrexate resistance plasmid and maintained alongside …
Figure 3 with 1 supplement
A subset a full-length transcription factors (TFs) cluster in Schneider-2 (S2) cells.
S2 cell lines expressing mNeonGreen-tagged intrinsically disordered regions (IDRs) or full-length proteins and mRuby3-tagged His2Av. The top four panels indicate control cell lines. IDRs and their …
Figure 3—figure supplement 1
Viterbi plots for candidate transcription factors (TFs).
Plots showing the output of the intrinsically disordered region (IDR) prediction hidden Markov model (HMM) for each of the TFs in our data set. Schematics of the linear structure of each protein …
Figure 4 with 1 supplement
Intrinsically disordered regions (IDRs) vs full-length transcription factors (TFs) in embryos.
Expression of transgenic mNeonGreen-tagged IDRs (A) or full-length TFs tagged at the endogenous locus with eGFP (B) and His2Av-RFP in nuclear cycle 14 (NC14) embryos. The name of the TF is indicated …
Figure 4—figure supplement 1
Brk localizes to the histone locus body.
Nuclei from a nuclear cycle 14 (NC14) embryo expressing a transgenic mNeonGreen-tagged Brk intrinsically disordered region (IDR) and Mxc tagged at the endogenous locus with mRuby3. The image is a …
Figure 5 with 1 supplement
Transgenic full-length transcription factors (TFs).
Nuclear cycle 14 (NC14) embryos expressing transgenic mNeonGreen-tagged full-length TFs and His2Av-RFP. The name of the TF is indicated at the far left. Images are maximum intensity z-projections, …
Figure 5—figure supplement 1
Subnuclear localization patterns of intrinsically disordered region (IDR) deletion constructs are uniform across the embryo.
(A) Brk tagged at the endogenous locus with eGFP. The labeled protein is expressed at low levels in nuclei on the ventral side of the embryo. The ventral view panel shows a 2× zoom of the same …
Figure 6
Intrinsically disordered region (IDR) deletions do not affect transcription factor (TF) localization.
Nuclear cycle 14 (NC14) embryos expressing transgenic mNeonGreen-tagged TFs with IDR deletions and His2Av-RFP. The name of the TF is indicated at the far left. Images are maximum intensity …
Tables
Table 1
Panel of transcription factors (TFs) chosen for full-length expression constructs in Schneider-2 (S2) cells and Drosophila embryos.
| IDR # | FlyBase ID | TF name | IDR length (AAs) | Full length | IDR start | IDR end |
|---|---|---|---|---|---|---|
| 6 | FBpp0304504 | Da | 219 | 710 | 116 | 334 |
| 17 | FBpp0303090 | Rib | 249 | 661 | 413 | 661 |
| 18 | FBpp0071577 | CG10321 | 270 | 835 | 307 | 576 |
| 26 | FBpp0076735 | CG13287 | 245 | 461 | 1 | 246 |
| 44 | FBpp0081483 | Tgo | 251 | 642 | 392 | 642 |
| 64 | FBpp0083950 | Spps | 265 | 968 | 372 | 636 |
| 65 | FBpp0084158 | CG31510 | 260 | 1150 | 90 | 349 |
| 72 | FBpp0071007 | Brk | 264 | 704 | 1 | 264 |
| 76 | FBpp0074028 | Disco | 206 | 568 | 220 | 425 |
Additional files
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Source code 1
Python code used to generate the HMM IDR predictions, provided as a Jupyter Notebook.
- https://cdn.elifesciences.org/articles/88221/elife-88221-code1-v1.zip
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Supplementary file 1
It contains identifying information, amino acid, and DNA sequences of all intrinsically disordered regions (IDRs) expressed in Schneider-2 (S2) cells in Figure 2.
- https://cdn.elifesciences.org/articles/88221/elife-88221-supp1-v1.xlsx
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Supplementary file 2
It contains sequences of primers used to generate transgenic Drosophila lines expressing intrinsically disordered regions (IDRs) or full-length transcription factors (TFs) in Figures 4—6.
- https://cdn.elifesciences.org/articles/88221/elife-88221-supp2-v1.xlsx
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Supplementary file 3
It contains sequences of primers used to generate CRISPR tagging constructs, sgRNA sequences, screening primers to identify CRISPR insertions, and a list of injected fly lines to produce the endogenously tagged transcription factors (TFs) shown in Figure 4 and Figure 4—figure supplement 1.
- https://cdn.elifesciences.org/articles/88221/elife-88221-supp3-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/88221/elife-88221-mdarchecklist1-v1.pdf
