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Status |
Public on May 19, 2024 |
Title |
High Throughput Plant Activation Domain Identification and Mapping |
Organism |
Saccharomyces cerevisiae |
Experiment type |
Other
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Summary |
Arabidopsis gene expression is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for most Arabidopsis TFs, we lack knowledge about the presence, location, and transcriptional strength of their ADs. To address this gap, we experimentally identified Arabidopsis ADs on a proteome-wide scale, finding that over half of Arabidopsis TFs carry an AD. We annotated 1,553 ADs, the vast majority of which were previously unknown. We used the dataset generated to develop a neural network to accurately predict ADs and to identify sequence features necessary to recruit coactivator complexes. We uncovered six distinct sequence feature combinations that resulted in activation activity, providing a framework to interrogate activation domain sub-functionalization. Furthermore, we identified activation domains within the ancient AUXIN RESPONSE FACTOR (ARF) family of transcription factors, finding conservation of AD positioning in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examination of function within intrinsically disordered regions, and a predictive model of activation domains.
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Overall design |
Arabidopsis TFs (PADI), or ARF regions (ARF Evolution and Pilot) were fragmented into 40 amino acid tiles with a 10 amino acid step size were made as oligo pools and cloned into plasmid libraries. Yeast transformations ensured integration of a single synthetic TF, each expressing one tile, at the URA3 locus. TF activity was induced with beta-estradiol and TF activity was measured using cell sorting based on the ratio of reporter to synthetic TF (GFP:mcherry). The distribution of tiles across GFP:mCherry ratio bins was determined with Next-generation sequencing of the integrated TF. Median GFP:mcherry values were used to calculate activation domain scores.
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Contributor(s) |
Morffy N, Strader LC |
Citation(s) |
39020176 |
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Submission date |
Jun 06, 2023 |
Last update date |
Aug 11, 2024 |
Contact name |
Lucia C. Strader |
E-mail(s) |
lucia.strader@duke.edu
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Organization name |
Duke University
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Department |
Biology
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Lab |
Strader Lab
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Street address |
124 Science Drive 3332 French Family Science Center
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City |
Durham |
State/province |
NC |
ZIP/Postal code |
27708 |
Country |
USA |
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Platforms (2) |
GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
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Samples (164)
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GSM7457349 |
PADI Library 10, Bin 1 |
GSM7457350 |
PADI Library 10, Bin 2 |
GSM7457351 |
PADI Library 10, Bin 3 |
GSM7457352 |
PADI Library 10, Bin 4 |
GSM7457353 |
PADI Library 10, Bin 5 |
GSM7457354 |
PADI Library 10, Bin 6 |
GSM7457355 |
PADI Library 10, Bin 7 |
GSM7457356 |
PADI Library 10, Bin 8 |
GSM7457357 |
PADI Library 10, Bin 9 |
GSM7457358 |
PADI Library 1, Bin 10 |
GSM7457359 |
ARF Evolution Library, Bin 10 |
GSM7457360 |
ARF Evolution Library, Bin 11 |
GSM7457361 |
ARF Evolution Library, Bin 12 |
GSM7457362 |
PADI Library 1, Bin 11 |
GSM7457363 |
ARF Evolution Library, Bin 1 |
GSM7457364 |
PADI Library 1, Bin 12 |
GSM7457365 |
ARF Evolution Library, Bin 2 |
GSM7457366 |
ARF Evolution Library, Bin 3 |
GSM7457367 |
ARF Evolution Library, Bin 4 |
GSM7457368 |
ARF Evolution Library, Bin 5 |
GSM7457369 |
ARF Evolution Library, Bin 6 |
GSM7457370 |
ARF Evolution Library, Bin 7 |
GSM7457371 |
ARF Evolution Library, Bin 8 |
GSM7457372 |
ARF Evolution Library, Bin 9 |
GSM7457373 |
PADI Library 1, Bin 1 |
GSM7457374 |
PADI Library 1, Bin 2 |
GSM7457375 |
PADI Library 1, Bin 3 |
GSM7457376 |
PADI Library 1, Bin 4 |
GSM7457377 |
PADI Library 1, Bin 5 |
GSM7457378 |
PADI Library 1, Bin 6 |
GSM7457379 |
PADI Library 1, Bin 7 |
GSM7457380 |
PADI Library 1, Bin 8 |
GSM7457381 |
PADI Library 1, Bin 9 |
GSM7457382 |
PADI Library 2, Bin 10 |
GSM7457383 |
PADI Library 2, Bin 11 |
GSM7457384 |
PADI Library 2, Bin 12 |
GSM7457385 |
PADI Library 2, Bin 1 |
GSM7457386 |
PADI Library 2, Bin 2 |
GSM7457387 |
PADI Library 2, Bin 3 |
GSM7457388 |
PADI Library 2, Bin 4 |
GSM7457389 |
PADI Library 2, Bin 5 |
GSM7457390 |
PADI Library 2, Bin 6 |
GSM7457391 |
PADI Library 2, Bin 7 |
GSM7457392 |
PADI Library 2, Bin 8 |
GSM7457393 |
PADI Library 2, Bin 9 |
GSM7457394 |
PADI Library 3, Bin 10 |
GSM7457395 |
PADI Library 3, Bin 11 |
GSM7457396 |
PADI Library 3, Bin 12 |
GSM7457397 |
PADI Library 3, Bin 1 |
GSM7457398 |
PADI Library 3, Bin 2 |
GSM7457399 |
PADI Library 3, Bin 3 |
GSM7457400 |
PADI Library 3, Bin 4 |
GSM7457401 |
PADI Library 3, Bin 5 |
GSM7457402 |
PADI Library 3, Bin 6 |
GSM7457403 |
PADI Library 3, Bin 7 |
GSM7457404 |
PADI Library 3, Bin 8 |
GSM7457405 |
PADI Library 3, Bin 9 |
GSM7457406 |
PADI Library 4, Bin 10 |
GSM7457407 |
PADI Library 4, Bin 11 |
GSM7457408 |
PADI Library 4, Bin 12 |
GSM7457409 |
PADI Library 4, Bin 1 |
GSM7457410 |
PADI Library 4, Bin 2 |
GSM7457411 |
PADI Library 4, Bin 3 |
GSM7457412 |
PADI Library 4, Bin 4 |
GSM7457413 |
PADI Library 4, Bin 5 |
GSM7457414 |
PADI Library 4, Bin 6 |
GSM7457415 |
PADI Library 4, Bin 7 |
GSM7457416 |
PADI Library 4, Bin 8 |
GSM7457417 |
PADI Library 4, Bin 9 |
GSM7457418 |
PADI Library 5, Bin 10 |
GSM7457419 |
PADI Library 5, Bin 11 |
GSM7457420 |
PADI Library 5, Bin 12 |
GSM7457421 |
PADI Library 5, Bin 1 |
GSM7457422 |
PADI Library 5, Bin 2 |
GSM7457423 |
PADI Library 5, Bin 3 |
GSM7457424 |
PADI Library 5, Bin 4 |
GSM7457425 |
PADI Library 5, Bin 5 |
GSM7457426 |
PADI Library 5, Bin 6 |
GSM7457427 |
PADI Library 5, Bin 7 |
GSM7457428 |
PADI Library 5, Bin 8 |
GSM7457429 |
PADI Library 5, Bin 9 |
GSM7457430 |
PADI Library 6, Bin 10 |
GSM7457431 |
PADI Library 6, Bin 11 |
GSM7457432 |
PADI Library 6, Bin 12 |
GSM7457433 |
PADI Library 6, Bin 1 |
GSM7457434 |
PADI Library 6, Bin 2 |
GSM7457435 |
PADI Library 6, Bin 3 |
GSM7457436 |
PADI Library 6, Bin 4 |
GSM7457437 |
PADI Library 6, Bin 5 |
GSM7457438 |
PADI Library 6, Bin 6 |
GSM7457439 |
PADI Library 6, Bin 7 |
GSM7457440 |
PADI Library 6, Bin 8 |
GSM7457441 |
PADI Library 6, Bin 9 |
GSM7457442 |
PADI Library 7, Bin 10 |
GSM7457443 |
PADI Library 7, Bin 11 |
GSM7457444 |
PADI Library 7, Bin 12 |
GSM7457445 |
PADI Library 7, Bin 1 |
GSM7457446 |
PADI Library 7, Bin 2 |
GSM7457447 |
PADI Library 7, Bin 3 |
GSM7457448 |
PADI Library 7, Bin 4 |
GSM7457449 |
PADI Library 7, Bin 5 |
GSM7457450 |
PADI Library 7, Bin 6 |
GSM7457451 |
PADI Library 7, Bin 7 |
GSM7457452 |
PADI Library 7, Bin 8 |
GSM7457453 |
PADI Library 7, Bin 9 |
GSM7457454 |
PADI Library 9, Bin 10 |
GSM7457455 |
PADI Library 9, Bin 11 |
GSM7457456 |
PADI Library 9, Bin 12 |
GSM7457457 |
PADI Library 9, Bin 1 |
GSM7457458 |
PADI Library 9, Bin 2 |
GSM7457459 |
PADI Library 9, Bin 3 |
GSM7457460 |
PADI Library 9, Bin 4 |
GSM7457461 |
PADI Library 9, Bin 5 |
GSM7457462 |
PADI Library 9, Bin 6 |
GSM7457463 |
PADI Library 9, Bin 7 |
GSM7457464 |
PADI Library 9, Bin 8 |
GSM7457465 |
PADI Library 9, Bin 9 |
GSM7457466 |
GFP-Only Library, Bin 1 |
GSM7457467 |
GFP-Only Library, Bin 2 |
GSM7457468 |
GFP-Only Library, Bin 3 |
GSM7457469 |
GFP-Only Library, Bin 4 |
GSM7457470 |
GFP-Only Library, Bin 5 |
GSM7457471 |
GFP-Only Library, Bin 6 |
GSM7457472 |
mCherry-Only Library, Bin 1 |
GSM7457473 |
mCherry-Only Library, Bin 2 |
GSM7457474 |
mCherry-Only Library, Bin 3 |
GSM7457475 |
mCherry-Only Library, Bin 4 |
GSM7457476 |
mCherry-Only Library, Bin 5 |
GSM7457477 |
mCherry-Only Library, Bin 6 |
GSM7457478 |
PADI Library 8, Bin 10 |
GSM7457479 |
PADI Library 8, Bin 11 |
GSM7457480 |
PADI Library 8, Bin 12 |
GSM7457481 |
PADI Library 8, Bin 1 |
GSM7457482 |
PADI Library 8, Bin 2 |
GSM7457483 |
PADI Library 8, Bin 3 |
GSM7457484 |
PADI Library 8, Bin 4 |
GSM7457485 |
PADI Library 8, Bin 5 |
GSM7457486 |
PADI Library 8, Bin 6 |
GSM7457487 |
PADI Library 8, Bin 7 |
GSM7457488 |
PADI Library 8, Bin 8 |
GSM7457489 |
PADI Library 8, Bin 9 |
GSM7457490 |
Pilot Library, Bin 1 |
GSM7457491 |
Pilot Library, Bin 2 |
GSM7457492 |
Pilot Library, Bin 3 |
GSM7457493 |
Pilot Library, Bin 4 |
GSM7457494 |
Pilot Library, Bin 5 |
GSM7457495 |
Pilot Library, Bin 6 |
GSM7457496 |
Pilot Library, Bin 7 |
GSM7457497 |
Pilot Library, Bin 8 |
GSM7920223 |
PADI Library Replicate 3B, Bin 1 |
GSM7920224 |
PADI Library Replicate 3B, Bin 10 |
GSM7920225 |
PADI Library Replicate 3B, Bin 11 |
GSM7920226 |
PADI Library Replicate 3B, Bin 12 |
GSM7920227 |
PADI Library Replicate 3B, Bin 2 |
GSM7920228 |
PADI Library Replicate 3B, Bin 3 |
GSM7920229 |
PADI Library Replicate 3B, Bin 4 |
GSM7920230 |
PADI Library Replicate 3B, Bin 5 |
GSM7920231 |
PADI Library Replicate 3B, Bin 6 |
GSM7920232 |
PADI Library Replicate 3B, Bin 7 |
GSM7920233 |
PADI Library Replicate 3B, Bin 8 |
GSM7920234 |
PADI Library Replicate 3B, Bin 9 |
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Relations |
BioProject |
PRJNA980550 |
Supplementary file |
Size |
Download |
File type/resource |
GSE234215_RAW.tar |
54.3 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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