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| Status |
Public on Mar 09, 2009 |
| Title |
Genome-wide characterization of light-inducible responses reveals a hierarchical light-sensing cascade in N. crassa |
| Organism |
Neurospora crassa |
| Experiment type |
Expression profiling by array
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| Summary |
To better understand the roles of WC-1, WC-2 and other putative photoreceptors in mediation of light signals and to identify new components in light sensing cascades, we used microarrays with genome-wide coverage to characterize light-inducible transcriptional changes in Neurospora crassa. After unsupervised hierarchical clustering of 90 microarrays, 316 genes, representing about 3.21% of the total genome, showed robust and consistent light responses. As expected, WC-1 and WC-2 knockout strains both exhibited severe impairments in response to a continuous white light stimulus, confirming their dominant roles in light sensing cascades. Knockout strains of 5 newly-identified light-inducible transcription factors were further characterized for their potential function in mediating light signals. Interestingly, one early light-inducible transcription factor, Submerged Protoperithecia-1 (SUB-1), appeared to be essential in mediating a large number of late light response, providing a direct molecular connection between early and late light responses. Furthermore, a novel motif, which is overrepresented among late light responsive genes, was demonstrated to be necessary for full induction of late light responses in vivo. Taken together, these results reveal a simple hierarchical light-sensing cascade in Neurospora, which is initially invoked by light-activated White Collar Complex (WCC) binding to Light Response Elements (LREs) of the primary target genes, including SUB-1. Subsequently, the induction of SUB-1 and other activators activate downstream targets. Thus, light responses of well-defined timing and amplitude can be orchestrated to meet the differential needs of underlying biological processes.
Keywords: time course, light response
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| Overall design |
Two-color microarray, totally 135 arrays were used to characterize light response in different photoreceptor knockout strains. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.
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| Contributor(s) |
Chen C, Ringelberg CS, Gross RH, Loros J, Dunlap JC |
| Citation(s) |
19262566, 20305004 |
| |
| Submission date |
Aug 31, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Chen-Hui Chen |
| E-mail(s) |
chen-hui.chen@dartmouth.edu
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| Phone |
603-650-1120
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| Fax |
603-650-1233
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| Organization name |
Dartmouth College
|
| Department |
Genetics
|
| Lab |
Dunlap and Loros lab
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| Street address |
702 Remsen
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| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
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| Platforms (1) |
| GPL5796 |
FGSC-N. crassa-10918-NC_10/04/05 UCB_11k oligo array |
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| Samples (135)
|
| GSM226380 |
74A-LL15-1 |
| GSM226381 |
74A-LL30-1 |
| GSM226382 |
74A-LL45-1 |
| GSM226383 |
74A-LL60-1 |
| GSM226384 |
74A-LL90-1 |
| GSM226385 |
74A-LL120-1 |
| GSM226386 |
74A-LL240-1 |
| GSM226387 |
phy-1 KO-DD-1 |
| GSM226388 |
phy-1 KO-LL5-1 |
| GSM226389 |
phy-1 KO-LL10-1 |
| GSM226390 |
phy-1 KO-LL15-1 |
| GSM226391 |
phy-1 KO-LL30-1 |
| GSM226392 |
phy-1 KO-LL45-1 |
| GSM226393 |
phy-1 KO-LL60-1 |
| GSM226394 |
phy-1 KO-LL90-1 |
| GSM226395 |
phy-1 KO-LL120-1 |
| GSM226396 |
phy-1 KO-LL240-1 |
| GSM226397 |
phy-2 KO-DD-1 |
| GSM226398 |
phy-2 KO-LL5-1 |
| GSM226399 |
phy-2 KO-LL10-1 |
| GSM226400 |
phy-2 KO-LL15-1 |
| GSM226401 |
phy-2 KO-LL30-1 |
| GSM226402 |
phy-2 KO-LL45-1 |
| GSM226403 |
phy-2 KO-LL60-1 |
| GSM226404 |
phy-2 KO-LL90-1 |
| GSM226405 |
phy-2 KO-LL120-1 |
| GSM226406 |
phy-2 KO-LL240-1 |
| GSM226407 |
phy-1, phy-2 KO-DD-1 |
| GSM226408 |
phy-1, phy-2 KO-LL5-1 |
| GSM226409 |
phy-1, phy-2 KO-LL10-1 |
| GSM226410 |
phy-1, phy-2 KO-LL15-1 |
| GSM226411 |
phy-1, phy-2 KO-LL30-1 |
| GSM226412 |
phy-1, phy-2 KO-LL45-1 |
| GSM226413 |
phy-1, phy-2 KO-LL60-1 |
| GSM226414 |
phy-1, phy-2 KO-LL90-1 |
| GSM226415 |
phy-1, phy-2 KO-LL120-1 |
| GSM226416 |
phy-1, phy-2 KO-LL240-1 |
| GSM226417 |
frq7-DD-1 |
| GSM226418 |
frq7-LL5-1 |
| GSM226419 |
frq7-LL10-1 |
| GSM226420 |
frq7-LL15-1 |
| GSM226421 |
frq7-LL30-1 |
| GSM226422 |
frq7-LL45-1 |
| GSM226423 |
frq7-LL60-1 |
| GSM226424 |
frq7-LL90-1 |
| GSM226425 |
frq7-LL120-1 |
| GSM226426 |
frq7-LL240-1 |
| GSM226427 |
wc-1 KO-DD-1 |
| GSM226428 |
wc-1 KO-LL5-1 |
| GSM226429 |
wc-1 KO-LL10-1 |
| GSM226430 |
wc-1 KO-LL15-1 |
| GSM226431 |
wc-1 KO-LL30-1 |
| GSM226432 |
wc-1 KO-LL45-1 |
| GSM226433 |
wc-1 KO-LL60-1 |
| GSM226434 |
wc-1 KO-LL90-1 |
| GSM226435 |
wc-1 KO-LL120-1 |
| GSM226436 |
wc-1 KO-LL240-1 |
| GSM226437 |
wc-2 KO-DD-1 |
| GSM226438 |
wc-2 KO-LL5-1 |
| GSM226439 |
wc-2 KO-LL10-1 |
| GSM226440 |
wc-2 KO-LL15-1 |
| GSM226441 |
wc-2 KO-LL30-1 |
| GSM226442 |
wc-2 KO-LL45-1 |
| GSM226443 |
wc-2 KO-LL60-1 |
| GSM226444 |
wc-2 KO-LL90-1 |
| GSM226445 |
wc-2 KO-LL120-1 |
| GSM226446 |
wc-2 KO-LL240-1 |
| GSM226447 |
wc-1, wc-2 KO-DD-1 |
| GSM226448 |
wc-1, wc-2 KO-LL5-1 |
| GSM226449 |
wc-1, wc-2 KO-LL10-1 |
| GSM226450 |
wc-1, wc-2 KO-LL15-1 |
| GSM226451 |
wc-1, wc-2 KO-LL30-1 |
| GSM226452 |
wc-1, wc-2 KO-LL45-1 |
| GSM226453 |
wc-1, wc-2 KO-LL60-1 |
| GSM226454 |
wc-1, wc-2 KO-LL90-1 |
| GSM226455 |
wc-1, wc-2 KO-LL120-1 |
| GSM226456 |
wc-1, wc-2 KO-LL240-1 |
| GSM226457 |
74A-DD-2 |
| GSM226458 |
74A-DD5-1 |
| GSM226459 |
74A-DD10-1 |
| GSM226460 |
74A-DD15-1 |
| GSM226461 |
74A-DD30-1 |
| GSM226462 |
74A-DD45-1 |
| GSM226463 |
74A-DD60-1 |
| GSM226464 |
74A-DD90-1 |
| GSM226465 |
74A-DD120-1 |
| GSM226466 |
74A-DD240-1 |
| GSM226467 |
74A-DD-3 |
| GSM226468 |
74A-LL15-2 |
| GSM226469 |
74A-LL30-2 |
| GSM226470 |
74A-LL60-2 |
| GSM226471 |
74A-LL120-2 |
| GSM226472 |
T1 KO-DD-1 |
| GSM226473 |
T1 KO-LL15-1 |
| GSM226474 |
T1 KO-LL30-1 |
| GSM226475 |
T1 KO-LL60-1 |
| GSM226476 |
T1 KO-LL120-1 |
| GSM226477 |
T2 KO-DD-1 |
| GSM226478 |
T2 KO-LL15-1 |
| GSM226479 |
T2 KO-LL30-1 |
| GSM226480 |
T2 KO-LL60-1 |
| GSM226481 |
T2 KO-LL120-1 |
| GSM226482 |
T3 KO-DD-1 |
| GSM226483 |
T3 KO-LL15-1 |
| GSM226484 |
T3 KO-LL30-1 |
| GSM226485 |
T3 KO-LL60-1 |
| GSM226486 |
T3 KO-LL120-1 |
| GSM226487 |
T4 KO-DD-1 |
| GSM226488 |
T4 KO-LL15-1 |
| GSM226489 |
T4 KO-LL30-1 |
| GSM226490 |
T4 KO-LL60-1 |
| GSM226491 |
T4 KO-LL120-1 |
| GSM226492 |
T5 KO-DD-1 |
| GSM226493 |
T5 KO-LL15-1 |
| GSM226494 |
T5 KO-LL30-1 |
| GSM226495 |
T5 KO-LL60-1 |
| GSM226496 |
T5 KO-LL120-1 |
| GSM226497 |
cry KO-DD-1 |
| GSM226498 |
cry KO-LL15-1 |
| GSM226499 |
cry KO-LL30-1 |
| GSM226500 |
cry KO-LL60-1 |
| GSM226501 |
cry KO-LL120-1 |
| GSM226502 |
vvd KO-DD-1 |
| GSM226503 |
vvd KO-LL15-1 |
| GSM226504 |
vvd KO-LL30-1 |
| GSM226505 |
vvd KO-LL60-1 |
| GSM226506 |
vvd KO-LL120-1 |
| GSM226507 |
opsin KO-DD-1 |
| GSM226508 |
opsin KO-LL15-1 |
| GSM226509 |
opsin KO-LL30-1 |
| GSM226510 |
opsin KO-LL60-1 |
| GSM226511 |
opsin KO-LL120-1 |
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| Relations |
| BioProject |
PRJNA102345 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8932_RAW.tar |
99.1 Mb |
(http)(custom) |
TAR (of DAT) |
| Processed data included within Sample table |
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