Transcriptional Modulation during Photomorphogenesis in Rice Seedlings
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material, Growth Conditions, and Treatment
2.2. Sample Preparation and Sequencing
2.3. RNA-seq Data Analysis
2.4. Functional Annotation
2.5. Alternative Splicing Analysis
2.6. Prediction of Long Non-Coding RNA (lncRNA)
3. Results
3.1. Light-Mediated Differential Gene Expression during Photomorphogenesis
3.2. Gene Function and Pathway Enrichment Analyses
3.3. Identifying Light-Regulated Transcription Factors
3.4. Transcript Splicing during Photomorphogenesis
3.5. Light-Mediated Shift in Gene Expression and Splicing Events
3.5.1. Circadian Clock Pathway Genes
3.5.2. MVA and MEP Pathway Genes
3.6. lncRNA Discovery and Splicing during Photomorphogenesis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Members of light-regulated transcription factor gene families | |||||
---|---|---|---|---|---|
Gene family | Upregulated | Downregulated | Gene family | Upregulated | Downregulated |
ABI3VP1 | 6 | 4 | GRF | 1 | 2 |
Alfin-like | 1 | 4 | HB | 21 | 24 |
AP2-EREBP | 23 | 32 | HSF | 3 | 10 |
ARF | 8 | 8 | LIM | 2 | 1 |
ARR-B | 1 | 4 | LOB | 2 | 1 |
BBR-BPC | 0 | 1 | MADS | 6 | 5 |
BES1 | 0 | 3 | mTERF | 9 | 4 |
bHLH | 19 | 27 | MYB | 28 | 14 |
BSD | 1 | 6 | MYB-related | 16 | 25 |
bZIP | 10 | 27 | NAC | 21 | 19 |
C2C2-CO-like | 4 | 7 | OFP | 2 | 1 |
C2C2-Dof | 5 | 4 | Orphans | 20 | 10 |
C2C2-GATA | 7 | 4 | PBF-2-like | 1 | 0 |
C2C2-YABBY | 3 | 1 | PLATZ | 1 | 4 |
C2H2 | 14 | 19 | RWP-RK | 4 | 2 |
C3H | 16 | 24 | S1Fa-like | 1 | 1 |
CAMTA | 0 | 3 | SBP | 3 | 5 |
CCAAT | 9 | 11 | Sigma 70-like | 4 | 0 |
CPP | 1 | 4 | SRS | 1 | 0 |
CSD | 0 | 1 | TAZ | 1 | 1 |
DBP | 2 | 3 | TCP | 4 | 6 |
E2F/DP | 2 | 1 | Tify | 6 | 2 |
EIL | 1 | 1 | Trihelix | 3 | 9 |
FAR1 | 5 | 10 | TUB | 2 | 5 |
FHA | 7 | 6 | ULT | 1 | 0 |
G2-like | 9 | 5 | VOZ | 0 | 2 |
GeBP | 0 | 3 | WRKY | 22 | 10 |
GRAS | 8 | 7 | zf-HD | 5 | 3 |
Members of other transcriptional regulator gene families | |||||
Gene family | Upregulated | Downregulated | Gene family | Upregulated | Downregulated |
ARID | 2 | 1 | PHD | 12 | 22 |
AUX/IAA | 3 | 19 | Pseudo ARR-B | 2 | 1 |
Coactivator p15 | 0 | 1 | RB | 0 | 1 |
DDT | 3 | 0 | Rcd1-like | 0 | 2 |
GNAT | 12 | 8 | SET | 11 | 6 |
HMG | 4 | 5 | SNF2 | 11 | 9 |
Jumonji | 4 | 5 | SOH1 | 0 | 2 |
LUG | 0 | 2 | SWI/SNF-BAF60b | 4 | 4 |
MBF1 | 0 | 1 | SWI/SNF-SWI3 | 2 | 1 |
MED6 | 0 | 1 | TRAF | 7 | 11 |
Chromosome # | Treatment | SpliceGrapher Prediction | IsoLasso | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Genes | IR | ES | Alt5’ | Alt3’ | Genes | IR | ES | Alt5’ | Alt3’ | ||
1 | Dark | 924 | 897 | 214 | 163 | 97 | 939 | 925 | 214 | 181 | 99 |
Light | 1028 | 994 | 264 | 184 | 109 | 1048 | 1021 | 264 | 191 | 112 | |
2 | Dark | 747 | 728 | 224 | 167 | 109 | 771 | 781 | 227 | 189 | 117 |
Light | 802 | 777 | 219 | 153 | 99 | 822 | 812 | 222 | 165 | 103 | |
3 | Dark | 825 | 797 | 216 | 136 | 94 | 858 | 868 | 216 | 162 | 120 |
Light | 945 | 893 | 219 | 143 | 98 | 960 | 920 | 219 | 153 | 118 | |
4 | Dark | 565 | 551 | 182 | 112 | 64 | 581 | 576 | 183 | 117 | 67 |
Light | 596 | 572 | 193 | 104 | 61 | 611 | 592 | 194 | 109 | 66 | |
5 | Dark | 519 | 503 | 139 | 139 | 70 | 538 | 534 | 140 | 114 | 75 |
Light | 552 | 537 | 144 | 103 | 80 | 562 | 550 | 144 | 109 | 92 | |
6 | Dark | 509 | 459 | 186 | 128 | 62 | 527 | 493 | 186 | 135 | 64 |
Light | 531 | 501 | 169 | 103 | 63 | 554 | 535 | 169 | 109 | 67 | |
7 | Dark | 466 | 432 | 166 | 77 | 48 | 482 | 468 | 166 | 85 | 51 |
Light | 481 | 473 | 129 | 72 | 52 | 498 | 498 | 129 | 82 | 56 | |
8 | Dark | 400 | 390 | 97 | 63 | 62 | 415 | 416 | 98 | 68 | 64 |
Light | 463 | 433 | 134 | 62 | 84 | 475 | 457 | 134 | 67 | 87 | |
9 | Dark | 341 | 342 | 79 | 53 | 32 | 349 | 359 | 79 | 64 | 37 |
Light | 375 | 361 | 118 | 49 | 38 | 382 | 377 | 118 | 53 | 39 | |
10 | Dark | 290 | 275 | 94 | 43 | 29 | 295 | 288 | 94 | 49 | 36 |
Light | 308 | 295 | 102 | 61 | 32 | 314 | 307 | 102 | 65 | 35 | |
11 | Dark | 304 | 266 | 113 | 49 | 35 | 313 | 278 | 113 | 53 | 36 |
Light | 363 | 306 | 150 | 51 | 35 | 374 | 325 | 150 | 57 | 37 | |
12 | Dark | 324 | 310 | 117 | 69 | 45 | 329 | 315 | 117 | 74 | 46 |
Light | 365 | 347 | 150 | 63 | 53 | 372 | 359 | 155 | 68 | 61 |
Known Spliced Genes | Spliced in | Light Regulation | Gene Description |
---|---|---|---|
Os01g0619000 | Dark, Light | Down | RNA recognition motif domain-containing protein |
Os01g0649900 | Dark, Light | - | GDSL esterase/lipase protein 20 |
Os01g0764000 | Dark, Light | Up | PHI glutathione s-transferase 2 |
Os01g0834400 | Dark | - | HAP3A subunit of CCAAT-box binding complex |
Os02g0122800 | Dark, Light | Down | Similar to Arginine/serine-rich splicing factor |
Os02g0130600 | Dark | Up | Conserved hypothetical protein |
Os02g0161900 | Dark, Light | Down | Rice ubiquitin2 |
Os02g0197900 | Dark, Light | Down | OsSTA53 |
Os02g0274900 | Dark, Light | Up | Similar to metabolite transport protein CSBC |
Os02g0577100 | Dark, Light | Down | Zinc finger, RING/PHD-type domain containing protein |
Os02g0666200 | Light | Down | Aquaporin |
Os02g0834000 | Dark, Light | Up | Rac-like GTP-binding protein 5 |
Os02g0291000 | - | Down | Calcineurin B-like protein 7 |
Os02g0291400 | - | - | Calcineurin B-like protein 8 |
Os02g0823100 | - | Up | Plasma membrane intrinsic protein 1;3 |
Os03g0265600 | Dark, Light | Down | Transformer-2-like protein |
Os03g0314100 | Dark, Light | Down | DEAD-like helicase |
Os03g0395900 | Dark, Light | Down | Splicing factor |
Os03g0670700 | Dark, Light | Down | Glycine-rich RNA-binding protein 3 |
Os03g0698500 | Dark, Light | Down | Similar to Yippee-like protein 3 |
Os03g0745000 | Dark, Light | - | Heat stress transcription factor A-2a |
Os03g0717600 | - | Down | Zinc finger, C2H2-type |
Os04g0115400 | Dark, Light | Down | D111/G-patch domain containing protein |
Os04g0649100 | Dark, Light | - | Shattering abortion 1 |
Os04g0656100 | Light | Down | H+-ATPase |
Os04g0665800 | Dark, Light | Up | Similar to H1005F08.12 protein |
Os04g0402300 | - | - | Cysteine-type peptidase |
Os04g0479200 | - | Up | Similar to NAD-dependent isocitrate dehydrogenase c;1 |
Os05g0348100 | Dark | Up | Similar to CRR23 (chlororespiratory reduction 23) |
Os05g0463800 | Dark, Light | Down | HAP3C subunit of CCAAT-box binding complex |
Os05g0554400 | Dark, Light | Down | Phosphatidyl serine synthase family protein |
Os05g0574700 | Dark, Light | - | Similar to cDNA clone:002-182-C01 |
Os05g0534400 | - | Up | Calcineurin B-like protein 4 |
Os05g0548900 | - | Up | Phosphoethanolamine N-Methyltransferase 2 |
Os06g0172800 | Light | - | Similar to alkaline alpha galactosidase 2 |
Os06g0651600 | Dark, Light | Down | Protein phosphatase 2C58 |
Os06g0727200 | Dark | Down | Catalase B |
Os06g0128500 | - | Up | Ribosomal protein L47, mitochondrial family protein |
Os06g0133000 | - | - | Glutinous endosperm, waxy |
Os06g0506600 | - | - | Ubiquitin-conjugating enzyme 17 |
Os07g0490400 | Dark, Light | Up | FK506 binding protein 20-2 |
Os07g0574800 | - | Up | Tubulin alpha-1 chain |
Os07g0613300 | - | - | Similar to PAUSED |
Os08g0191600 | Dark, Light | Up | Autophagy associated gene 8C |
Os08g0530400 | Dark, Light | Up | Moco containing protein, similar to sulfite oxidase |
Os08g0436200 | - | - | Zinc finger, RING/PHD-type domain containing protein |
Os10g0115600 | Dark, Light | Down | U1 snRNP 70K |
Os10g0535800 | Dark, Light | - | Cys-rich domain containing protein |
Os10g0564900 | Dark | Down | Similar to protein kinase CK2 regulatory subunit CK2B2 |
Os10g0567400 | Dark, Light | Up | Chlorophyll a oxygenase 1 |
Os10g0577900 | Dark, Light | - | Glycerol-3-phosphate acyltransferase |
Os10g0411500 | - | Down | Q calmodulin-binding region domain containing protein |
Os11g0157100 | Dark, Light | Down | Cyclin-T1-4 |
Os11g0700500 | Dark | - | MybAS1 |
Os11g0600700 | - | Up | Zinc finger, RING domain protein |
Os12g0567300 | Dark | Up | MybAS2, R2R3-Myb |
Os12g0632000 | Dark, Light | Down | Glycine-rich Protein GRP162 |
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Gupta, P.; Jaiswal, P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes 2024, 15, 1072. https://doi.org/10.3390/genes15081072
Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes. 2024; 15(8):1072. https://doi.org/10.3390/genes15081072
Chicago/Turabian StyleGupta, Parul, and Pankaj Jaiswal. 2024. "Transcriptional Modulation during Photomorphogenesis in Rice Seedlings" Genes 15, no. 8: 1072. https://doi.org/10.3390/genes15081072