| Sonstiges: |
- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article; Research Support, Non-U.S. Gov't
- Language: English
- [Nat Plants] 2023 Mar; Vol. 9 (3), pp. 473-485. <i>Date of Electronic Publication: </i>2023 Feb 16.
- MeSH Terms: Plant Proteins* / genetics ; Plant Proteins* / metabolism ; MADS Domain Proteins* / genetics ; MADS Domain Proteins* / metabolism ; Flowers ; Transcription Factors / genetics ; Transcription Factors / metabolism ; DNA / metabolism ; Gene Expression Regulation, Plant
- References: Ludwig, L. S. et al. Transcriptional states and chromatin accessibility underlying human erythropoiesis. Cell Rep. 27, 3228–3240.e7 (2019). (PMID: 31189107657911710.1016/j.celrep.2019.05.046) ; Argelaguet, R. et al. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature 576, 487–491 (2019). (PMID: 31827285692499510.1038/s41586-019-1825-8) ; Pawlak, M. et al. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome Res. 29, 506–519 (2019). (PMID: 30760547639641210.1101/gr.244491.118) ; Ibarra, I. L. et al. Mechanistic insights into transcription factor cooperativity and its impact on protein–phenotype interactions. Nat. Commun. 11, 124 (2020). (PMID: 31913281694924210.1038/s41467-019-13888-7) ; Slattery, M. et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147, 1270–1282 (2011). (PMID: 22153072331906910.1016/j.cell.2011.10.053) ; Smaczniak, C., Muiño, J. M., Chen, D., Angenent, G. C. & Kaufmann, K. Differences in DNA binding specificity of floral homeotic protein complexes predict organ-specific target genes. Plant Cell 29, 1822–1835 (2017). (PMID: 28733422559050310.1105/tpc.17.00145) ; Smaczniak, C., Immink, R. G. H., Angenent, G. C. & Kaufmann, K. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139, 3081–3098 (2012). (PMID: 2287208210.1242/dev.074674) ; Schwarz-Sommer, Z. et al. Characterization of the Antirrhinum floral homeotic MADS-box gene deficiens: evidence for DNA binding and autoregulation of its persistent expression throughout flower development. EMBO J. 11, 251–263 (1992). (PMID: 134676055644610.1002/j.1460-2075.1992.tb05048.x) ; Huang, H. et al. DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation. Plant Cell 8, 81–94 (1996). (PMID: 8597661161083) ; de Folter, S. et al. Comprehensive interaction map of the Arabidopsis MADS box transcription factors. Plant Cell 17, 1424–1433 (2005). (PMID: 15805477109176510.1105/tpc.105.031831) ; Folter, Sde & Angenent, G. C. trans meets cis in MADS science. Trends Plant Sci. 11, 224–231 (2006). (PMID: 1661658110.1016/j.tplants.2006.03.008) ; Theißen, G. Development of floral organ identity: stories from the MADS house. Curr. Opin. Plant Biol. 4, 75–85 (2001). (PMID: 1116317210.1016/S1369-5266(00)00139-4) ; Airoldi, C. A., Bergonzi, S. & Davies, B. Single amino acid change alters the ability to specify male or female organ identity. Proc. Natl Acad. Sci. USA 107, 18898–18902 (2010). (PMID: 20956314297388010.1073/pnas.1009050107) ; Que, K. et al. Regulatory switch enforced by basic helix–loop–helix and ACT-domain mediated dimerizations of the maize transcription factor R. Proc. Natl Acad. Sci. USA 109, E2091–E2097 (2012). ; Camille, S. et al. A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science 343, 645–648 (2014). (PMID: 10.1126/science.1248229) ; Lai, X. et al. The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors. Nat. Commun. 12, 4760 (2021). (PMID: 34362909834651710.1038/s41467-021-24978-w) ; Bemer, M. et al. FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture. J. Exp. Bot. 68, 3391–3403 (2017). (PMID: 28586421585340110.1093/jxb/erx184) ; Mandel, M. A. & Yanofsky, M. F. The Arabidopsis AGL8 MADS box gene is expressed in inflorescence meristems and is negatively regulated by APETALA1. Plant Cell 7, 1763–1771 (1995). (PMID: 8535133161036) ; Hempel, F. D. et al. Floral determination and expression of floral regulatory genes in Arabidopsis. Development 124, 3845–3853 (1997). (PMID: 936744010.1242/dev.124.19.3845) ; Ferrandiz, C., Gu, Q., Martienssen, R. & Yanofsky, M. F. Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development 127, 725–734 (2000). (PMID: 1064823110.1242/dev.127.4.725) ; Balanzà, V., Martínez-Fernández, I. & Ferrándiz, C. Sequential action of FRUITFULL as a modulator of the activity of the floral regulators SVP and SOC1. J. Exp. Bot. 65, 1193–1203 (2014). (PMID: 24465009393557410.1093/jxb/ert482) ; Balanzà, V. et al. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat. Commun. 9, 565 (2018). (PMID: 29422669580573510.1038/s41467-018-03067-5) ; Balanzà, V., Martínez-Fernández, I., Sato, S., Yanofsky, M. F. & Ferrándiz, C. Inflorescence meristem fate is dependent on seed development and FRUITFULL in Arabidopsis thaliana. Front. Plant Sci. 10, 1622 (2019). (PMID: 31921264693024010.3389/fpls.2019.01622) ; Ferrándiz, C., Liljegren, S. J. & Yanofsky, M. F. Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development. Science 289, 436–438 (2000). (PMID: 1090320110.1126/science.289.5478.436) ; Liljegren, S. J. et al. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature 404, 766–770 (2000). (PMID: 1078389010.1038/35008089) ; Roeder, A. H. K., Ferrándiz, C. & Yanofsky, M. F. The role of the REPLUMLESS homeodomain protein in patterning the Arabidopsis fruit. Curr. Biol. 13, 1630–1635 (2003). (PMID: 1367859510.1016/j.cub.2003.08.027) ; Liljegren, S. J. et al. Control of fruit patterning in Arabidopsis by INDEHISCENT. Cell 116, 843–853 (2004). (PMID: 1503598610.1016/S0092-8674(04)00217-X) ; Gu, Q., Ferrandiz, C., Yanofsky, M. F. & Martienssen, R. The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Development 125, 1509–1517 (1998). (PMID: 950273210.1242/dev.125.8.1509) ; Di Marzo, M. et al. SEEDSTICK controls Arabidopsis fruit size by regulating cytokinin levels and FRUITFULL. Cell Rep. 30, 2846–2857.e3 (2020). (PMID: 3210175610.1016/j.celrep.2020.01.101) ; José Ripoll, J. et al. microRNA regulation of fruit growth. Nat. Plants 1, 15036 (2015). (PMID: 2724703610.1038/nplants.2015.36) ; Smaczniak, C. et al. Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc. Natl Acad. Sci. USA 109, 1560–1565 (2012). (PMID: 22238427327718110.1073/pnas.1112871109) ; Smyth, D. R., Bowman, J. L. & Meyerowitz, E. M. Early flower development in Arabidopsis. Plant Cell 2, 755–767 (1990). (PMID: 2152125159928) ; Sudre, D. et al. Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an Arabidopsis ferritin mutant. J. Exp. Bot. 64, 2665–2688 (2013). (PMID: 23682113369794610.1093/jxb/ert112) ; Carbonell-Bejerano, P., Urbez, C., Carbonell, J., Granell, A. & Perez-Amador, M. A. A fertilization-independent developmental program triggers partial fruit development and senescence processes in pistils of Arabidopsis. Plant Physiol. 154, 163–172 (2010). (PMID: 20625003293816410.1104/pp.110.160044) ; Marsch-Martínez, N. & de Folter, S. Hormonal control of the development of the gynoecium. Curr. Opin. Plant Biol. 29, 104–114 (2016). (PMID: 2679913210.1016/j.pbi.2015.12.006) ; Kashkan, I. et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. N. Phytol. 233, 329–343 (2022). (PMID: 10.1111/nph.17792) ; Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J. L. & Meyerowitz, E. M. Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet. 2, e117 (2006). (PMID: 16789830152324710.1371/journal.pgen.0020117) ; Urbanus, S. L. et al. In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana. BMC Plant Biol. 9, 5 (2009). (PMID: 19138429263093010.1186/1471-2229-9-5) ; Muiño, J. M., Kaufmann, K., van Ham, R. C. H. J., Angenent, G. C. & Krajewski, P. ChIP–seq analysis in R (CSAR): an R package for the statistical detection of protein-bound genomic regions. Plant Methods 7, 11 (2011). (PMID: 21554688311401710.1186/1746-4811-7-11) ; Kaufmann, K. et al. Orchestration of floral initiation by APETALA1. Science 328, 85–89 (2010). (PMID: 2036010610.1126/science.1185244) ; Gregis, V. et al. Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis. Genome Biol. 14, R56 (2013). (PMID: 23759218370684510.1186/gb-2013-14-6-r56) ; Pajoro, A. et al. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 15, R41 (2014). (PMID: 24581456405484910.1186/gb-2014-15-3-r41) ; Akiva, S.-K. et al. The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development. Proc. Natl Acad. Sci. USA 116, 16127–16136 (2019). (PMID: 10.1073/pnas.1906405116) ; van Gelderen, K., van Rongen, M., Liu, A., Otten, A. & Offringa, R. An INDEHISCENT-controlled auxin response specifies the separation layer in early Arabidopsis fruit. Mol. Plant 9, 857–869 (2016). (PMID: 2699529610.1016/j.molp.2016.03.005) ; Yanofsky, M. F. et al. The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346, 35–39 (1990). (PMID: 197326510.1038/346035a0) ; Aichinger, E. et al. CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. PLoS Genet. 5, e1000605 (2009). (PMID: 19680533271883010.1371/journal.pgen.1000605) ; Li, G. et al. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J. 78, 706–714 (2014). (PMID: 2460621210.1111/tpj.12499) ; Yamaguchi, N. et al. Chromatin-mediated feed-forward auxin biosynthesis in floral meristem determinacy. Nat. Commun. 9, 5290 (2018). (PMID: 30538233628999610.1038/s41467-018-07763-0) ; Jolma, A. et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20, 861–873 (2010). (PMID: 20378718287758210.1101/gr.100552.109) ; Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. The MEME Suite. Nuceic Acids Res. https://doi.org/10.1093/nar/gkv416 (2015). ; Muiño, J. M., Smaczniak, C., Angenent, G. C., Kaufmann, K. & Van Dijk, A. D. J. Structural determinants of DNA recognition by plant MADS-domain transcription factors. Nucleic Acids Res. 42, 2138–2146 (2014). (PMID: 2427549210.1093/nar/gkt1172) ; Avila Cobos, F., Alquicira-Hernandez, J., Powell, J. E., Mestdagh, P. & De Preter, K. Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat. Commun. 11, 5650 (2020). (PMID: 33159064764864010.1038/s41467-020-19015-1) ; Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453–457 (2015). (PMID: 25822800473964010.1038/nmeth.3337) ; Eeckhoute, J., Métivier, R. & Salbert, G. Defining specificity of transcription factor regulatory activities. J. Cell Sci. 122, 4027–4034 (2009). (PMID: 1991049410.1242/jcs.054916) ; Jana, T., Brodsky, S. & Barkai, N. Speed-specificity trade-offs in the transcription factors search for their genomic binding sites. Trends Genet. 37, 421–432 (2021). (PMID: 3341401310.1016/j.tig.2020.12.001) ; Immink, R. G. H. et al. SEPALLATA3: the ‘glue’ for MADS box transcription factor complex formation. Genome Biol. 10, R24 (2009). (PMID: 19243611268827410.1186/gb-2009-10-2-r24) ; Gregis, V., Sessa, A., Dorca-Fornell, C. & Kater, M. M. The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes. Plant J. 60, 626–637 (2009). (PMID: 1965634310.1111/j.1365-313X.2009.03985.x) ; Alvarez-Buylla, E. R. et al. Flower development. Arab. B. 8, e0127 (2010). (PMID: 10.1199/tab.0127) ; Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). (PMID: 24695404410359010.1093/bioinformatics/btu170) ; Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). (PMID: 2310488610.1093/bioinformatics/bts635) ; Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014). (PMID: 2422767710.1093/bioinformatics/btt656) ; Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014). (PMID: 25516281430204910.1186/s13059-014-0550-8) ; Van Mourik, H., Muiño, J. M., Pajoro, A., Angenent, G. C. & Kaufmann, K. Characterization of in vivo DNA-binding events of plant transcription factors by ChIP–seq: experimental protocol and computational analysis. Methods Mol. Biol. 1284, 93–121 (2015). (PMID: 2575776910.1007/978-1-4939-2444-8_5) ; Kaufmann, K. et al. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP–seq) or hybridization to whole genome arrays (ChIP–ChIP). Nat. Protoc. 5, 457–472 (2010). (PMID: 2020366310.1038/nprot.2009.244) ; Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009). (PMID: 19451168270523410.1093/bioinformatics/btp324) ; Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010). (PMID: 20110278283282410.1093/bioinformatics/btq033) ; Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008). (PMID: 1902991010.1038/nbt.1511) ; Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011). (PMID: 2125476010.1021/pr101065j) ; Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016). (PMID: 2734871210.1038/nmeth.3901) ; Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020). (PMID: 3188299310.1093/bioinformatics/btz931) ; Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009). (PMID: 1949793310.1093/bioinformatics/btp336) ; Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003). (PMID: 1253823810.1093/bioinformatics/19.2.185)
- Substance Nomenclature: 0 (Plant Proteins) ; 0 (MADS Domain Proteins) ; 0 (Transcription Factors) ; 9007-49-2 (DNA)
- Entry Date(s): Date Created: 20230216 Date Completed: 20230322 Latest Revision: 20230516
- Update Code: 20240513
|
