PROTOCOL: Chromatin Immunoprecipitation from Arabidopsis Tissues

Yamaguchi, Nobutoshi; Winter, Cara M.; Wu, Miin-Feng; Kwon, Chang Seob; William, Dilusha A.; Wagner, Doris

doi:10.1199/tab.0170

Cited by 164 publications

(141 citation statements)

References 22 publications

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“…5F, region III), relative to surrounding locations. ACT2 and ZPR3 were also tested as negative and positive controls, respectively (26,27), and validated our results. Together these data demonstrate that REV represses MIR165/166 directly via a previously characterized conserved cis-element (25).…”

Section: Hd-zipiis and Hd-zipiiis Repress Mir165/166 Expression Via Asupporting

confidence: 71%

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Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity

Merelo

Ram

Caggiano

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

109

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A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial-abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets. T he morphogenesis of lateral organs in plants and animals is dependent on the specification of distinct cell types early in development. In particular, the correct patterning of adaxialabaxial tissues in plant organs such as leaves is critical for the generation of a lamina shape and the formation of a polar vascular system (1-4). Adaxial-abaxial cell-type patterning in turn depends on the restricted expression of several genes known to specify these cell types, including the class III homeodomain leucine zipper genes (HD-ZIPIIIs), KANADI genes, HD-ZIPIIs, and microRNA (MIR)165/166 (1, 2, 4-11). In general, genetic analyses have indicated that adaxial and abaxial factors act oppositely in organ patterning (1,2,4,(8)(9)(10)(11). Hence, loss-of-function mutations in genes promoting adaxial cell identity typically cause an abaxialized phenotype that correlates with the ectopic expression of abaxial genes, whereas loss-of-function mutations in abaxial genes produce an adaxialized phenotype that is accompanied by the expanded expression of adaxial genes. This antagonistic interaction between adaxial and abaxial factors may be mediated by mutually antagonistic regulation (12) or through opposing regulation of common targets (9, 13-16).A key set of transcription factors involved in plant organ polarity are the HD-ZIPIII proteins, such as REVOLUTA (REV), which specify adaxial cell fate (1, 2, 4, 17). The expression of these genes is restricted specifically to adaxial tissues via the action of two miRNA families, MIR165 and MIR166 (2, 7). In turn, the expression of these miRNAs is restricted to abaxial tissues and this restriction is essential for maintaining proper organ polarity (18).Here, we address the question of how MIR165/166 are regulated. We show that the HD-ZIPII proteins HAT3 and ATHB4 physically interact with HD-ZIPIII proteins and directly repress MIR165/166 expression via a conserved cis-element located in their promoters. This regulatory interaction largely accounts for HAT3 and ATHB4 function and reveals the molecular nature of a bidirectional repressive circuit essential to maintain balance between adaxial and abaxial tissue sp...

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Section: Hd-zipiis and Hd-zipiiis Repress Mir165/166 Expression Via Asupporting

confidence: 71%

“…Error bars show means ± SD of three biological replicates treated with 10 μM DEX (+DEX; yellow and blue bars) or mock (0.1% ethanol; −DEX; gray bars). ACT2 and ZPR3 were also tested as negative and positive controls, respectively (26,27). *P ≤ 0.05; **P ≤ 0.01.…”

Section: Hd-zipiis and Hd-zipiiis Repress Mir165/166 Expression Via Amentioning

confidence: 99%

Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity

Merelo

Ram

Caggiano

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

109

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“…4C). Primers for the TA3 promoter were used as the negative control (26). The occupancy of HY5 was remarkably high in the "P1" and "P2" regions, which contain ERSE1 and ERSE2 of the BIP3 promoter, respectively, compared with that in negative control site in P 35S :Y-HY5/hy5 plants but not in the hy5 mutants (Fig.…”

Section: Resultsmentioning

confidence: 99%

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response inArabidopsis

Nawkar

Kang

Maibam

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

111

102

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Light influences essentially all aspects of plant growth and development. Integration of light signaling with different stress response results in improvement of plant survival rates in ever changing environmental conditions. Diverse environmental stresses affect the protein-folding capacity of the endoplasmic reticulum (ER), thus evoking ER stress in plants. Consequently, the unfolded protein response (UPR), in which a set of molecular chaperones is expressed, is initiated in the ER to alleviate this stress. Although its underlying molecular mechanism remains unknown, light is believed to be required for the ER stress response. In this study, we demonstrate that increasing light intensity elevates the ER stress sensitivity of plants. Moreover, mutation of the ELONGATED HYPOCOTYL 5 (HY5), a key component of light signaling, leads to tolerance to ER stress. This enhanced tolerance of hy5 plants can be attributed to higher expression of UPR genes. HY5 negatively regulates the UPR by competing with basic leucine zipper 28 (bZIP28) to bind to the G-box-like element present in the ER stress response element (ERSE). Furthermore, we found that HY5 undergoes 26S proteasome-mediated degradation under ER stress conditions. Conclusively, we propose a molecular mechanism of crosstalk between the UPR and light signaling, mediated by HY5, which positively mediates light signaling, but negatively regulates UPR gene expression.endoplasmic reticulum stress | light signaling | protein-folding capacity | crosstalk | unfolded protein response

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“…ChIP experiments were performed according to previous publications (Haring et al, 2007;Cao et al, 2014;Yamaguchi et al, 2014;Pchelintsev et al, 2016) with minor modifications. Briefly, we initially harvested 1.5 to 2 g of 10-d-old, long-day-grown, transgenic (p35S:CO-YFP/HA) seedlings at 14 h after lights on.…”

Section: Chipmentioning

confidence: 99%