Chromatin techniques for plant cells

Bowler, Chris; Benvenuto, Giovanna; Laflamme, Pierre; Molino, Diana; Probst, Aline V.; Tariq, Muhammad; Paszkowski, Jerzy

doi:10.1111/j.1365-313x.2004.02169.x

Cited by 355 publications

(323 citation statements)

References 58 publications

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“…A nonionic surfactant (e.g. Triton X-100 or Igepal CA 630) is normally used at concentrations between 0.3% and 1% (v/v) depending on the specific requirement of each experiment (Bowler et al, 2004;Wagschal et al, 2007). Normally, a 15-min treatment with cell lysis buffer containing 0.5% Triton X-100 is sufficient for most Arabidopsis green tissues.…”

Section: Isolation Of Nucleimentioning

confidence: 99%

“…Normally, a 15-min treatment with cell lysis buffer containing 0.5% Triton X-100 is sufficient for most Arabidopsis green tissues. It is advisable to include Suc or hexylene glycol in the buffer (Bowler et al, 2004) to maintain a physiological osmotic pressure. Such an osmotic agent also increases the viscosity of the buffer system slightly and forms an additional protection for the nuclei.…”

Section: Isolation Of Nucleimentioning

confidence: 99%

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Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

Shu¹,

Gruissem

Hennig

2013

Plant Physiol.

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Section: Isolation Of Nucleimentioning

confidence: 99%

Section: Isolation Of Nucleimentioning

confidence: 99%

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

Shu¹,

Gruissem

Hennig

2013

Plant Physiol.

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“…S2; Bowler et al, 2004;Sandoval et al, 2004;Tsuji et al, 2006;Chung et al, 2009). The antibody used in the ChIP experiments herein was antiPol II CTD (sc-900; Santa Cruz Biotechnology).…”

Section: Rna Pol Ii-chipmentioning

confidence: 99%

Posttranscriptional Control of Photosynthetic mRNA Decay under Stress Conditions Requires 3′ and 5′ Untranslated Regions and Correlates with Differential Polysome Association in Rice

et al. 2012

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Abiotic stress, including drought, salinity, and temperature extremes, regulates gene expression at the transcriptional and posttranscriptional levels. Expression profiling of total messenger RNAs (mRNAs) from rice (Oryza sativa) leaves grown under stress conditions revealed that the transcript levels of photosynthetic genes are reduced more rapidly than others, a phenomenon referred to as stress-induced mRNA decay (SMD). By comparing RNA polymerase II engagement with the steady-state mRNA level, we show here that SMD is a posttranscriptional event. The SMD of photosynthetic genes was further verified by measuring the half-lives of the small subunit of Rubisco (RbcS1) and Chlorophyll a/b-Binding Protein1 (Cab1) mRNAs during stress conditions in the presence of the transcription inhibitor cordycepin. To discern any correlation between SMD and the process of translation, changes in total and polysome-associated mRNA levels after stress were measured. Total and polysome-associated mRNA levels of two photosynthetic (RbcS1 and Cab1) and two stress-inducible (Dehydration Stress-Inducible Protein1 and Salt-Induced Protein) genes were found to be markedly similar. This demonstrated the importance of polysome association for transcript stability under stress conditions. Microarray experiments performed on total and polysomal mRNAs indicate that approximately half of all mRNAs that undergo SMD remain polysome associated during stress treatments. To delineate the functional determinant(s) of mRNAs responsible for SMD, the RbcS1 and Cab1 transcripts were dissected into several components. The expressions of different combinations of the mRNA components were analyzed under stress conditions, revealing that both 39 and 59 untranslated regions are necessary for SMD. Our results, therefore, suggest that the posttranscriptional control of photosynthetic mRNA decay under stress conditions requires both 39 and 59 untranslated regions and correlates with differential polysome association.

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“…The reaction was stopped by adding 0.1 M Gly. Fixed tissues were ground in liquid nitrogen, nuclei were isolated, and chromatin was extracted and sheared by sonication (Microson MS-50; 10 s on and 10 s off for 10 times) to generate 0.5-to 2-kb fragments (Bowler et al, 2004). Anti-H3K27me3 (Millipore) and anti-H3K4me3 (Abcam) antibodies were used to immunoprecipitate the fragmented chromatin.…”

Section: Chip and Chip-qpcrmentioning

confidence: 99%

EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis Development and Stress Response

Liu

Kim

et al. 2013

Plant Physiology

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Epigenetic regulation of gene expression is of fundamental importance for eukaryotic development. EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene that participates in Polycomb group-mediated transcriptional repression of target genes such as the flower MADS box genes AGAMOUS, APETALA3, and PISTILLATA. Here, we investigated the molecular mechanism underlying the curly leaf and early flowering phenotypes caused by reducing EMF1 activity in the leaf primordia of LFYasEMF1 transgenic plants and propose a combined effect of multiple flower MADS box gene activities on these phenotypes. ULTRAPETALA1 (ULT1) functions as a trithorax group factor that counteracts Polycomb group action in Arabidopsis (Arabidopsis thaliana). Removing ULT1 activity rescues both the abnormal developmental phenotypes and most of the misregulated gene expression of LFYasEMF1 plants. Reducing EMF1 activity increases salt tolerance, an effect that is diminished by introducing the ult1-3 mutation into the LFYasEMF1 background. EMF1 is required for trimethylating lysine-27 on histone 3 (H3K27me3), and ULT1 associates with ARABIDOPSIS TRITHORAX1 (ATX1) for trimethylating lysine-3 on histone 4 (H3K4me3) at flower MADS box gene loci. Reducing EMF1 activity decreases H3K27me3 marks and increases H3K4me3 marks on target gene loci. Removing ULT1 activity has the opposite effect on the two histone marks. Removing both gene activities restores the active and repressive marks to near wild-type levels. Thus, ULT1 acts as an antirepressor that counteracts EMF1 action through modulation of histone marks on target genes. Our analysis indicates that, instead of acting as off and on switches, EMF1 and ULT1 mediate histone mark deposition and modulate transcriptional activities of the target genes.

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Chromatin techniques for plant cells

Cited by 355 publications

References 58 publications

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

Posttranscriptional Control of Photosynthetic mRNA Decay under Stress Conditions Requires 3′ and 5′ Untranslated Regions and Correlates with Differential Polysome Association in Rice

EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis Development and Stress Response

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