ChIP-Seq Information For P1


General Information


TF Name: ZmMYB3
Species: Maize
TF Family: MYB
Gene Name (Synonym): P1
Gene ID: GRMZM2G084799


Summary


Title: A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes
Overall Design: Comparison of pericarp chromatin inmunoprecipitated material P-rr_14DAP (P1 expressed) vs. P-ww_14DAP (P1 not expressed) to determine P1 direct targets
Antibody: anti-ZmP1
Library Construction Protocol: Chromatin immunoprecipitation (ChIP) was performed by methods previously described (Morohashi and Grotewold, 2009; Morohashi et al., 2009; Falcone Ferreyra et al., 2010), with modifications to accommodate for the high concentration of flavonoids present in P1-rr pericarps. Briefly, 0.3 g of dissected pericarps were fixed in Buffer A (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1 mM phenylmethylsulfonyl fluoride, and 0.1% formaldehyde) for 10 minutes under vacuum conditions. Glycine was added to a final concentration of 0.1 M and incubation was continued for an additional 5 minutes. Fixed pericarps were washed in distilled water and frozen in liquid N2. The tissue was ground in liquid N2, followed by nuclear isolation using the Plant Nuclei Isolation/Extraction Kit according to the manufacturer's instruction (Sigma). Nuclear-enriched extracts were resuspended in 100 ul Lysis Buffer (50 mM HEPES, pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS, 1 mM phenylmethylsulfonyl fluoride, 10 mM sodium butyrate) and plant proteinase inhibitor cocktail (Sigma), followed by sonication with a Bioruptor (Diangenode) to approximately 300 bp of average fragment size, estimated by agarose electrophoresis.
Data Processing: ChIP-Seq reads were aligned to the maize genome assembly version 2 using Bowtie. MACS ver. 1.4.0beta was used for calling peaks by using uniquely aligned reads.
Authors: Kengo Morohashi, Maria Isabel Casas, Lorena Falcone Ferreyra, Maria Katherine Mejia-Guerra, Lucille Pourcel, Alper Yilmaz, Antje Feller, Bruna Carvalho, Julia Emiliani, Eduardo Rodriguez, Silvina Pellegrinet, Michael McMullen, Paula Casati, and Erich Grotewold
Reference: Plant Cell. 2012; 24(7):2745-64. PubMed link: 22822204


Figures and Tables


Zea mays cobs (P_rr_14DAP; P1 expressed) in the stage used to collect pericarps for ChIP experiments. Picture provided by Maria Isabel Casas (Grotewold lab)

Zea mays cobs (P_rr_25DAP; P1 expressed) in the stage used to collect pericarps for RNA-Seq experiments. Pictures provided by Maria Isabel Casas (Grotewold Lab)



Download ChIP-Seq Files


Description File Type Name
Pericarp_P-rr_14DAP_ChIP_1 Alignment *bam *bai Pericarp_P-rr_14DAP_ChIP_1.tar
Pericarp_P-rr_14DAP_ChIP_2 Alignment *bam *bai Pericarp_P-rr_14DAP_ChIP_2.tar
Pericarp_P-ww_14DAP_ChIP_1 Alignment *bam *bai Pericarp_P-ww_14DAP_ChIP_1.tar
Pericarp_P-ww_14DAP_ChIP_2 Alignment *bam *bai Pericarp_P-ww_14DAP_ChIP_2.tar
P1_Prr-14_Pww-14_1_peaks Peaks Position *.bed P1_Prr-14_Pww-14_1_peaks.bed
P1_Prr-14_Pww-14_2_peaks Peaks Position *.bed P1_Prr-14_Pww-14_2_peaks.bed
P1_Prr-14_Pww-14_1.wig Peaks position and shape *wig P1_Prr-14_Pww-14_1.wig.tar
P1_Prr-14_Pww-14_2.wig Peaks position and shape *wig P1_Prr-14_Pww-14_2.wig.tar


Scripts


Description Language Name
Script to calculate mean of; counts, positions, and values within a given bin Perl mean_of_bin.pl


GEO Accession Numbers


ChIP-Seq: GSE38587
RNA-Seq: GSE38413,GSE38414


Others


Explore Targets information in the GRASSIUS Gene Regulatory Grid Explorer GRG-X