Identification of Direct p73 Target Genes Combining DNA Microarray and Chromatin Immunoprecipitation Analyses

Background: Vitamin D is a liposoluble vitamin essential for calcium metabolism. The ligand-bound vitamin D receptor (VDR), heterodimerized with retinoid X receptor, interacts with vitamin D response elements (VDREs) to regulate gene expression. Vitamin D deficiency due to insufficient sunlight exposure confers an increased risk for multiple sclerosis (MS). Objective: To study a protective role of vitamin D in multiple sclerosis (MS), it is important to characterize the global molecular network of VDR target genes (VDRTGs) in immune cells. Methods: We identified genome-wide VDRTGs collectively from two distinct chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) datasets of VDR-binding sites derived from calcitriol-treated human cells of B cell and monocyte origins. We mapped short reads of next generation sequencing (NGS) data on hg19 with Bowtie, detected the peaks with Model-based Analysis of ChIP-Seq (MACS), and identified genomic locations by GenomeJack, a novel genome viewer for NGS platforms. Results: We found 2997 stringent peaks distributed on protein-coding genes, chiefly located in the promoter and the intron on VDRE DR3 sequences. However, the corresponding transcriptome data verified calcitriol-induced upregulation of only a small set of VDRTGs. The molecular network of 1541 calcitriol-responsive VDRTGs showed a significant relationship with leukocyte transendothelial migration, Fcγ receptor-mediated phagocytosis, and transcriptional regulation by VDR, suggesting a pivotal role of genome-wide VDRTGs in immune regulation. Conclusion: These results suggest the working hypothesis that persistent deficiency of vitamin D might perturb the complex network of VDRTGs in immune cells, being responsible for induction of an autoimmune response causative for MS.

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Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing

Methods in Molecular Biology - Brassinosteroids ◽

10.1007/978-1-4939-6813-8_7 ◽

2017 ◽

pp. 63-79 ◽

Cited By ~ 4

Author(s):

Trevor Nolan ◽

Sanzhen Liu ◽

Hongqing Guo ◽

Lei Li ◽

Patrick Schnable ◽

...

Keyword(s):

Rna Sequencing ◽

High Throughput ◽

Chromatin Immunoprecipitation ◽

High Throughput Sequencing ◽

Target Genes

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A Multiplicity of Coactivators Is Required by Gcn4p at Individual Promoters In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.23.8.2800-2820.2003 ◽

2003 ◽

Vol 23 (8) ◽

pp. 2800-2820 ◽

Cited By ~ 108

Author(s):

Mark J. Swanson ◽

Hongfang Qiu ◽

Laarni Sumibcay ◽

Anna Krueger ◽

Soon-ja Kim ◽

...

Keyword(s):

Amino Acid ◽

Chromatin Immunoprecipitation ◽

Target Gene ◽

Target Genes ◽

Yeast Cells ◽

Histone Acetyltransferases ◽

Vitro Binding ◽

Paf1 Complex

ABSTRACT Transcriptional activators interact with multisubunit coactivators that modify chromatin structure or recruit the general transcriptional machinery to their target genes. Budding yeast cells respond to amino acid starvation by inducing an activator of amino acid biosynthetic genes, Gcn4p. We conducted a comprehensive analysis of viable mutants affecting known coactivator subunits from the Saccharomyces Genome Deletion Project for defects in activation by Gcn4p in vivo. The results confirm previous findings that Gcn4p requires SAGA, SWI/SNF, and SRB mediator (SRB/MED) and identify key nonessential subunits of these complexes required for activation. Among the numerous histone acetyltransferases examined, only that present in SAGA, Gcn5p, was required by Gcn4p. We also uncovered a dependence on CCR4-NOT, RSC, and the Paf1 complex. In vitro binding experiments suggest that the Gcn4p activation domain interacts specifically with CCR4-NOT and RSC in addition to SAGA, SWI/SNF, and SRB/MED. Chromatin immunoprecipitation experiments show that Mbf1p, SAGA, SWI/SNF, SRB/MED, RSC, CCR4-NOT, and the Paf1 complex all are recruited by Gcn4p to one of its target genes (ARG1) in vivo. We observed considerable differences in coactivator requirements among several Gcn4p-dependent promoters; thus, only a subset of the array of coactivators that can be recruited by Gcn4p is required at a given target gene in vivo.

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Research on the Typical miRNA and Target Genes in Squamous Cell Carcinoma and Adenocarcinoma of Esophagus Cancer with DNA Microarray

Pathology & Oncology Research ◽

10.1007/s12253-013-9688-z ◽

2014 ◽

Vol 20 (2) ◽

pp. 245-252 ◽

Cited By ~ 12

Author(s):

Hong Bin Wang ◽

Zhi Biao Jiang ◽

Min Li

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Dna Microarray ◽

Squamous Cell ◽

Target Genes ◽

Esophagus Cancer ◽

Adenocarcinoma Of Esophagus

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Ets-dependent Regulation of Target Gene Expression during Megakaryopoiesis

Journal of Biological Chemistry ◽

10.1074/jbc.m407489200 ◽

2004 ◽

Vol 279 (50) ◽

pp. 52183-52190 ◽

Cited By ~ 57

Author(s):

Pascale Jackers ◽

Gabor Szalai ◽

Omar Moussa ◽

Dennis K. Watson

Keyword(s):

Transcription Factors ◽

Rna Polymerase Ii ◽

Chromatin Immunoprecipitation ◽

Target Genes ◽

Hematopoietic Stem ◽

Exogenous Expression ◽

Direct Target ◽

Transcriptional Complex

Megakaryopoiesis is the process by which hematopoietic stem cells in the bone marrow differentiate into mature megakaryocytes. The expression of megakaryocytic genes during megakaryopoiesis is controlled by specific transcription factors. Fli-1 and GATA-1 transcription factors are required for development of megakaryocytes and promoter analysis has definedin vitrofunctional binding sites for these factors in several megakaryocytic genes, includingGPIIb,GPIX, andC-MPL. Herein, we utilize chromatin immunoprecipitation to examine the presence of Ets-1, Fli-1, and GATA-1 on these promotersin vivo. Fli-1 and Ets-1 occupy the promoters ofGPIIb,GPIX, andC-MPLgenes in both Meg-01 and CMK11-5 cells. WhereasGPIIbis expressed in both Meg-01 and CMK11-5 cells,GPIXandC-MPLare only expressed in the more differentiated CMK11–5 cells. Thus,in vivooccupancy by an Ets factor is not sufficient to promote transcription of some megakaryocytic genes. GATA-1 and Fli-1 are both expressed in CMK11-5 cells and co-occupy theGPIXandC-MPLpromoters. Transcription of all three megakaryocytic genes is correlated with the presence of acetylated histone H3 and phosphorylated RNA polymerase II on their promoters. We also show that exogenous expression of GATA-1 in Meg-01 cells leads to the expression of endogenous c-mpl and gpIX mRNA. WhereasGPIIb,GPIX, andC-MPLare direct target genes for Fli-1, both Fli-1 and GATA-1 are required for formation of an active transcriptional complex on theC-MPLandGPIXpromotersin vivo. In contrast,GPIIbexpression appears to be independent of GATA-1 in Meg-01 cells.

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