ZIP-seq for functional characterizations of Z-DNA in rice
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ABSTRACT:
PROVIDER: PRJNA1063304 | ENA |
REPOSITORIES: ENA
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Project description:A Z-DNA is a left-handed DNA double helix functioning in various DNA templated events. However, antibody based high throughput methodologies for Z-DNA profiling are still missing in both humans and plants. We here developed the Z-DNA antibody-based IP-seq, termed ZIP-seq, for characterization of Z-DNA across the rice genome.
2025-01-09 | GSE252954 | GEO
Project description:Functional characterizations of the Hippo pathway effectors YAP and TAZ
| PRJNA437466 | ENA
Project description:Single-base resolution DNA methylomes of rice and functional roles of DNA methylation
| PRJNA124663 | ENA
Project description:To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. Most interestingly, we discovered for the first time that methylation in gene transcriptional termination regions can significantly repress gene expression, and the effect is even stronger than promoter methylation, which opens a new direction in the study of epigenetic regulation of gene expressions. Through integrated analysis of genetic, methylome and expression variation between cultivated and wild rice, we found that the genetic factor reflected by DNA variations may be the major determinant for methylation patterns at the whole-genome level and that methylation variation can only account for limited expression variation of genes between cultivated and wild rice.
2011-11-04 | GSE20871 | GEO
Project description:To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. Most interestingly, we discovered for the first time that methylation in gene transcriptional termination regions can significantly repress gene expression, and the effect is even stronger than promoter methylation, which opens a new direction in the study of epigenetic regulation of gene expressions. Through integrated analysis of genetic, methylome and expression variation between cultivated and wild rice, we found that the genetic factor reflected by DNA variations may be the major determinant for methylation patterns at the whole-genome level and that methylation variation can only account for limited expression variation of genes between cultivated and wild rice. A single young panicle from each of the cultivated rice subspecies and the two wild rice species was ground in liquid nitrogen to fine powder using mortar and pestle. Total RNAs were isolated using the RNeasy Plant Mini Kit (Qiagen). DGE-tag libraries were constructed using the DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina) according to the manufacturer's instructions. This submission represents the gene expression component of the study.
2011-11-04 | E-GEOD-20871 | biostudies-arrayexpress
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
2014-11-01 | GSE57252 | GEO
Project description:Several homeobox genes belonging to HD-ZIP I subfamily are highly induced by drought stress at various developmental stages in rice. To analyze the role of a candidate HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in rice. The physiological analyses revealed that overexpression of OsHOX24 gene reduced drought stress tolerance in transgenic plants as compared to wild-type. We used microarrays to study the global effect of OsHOX24 overexpression in rice as compared to wild-type under control and drought stress condition.
2017-06-12 | GSE79212 | GEO
Project description:The Epstein-Barr virus (EBV) B-ZIP transcription factor (TF) Zta binds to many DNA sequences containing methylated CG dinucleotides. Using protein binding microarrays (PBMs), we analyzed the binding of Zta to four kinds of double-stranded DNA: 1) DNA containing cytosine on both strands, 2) DNA with 5-methylcytosine (5mC) on one strand and cytosine on the second strand, 3) DNA with 5-hydroxymethylcytosine (5hmC) on one strand and cytosine on the second strand, and 4) DNA where both cytosines in all CG dinucleotides contain 5mC. We compared the resulting data to PBM data for three other B-ZIP proteins (CREB1 and CEBPB homodimers, and cFos-cJun heterodimers). With cytosine, Zta binds the TRE motif TGAC/GTCA as previously reported. With CG dinucleotides containing 5mC on both strands, many TRE motif variants containing a methylated CG dinucleotide at two positions in the motif, such as MGAGTCA and TGAGMGA (where M=5mC) were preferentially bound. 5mC inhibits Zta binding to both TRE motif half sites GTCA and CTCA. Like the CREB1 homodimer, the Zta homodimer and the cJun|cFos heterodimer bind the C/EBP half site tetranucleotide GCAA stronger when it contains 5mC. Our results identify new DNA sequences that are well-bound by the viral B-ZIP protein Zta only when they contain 5mC or 5hmC, opening the potential for discovery of new viral and host regulatory programs controlled by EBV.
2017-10-26 | GSE100870 | GEO
Project description:The Epstein-Barr virus (EBV) B-ZIP transcription factor (TF) Zta binds to many DNA sequences containing methylated CG dinucleotides. Using protein binding microarrays (PBMs), we analyzed the binding of Zta to four kinds of double-stranded DNA: 1) DNA containing cytosine on both strands, 2) DNA with 5-methylcytosine (5mC) on one strand and cytosine on the second strand, 3) DNA with 5-hydroxymethylcytosine (5hmC) on one strand and cytosine on the second strand, and 4) DNA where both cytosines in all CG dinucleotides contain 5mC. We compared the resulting data to PBM data for three other B-ZIP proteins (CREB1 and CEBPB homodimers, and cFos-cJun heterodimers). With cytosine, Zta binds the TRE motif TGAC/GTCA as previously reported. With CG dinucleotides containing 5mC on both strands, many TRE motif variants containing a methylated CG dinucleotide at two positions in the motif, such as MGAGTCA and TGAGMGA (where M=5mC) were preferentially bound. 5mC inhibits Zta binding to both TRE motif half sites GTCA and CTCA. Like the CREB1 homodimer, the Zta homodimer and the cJun|cFos heterodimer bind the C/EBP half site tetranucleotide GCAA stronger when it contains 5mC. Our results identify new DNA sequences that are well-bound by the viral B-ZIP protein Zta only when they contain 5mC or 5hmC, opening the potential for discovery of new viral and host regulatory programs controlled by EBV.
2017-10-26 | GSE100869 | GEO
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress. We sequenced mRNA from soybean cv. "Williams 82" root samples that includes three control samples (0 hr), and three biological replicates for each of the three time points 1, 6 and 12 hr under dehydration and salt stress
2014-11-01 | E-GEOD-57252 | biostudies-arrayexpress