Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplex genome editing uncovers a class of non-CG methylation specific for GC-rich regions in rice

ABSTRACT: We report the BS-Seq, mRNA-Seq and sRNA-Seq of the homozygous mutants and wide type in rice T1 plants, including single and multiple knock-out mutants. We found the major DNA methyltransfereases in regulating DNA methylation of rice.

ORGANISM(S): Oryza sativa

PROVIDER: GSE138705 | GEO | 2021/06/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Multiplex genome editing uncovers a class of non-CG methylation specific for GC-rich regions in rice

Project description:Multiplex genome editing uncovers a class of non-CG methylation specific for GC-rich regions in rice

| PRJNA576905 | ENA

Transcriptome and methylome interactions in rice hybrids

Project description:This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrative maps of whole genome cytosine methylation profiles (BS-Seq), transcriptional profiles (RNA-seq), and small RNA profiles (sRNA-seq) to characterize two rice subspecies, Oryza sativa spp japonica (Nipponbare) and Oryza sativa spp indica (93-11) and their two reciprocal hybrid offspring using Illumina's sequencing-by-synthesis (SBS) platform .

2012-07-10 | E-GEOD-38480 | biostudies-arrayexpress

Transcriptome and methylome interactions in rice hybrids

2012-07-10 | GSE38480 | GEO

The SWR1 Complex Regulates Active DNA Demethylation in Arabidopsis

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in 35S-SUC2 WT and antisilencing mutants (arp6, pie1, h2a.z, idm1, and ros1)

2020-12-06 | GSE107751 | GEO

mRNA-seq of Arabidopsis bz1728, nobiro6, nbr-t1 and taf12-t1 mutants

Project description:mRNA-seq of Arabidopsis bz1728, nobiro6, nbr-t1 and taf12-t1 mutants

| PRJNA688172 | ENA

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (BS_Seq)

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

2021-01-16 | GSE164914 | GEO

Microarray analyses of rachis tissue extracted from control and BS affected grape clusters

Project description:Transcriptional expression in the rachis of pre-sympotmatic (T1) and symptomatic (T2) berry shrivel (BS) clusters in comparison to control samples. Samples were collected from a vineyard in Mailberg, Lower Austria, in 2011 from cultivar Blauer Zweigelt (Vitis vinifera) grafted on Kober 5BB. The objetive of the study was to identify metabolic processes changed in the rachis due to BS induction and symptom development

2022-09-01 | E-MTAB-12113 | biostudies-arrayexpress

CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

Project description:To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. mRNA-seq of primary female mouse dermal fibroblasts with and without thapsigargin identified differentially expressed genes. Genes that are commonly bound by CEBPB and ATF4 to TGAT|GCAA (the best-bound 8-mer in the array) at the promoters were highly expressed and up-regulated or remained unchanged in the thapsigargin treated primary female mouse dermal fibroblasts. RNA-Seq: Examination of whole genome transcriptome profiles (RNA-seq) of primary mouse dermal fibroblasts with and without Thapsigargin treatment ChIP-Seq: Examination of transcription factor binding in dermal fibroblasts with and without Thapsigargin teratment BS-Seq: Determination of whole genome DNA methylation profiles (BS-seq) of primary mouse dermal fibroblasts

2013-03-08 | E-GEOD-44942 | biostudies-arrayexpress

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes. Eighteen mRNA-seq samples, five smRNA-seq samples, five bisulfite-seq samples, twenty ChIP-seq samples. Bisulfite-seq data for cmt2-7 single mutants, cmt3 single mutants, drm1/2 double mutants, drm1/2 cmt3 triple mutants are deposited in GSE39901. Processed wiggle format files for all datasets can be downloaded at http://genomes.mcdb.ucla.edu/AthBSseq/

2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.

Project description: Not available

| S-EPMC7709200 | biostudies-literature