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Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ncRNA-Seq]

ABSTRACT: Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ncRNA-Seq]

PROVIDER: PRJNA895402 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22081629.fastq.gz	Fastqsanger.gz
	SRR22081630.fastq.gz	Fastqsanger.gz
	SRR22081631.fastq.gz	Fastqsanger.gz
	SRR22081632.fastq.gz	Fastqsanger.gz
	SRR22081633.fastq.gz	Fastqsanger.gz

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Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ncRNA-Seq]

Project description:Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). We found that HDA6 silenced 517 TEs by itself, LDL1/2 silenced 2 TEs alone and HDA6 silenced 15 TEs in cooperation with LDL1/2; suggesting that HDA6 has a stronger impact on TE silencing than LDL1/2; the effect of HDA6 is mostly independent of LDL1/2 whereas most LDL1/2 effect requires HDA6. Also, we observed that the expression of TE showed clear synergistic (enhanced de-repression in hda6/ldl1/2) and antagonistic (lower de-repression in hda6/ldl1/2) effects at different sets of TEs. Further analysis showed that the TEs targeted by either of the two effects exhibited totally different epigenome patterns.

2024-11-06 | GSE216788 | GEO

Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS]

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Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ATAC-Seq]

2024-11-06 | GSE216786 | GEO

RNA-seq of 14 days old arabidopsis in Col hda6 ldl1/2 and hda6/ldl1/2

Project description:We report the application ofr high-throughput profiling of total transcript in WT, hda6, ldl1/2 and hda6/ldl1/2. The total RNA were extracted and analysed by NGS to identify the differential expressed genes between WT with hda6, ldl1/2 and hda6/ldl1/2.

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Genome-wide maps of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3AC levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K9K14Ac antibody (Millipore; 06-599), and ChIP DNA were analyzed by Illumina HiSeq 2500.

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Genome-wide maps of H3K4me2 in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3K4me2 in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3K4me2 levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K4me2 antibody (diagenode; C15410035), and ChIP DNA were analyzed by Illumina HiSeq 2500.

2021-03-30 | GSE133005 | GEO

Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2

Project description:Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2

| PRJNA895399 | ENA

Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS]

Project description:Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS]

| PRJNA895401 | ENA

Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ATAC-Seq]

Project description:Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ATAC-Seq]

| PRJNA895400 | ENA

RNA-seq of 14 days old arabidopsis in Col hda6 ldl1/2 and hda6/ldl1/2

Project description:RNA-seq of 14 days old arabidopsis in Col hda6 ldl1/2 and hda6/ldl1/2