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Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)

ABSTRACT: Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)

PROVIDER: PRJNA719557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14140121_1.fastq.gz	Fastqsanger.gz
	SRR14140121_2.fastq.gz	Fastqsanger.gz
	SRR14140122_1.fastq.gz	Fastqsanger.gz
	SRR14140122_2.fastq.gz	Fastqsanger.gz
	SRR14140123_1.fastq.gz	Fastqsanger.gz

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Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)

Project description:Purpose: The goals of this study are to compare transcriptome of ldl1ldl2 double mutants with that of wild-type Columbia-0 plants and to identify genes whose expression are tightly regualted by LDL1/LDL2 prtoeins in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and ldl1ldl2 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 27~31 million sequence reads per sample to the Arabidopsis genome (TAIR10). Conclusions: Our results show that LDL1 and LDL2 protein had significant effects on transcription of genes important for plant immune reponses against Pseudomonas infection.

2021-04-04 | GSE171433 | GEO

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

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 | GSE216787 | GEO

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

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

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Genome-wide map of lysine specific demethylase 1 (LSD1) in mouse embryonic stem cells.

Project description:We report the identification of LSD1 binding genomic regions in mouse embryonic stem cells (ESC) by high throughput sequencing. By obtaining over 10 million 36 bp reads of sequence from each chromatin immunoprecipitated DNA, we generated genome-wide maps for LSD1 and histone H3 dimethylated on lysine 4 (H3K4me2), the substrate for LSD1 in mouse ESCs. Our results showed an extensive overlap between the LSD1 and H3K4me2 genomic regions and a correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ESC genes. LSD1 is recruited to the chromatin of cells in the G1/S/G2 phases and is displaced from the chromatin of M phase cells, suggesting that LSD1 or H3K4me2 alternatively occupies LSD1 genomic regions during cell cycle progression. LSD1 knockdown by RNA interference or its displacement from the chromatin by anti-neoplastic agents caused an increase in the levels of a subset of LSD1 target genes. Taken together, these results suggest that cell-cycle dependent association and dissociation of LSD1 with chromatin mediates short-time scale gene expression changes during ES cell cycle progression. Examination of LSD1 and lysine 4 dimethylated histone H3 (H3K4me2) binding genomic regions in embryonic stem cells. Input genomic DNA and DNA immunoprecipitaed with control IgG was included as controls.

2012-10-03 | E-GEOD-18515 | biostudies-arrayexpress

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.

2021-03-30 | GSE132873 | GEO

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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

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.

2021-03-30 | GSE132636 | GEO

Genome-wide maps of LDL1pro::LDL1:GFP in 14 days old arabidopsis

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3K4 demethylase LDL1 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide LDL1-binding maps of 14 days old arabidopsis. To reveal bound genes by LDL1, chimeric protein LDL1-GFP was expressed under LDL1 promoter in ldl1 (LDL1pro:LDL1:GFP/ ldl1). ChIP was performed using anti-GFP antibody (ab290; ABCAM), and ChIP DNA were analyzed by Illumina HiSeq 2500.

2018-08-19 | GSE118025 | GEO

Uncoupling Histone Modification Crosstalk by Engineering Lysine Demethylase LSD1

Project description:Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation but its functional significance in cells has been difficult to discern. Prior enzymatic studies have revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine specific demethylase 1 (LSD1). Here we have engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. Y391K LSD1 knockin cells show increased repression of a set of genes associated with cellular adhesion. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation than the baseline in unedited, parental cells. Y391K LSD1 knockin cells show diminished H3 mono-methyl Lys4 in the vicinity of these silenced genes, consistent with a role for enhanced LSD1 demethylase activity in these regions. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme in gene and chromatin regulation.

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