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Lamina joint positioning and differentiation

ABSTRACT: Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling

PROVIDER: PRJEB40447 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4613251_1.fastq.gz	Fastqsanger.gz
	ERR4613251_2.fastq.gz	Fastqsanger.gz
	ERR4613252_1.fastq.gz	Fastqsanger.gz
	ERR4613252_2.fastq.gz	Fastqsanger.gz
	ERR4613253_1.fastq.gz	Fastqsanger.gz

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lamina joint initiation in rice

Project description:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling

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Genome-wide gene expression profiling of rice Zhonghua11 and ila1 lamina joint

Project description:The leaf lamina joint joins the rice leaf blade and sheath, contributing significantly to the leaf angle trait. A more erect leaf facilitates the penetration of sunlight, enhancing photosynthetic efficiency and occupying less space in dense planting. Genetic screening found a mutant increased leaf angle1, ila1 from rice T-DNA insertional mutants library. We used microarrays to detail the transcriptional profile changes in the mutant ila1 lamina joint. Two biological replicate sample of leaf lamina joints from the ila1 and wild-type plants at tillering stage were collected for RNA extraction. Total RNAs were isolated from each replicate via the TRIzol method (Invitrogen) and used in target synthesis for the Rice Genome Array from Affymetrix. The microarray analyses were performed through following standard protocols (Affymetrix).

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Microarray using WT (Dongjin rice) and OsBUL1KO Lamina joint samples

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Microarray using WT (TNG67) and pOsBUL1:OsBDG1 Lamina joint samples (TNG67 vs. #13 vs. #20)

Project description:We compared transcripts using microarray hybridization between lamina joint samples of WT and pOsBUL1:OsBDG1 plants.

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Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

Project description:Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confers structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains elusive, however. We examined changes in the association of lamin B1 with the genome in the first 72 hours of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. In addition, differentially expressed genes in LADs are linked to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.

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Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

Project description:Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage

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A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]

Project description:A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts. We characterized DNA regions within LADs that are functionally capable of positioning chromatin domains at the inner nuclear membrane (INM) lamina. We mapped and characterized the IgH and other LADs in murine fibroblasts. We show that these murine LADs have a unique chromatin structure with discrete boundaries. We demonstrate DNA regions within LADs that are capable of directing the association of chromatin domains with the INM-lamina as well as the silencing of a co-integrated reporter gene.

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Expression analysis of genes in the lamina joint of lc1 mutant compared with that of wild-type

Project description:The angle of rice leaf inclination is an important agronomic trait and closely related to the yield and architecture of crops. Through genetic screening, a rice gain-of-function mutant leaf inclination1, lc1, was identified . Phenotypic analysis confirmed the exaggerated leaf angels of lc1 due to the stimulated cell elongation at the collar.In this series, we compare the transcriptome of zhonghua11 and lc1 collar. The lamina joint (1-cm long) of the flag leaves of lc1 and WT plants were collected and frozen in liquid nitrogen, which were then used for RNAs extraction. The obtained RNA samples were processed as recommended by Affymetrix, including RNA extraction, converting to double-stranded cDNA, and synthesis of biotin-labeled copy RNA. Fifteen micrograms of biotin-labeled copy RNA was purified and fragmented into 35- to 300-nucleotide fragments and then hybridized with a Rice genome array (Affymetrix). The hybridization was performed with two biological replicates for each sample. After hybridization, arrays were scanned using an Agilent GeneArray scanner (Affymetrix G2500A). Microarray data were normalized using the Affymetrix Microarray Suit program (version 5.0). The algorithm absolute call flag was set to indicate the reliability of the data points according to P (present), M (marginal), and A (absent). Significant differences for each gene between the WT and lc1 mutant plants were examined using the Wilcoxon rank test of the Affymetrix Microarray Suit program (P<0.01) and analysis of variance by fitting a mixed model in the MAANOVA package under R 1.8.0 for multiple testing (false discovery rate-corrected P<0.05). Genes with the consensus significant difference in two independent samples were selected and listed. Annotations for the selected probe set identification were rechecked at the Affymetrix website.

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