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Mitochondria-originating novel coding gene sORF2146 controls flowering

ABSTRACT: Mitochondria-originating novel coding gene sORF2146 controls flowering

PROVIDER: PRJNA765670 | ENA |

REPOSITORIES: ENA

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Mitochondria-originating novel coding gene sORF2146 controls flowering

Project description:It has been reported that a number of small coding genes (30–100 amino acids) tend to be lineage-specifically emerged in evolution but such de-novo genes tend to be missed in genomes. Plant mitochondrial genomes might be fostering sources of de-novo genes because of a high rearrangement rate. However, the functional role of de-novo genes derived from mitochondria is unclear. Here, in the best model species of plants (Arabidopsis thaliana), we showed that Arabidopsis-specifically emerged de-novo genes derived from mitochondrial genome contributed to phenotypic variation in a species. We previously identified 49 candidates of small coding genes inducing abnormal morphological changes on overexpression in the nuclear genome. Among them, we focused on a candidate (sORF2146) potentially encoding 66 amino acids in large-scale intergenic genomic transferring region from mitochondrial genome. Comparative genome analysis showed that sORF2146 had been appeared in Arabidopsis lineage. Mitochondrial sORF2146 is fixed among A. thaliana ecotypes but nucleus sORF2146 is not fixed in A. thaliana ecotypes. After showing evidence that nucleus sORF2146 was transcribed and translated as a coding gene, we performed transcriptome analysis in transgenic plant overexpressing sORF2146. Genes associated with flowering transition are highly regulated in the transgenic plant. We then examined phenotypic effects of overexpression and knockdown transgenic plant. Overexpression and knockdown transgenic plant induce late and early flowering, respectively. Taken together, we conclude that a nucleus de-novo gene derived from mitochondria contributes to the variation of floral timing in Arabidopsis population.

2021-09-24 | GSE184689 | GEO

An LKB1-mitochondria axis controls Th17 effector function

Project description:An LKB1-mitochondria axis controls Th17 effector function

| PRJNA856302 | ENA

An LKB1-mitochondria axis controls Th17 effector function [ATAC-Seq]

Project description:An LKB1-mitochondria axis controls Th17 effector function [ATAC-Seq]

| PRJNA856304 | ENA

An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 1]

Project description:An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 1]

| PRJNA658955 | ENA

An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 2]

Project description:An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 2]

| PRJNA856305 | ENA

Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana

Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP. The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change.

2013-09-19 | GSE48082 | GEO

RNA-Seq of early flowering Arabidopsis thaliana FLC mutants and wild type controls

Project description:RNA-Seq of early-flowering FLC mutants and wild type controls

| PRJEB89960 | ENA

Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana

Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-M-NM-2 and FLM-M-NM-4, which compete for interaction with the floral repressor SVP. The SVP/FLM-M-NM-2 complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-M-NM-4 complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change. ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)

2013-09-19 | E-GEOD-48082 | biostudies-arrayexpress

Flowering Mutant Experiment

Project description:Collection of Flowering mutants Keywords = flowering, growth and development, gene structure and expression Keywords: other

2005-04-09 | GSE2506 | GEO

Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

Project description:Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

| PRJNA353973 | ENA