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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos

ABSTRACT: Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h

ORGANISM(S): Hordeum vulgare subsp. vulgare

SUBMITTER: Qisen Zhang

PROVIDER: E-GEOD-66024 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Involvement of Alternative Splicing in Barley Seed Germination.

Zhang Qisen Q Zhang Xiaoqi X Wang Songbo S Tan Cong C Zhou Gaofeng G Li Chengdao C

PloS one 20160331 3

Seed germination activates many new biological processes including DNA, membrane and mitochondrial repairs and requires active protein synthesis and sufficient energy supply. Alternative splicing (AS) regulates many cellular processes including cell differentiation and environmental adaptations. However, limited information is available on the regulation of seed germination at post-transcriptional levels. We have conducted RNA-sequencing experiments to dissect AS events in barley seed germinatio ...[more]

PMID: 27031341

Similar Datasets

Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos

Project description:Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos

2016-02-18 | GSE66024 | GEO

An Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates

Project description:Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. Engineered skipping of the orthologous exon in chicken cells induces a large number of mammalian-like AS changes in PTBP1 target exons. These results thus reveal that a single exon skipping event in an RNA binding regulator directs numerous AS changes between species. The results further suggest that these changes contributed to evolutionary differences in the formation of vertebrate nervous systems. This study contains two sets of samples: (Set 1) mRNA profiling of human 293 cells subjected to four different conditions in two biological replicates: non-targetting control siRNA, PTBP1 and PTBP2 siRNA, PTBP1 and PTBP2 siRNA with overexpression of full-length human PTBP1, PTBP1 and PTBP2 siRNA with overexpression of exon-excluded human PTBP1. (Set 2) mRNA profiling of chicken DT40 cells with 3 genotypes in two bioligcal replicates: wildtype cells, cells with PTBP1 exon 8 (orthologous to human PTBP1 exon 9) deleted in one allele, and cells with PTBP1 exon 8 deleted in both alleles.

2015-09-01 | E-GEOD-69656 | biostudies-arrayexpress

Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

Project description:Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions. RNA-seq for wide type (WT) and SRSF10-deficient (KO) chicken DT40 cells

2014-01-22 | E-GEOD-53354 | biostudies-arrayexpress

Genome-wide analysis of Dengue virus 2 infected cells

Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of Dengue virus 2 and mock infected cells at 24 and 36 hours post infection. Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses. Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication. A549 cells where infected with Dengue virus 2 or mock and after 24 and 36 hours post infection mRNA was purified. Then the transcriptional profile of these cells was analyzed using RNA-seq.

2016-08-09 | E-GEOD-84285 | biostudies-arrayexpress

SRSF10 regulates alternative splicing and is required for adipocyte differentiation.

Project description:During adipocyte differentiation, significant alternative splicing changes occur in association with the adipogenic process. However, little is known about roles played by splicing factors in this process. We observed that mice deficient for the splicing factor SRSF10 exhibit severely impaired development of subcutaneous white adipose tissue as a result of defects in adipogenic differentiation. To identify splicing events responsible for this, RNA-seq analysis was performed using embryonic fibroblast cells. Several SRSF10-affected splicing events that are implicated in adipogenesis have been identified. Skipping of lipin1 exon 7 is controlled by SRSF10-regulated cis-element located in the constitutive exon 8. The activity of this element depends on the binding of SRSF10 and correlates with the relative abundance of lipin1a mRNA. A series of experiments demonstrated that SRSF10 controls the production of lipin1a and thus promotes adipocyte differentiation. Indeed, lipin1a expression could rescue SRSF10-mediated adipogenic defects. Taken together, our results identify SRSF10 as an essential regulator for adipocyte differentiation and also provide new insights into splicing control by SRSF10 in lipin1 pre-mRNA splicing. RNA-seq for wide type (WT) and SRSF10-deficient (KO) mouse MEF cells

2014-05-12 | E-GEOD-54226 | biostudies-arrayexpress

Transcription profiling of barley maturing and germinating grains

Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.

2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress

Transcriptome in developing caeca

Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Transcriptional activity at the HoxD locus in developing caeca at E13.5 Transcriptional activity at the HoxD locus in developing caeca at E13.5

2013-10-23 | E-GEOD-44367 | biostudies-arrayexpress

The metabolic regulation of sporulation and parasporal crystal formation in Bacillus thuringiensis revealed by transcriptomics and proteomics

Project description:Proteomics on B. thuringiensis CT_43 cells in GYS medium. Two biological replicate cell samples were collected at time points of 7 h, 9 h, 13 h and 22 h, respectively. The crude proteins were purified using the ReadyPrep 2-D Cleanup Kit, underwent the reductive alkylation, tryptically digested, and were labeled with 8-plex iTRAQ reagents as follows: 7 h-1, 113; 7 h-2, 114; 9 h-1, 115; 9 h-2, 116; 13 h-1, 117; 13 h-2, 118; 22 h-1, 119; and 22 h-2, 121. The labeled samples were pooled and resolved into 12 fractions, which were loaded onto LC-MSMS.

2019-11-22 | PXD000020 | Pride

Transcriptome analysis of HeLa cells upon deprivation of methionine and cysteine (Met/Cys)

Project description:We have previously shown that deprivation of essential amino acids, namely methionine/cysteine or tyrosine, leads to the transcriptional reactivation of integrated silenced transgenes, and latent HIV-1 provirus. In an effort to understand the underlying mechanisms, here we investigate the overall transcriptional profile of HeLa cells upon Met/Cys starvation for different time points, including the expression of repeated and transposable elements. HeLa cells carrying a stably integrated and silenced plasmid expressing the OA1/GPR143 gene (pcDNA3.1-OA1) were cultured in regular DMEM medium for 6-30-120 hours, or in absence of Met/Cys for 6-15-30-72-120 hours, and the changes in the expression of genes and repeated elements was evaluated by RNAseq

2018-07-21 | E-MTAB-6452 | biostudies-arrayexpress

LncRNA Sequencing Analysis of Mouse spermatogonial stem cells during Glial cell-derived neurotrophic factor?GDNF?treatment

Project description:Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides and have little or no potential for translation. More and more studies have domenstrated mammalian lncRNAs are intrinsically functional and growing data indicate lncRNAs are determinants of stem cell fate by regulating potency, self-renewal and differentiation. There is no report of lncRNAs in spermatogonial stem cells?SSCs?, and importance of lncRNAs in germline linage stem cell has not been investigated yet. here, we presents a large –scale profiling of all lncRNAs in SSCs as well as those lncRNAs regulated by SSC dependent growth factor GDNF through high throughput sequencing. Spermatogonial stem cells were first suffered from an 18 hr GDNF withdrawal followed by refreshment with GDNF for 8 hrs and RNA samples were collected from normal culture wells (N), GDNF 18hr withdrawal wells (0hr), and GDNF 8 hr refreshed cells (8hr). After all GDNF treatment, cultured germ cell clumps were gently blowed with a 200?l pipette, and followed by Total RNA isolation and sequencing by Illumina HiSeqTM 2000

2015-04-15 | E-GEOD-66998 | biostudies-arrayexpress

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