Project description:Objectives: MicroRNA (miRNA) can be released to the extracellular medium and participates in neuronal communication. We investigate the mechanisms of miRNA exocytosis by vesicle fusion as a neuromodulator in a manner that are disparate from silencing gene expression. Methods: Small RNA sequencing data of large dense-core vesicle were generated by next-generation sequencing (NGS) in triplicate using Illumina Hiseq 2500. Results: Large dense-core vesicles contain a variety of known and novel miRNAs inside including miR-375. Conclusion: miRNAs can be novel neuromodulators, which are stored in LDCVs and released by vesicle fusion by SNARE assembly and synaptotagmin-1

2017-01-01 | GSE84834 | GEO

de novo re-construction of the core genome from ChIP-Seq for large-genome organisms

Project description:Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high accuracy, sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.

2018-05-27 | GSE107827 | GEO

A Spirodela polyrhiza genome and proteome reveal conserved chromosomal structure and translation favoring energy production

Project description:Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.

2022-10-26 | PXD017093 | Pride

CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (ChIP-Seq)

Project description:In this study we characterized the importance of CDK12-kinase activity in cell cycle regulation, using CDK12 anolog-sentive cells. Inhibition of analog-sensitive CDK12 reveals its catalytic activity is necessary for optimal G1/S progression. Mechanistically, CDK12 regulates transcription of core DNA replication genes and affects timely assembly of pre-replication DNA complex on chromatin. We have performed 3’-end RNA-sequencing after CDK12 inhibition and identified that the expression of core DNA replication genes were affected. To investigate further, we carried out nuclear RNA-seq coupled with ChIP-seq, and demonstrated that CDK12 regulates RNAPII processivity of core DNA replication genes and optimal G1/S progression.

2019-07-22 | GSE120069 | GEO

esBAF is an essential component of the core pluripotency transcriptional network

Project description:Distinctive SWI/SNF-like ATP-dependent chromatin remodeling esBAF complexes are indispensable for the maintenance and pluripotency of mouse embryonic stem (ES) cells. To understand the mechanism underlying the roles of these complexes in ES cells, we performed high-resolution genome-wide mapping of the core ATPase subunit, Brg, using ChIP-Seq technology. We find that that esBAF, as represented by Brg, binds to genes encoding components of the core ES transcriptional circuitry, including Polycomb group proteins. esBAF colocalizes extensively with Oct4, Sox2 and Nanog genome-wide, and shows distinct functional interactions with Oct4 and Sox2 at its target genes. Surprisingly, no significant colocalization of esBAF with PRC2 complexes, represented by Suz12, is observed. Lastly, esBAF co-binds with Stat3 and Smad1 genome-wide, consistent with a direct and critical role in LIF and BMP signaling essential to maintain pluripotency. Taken together, our studies indicate that esBAF is both an essential component of the core pluripotency transcriptional network, and might also be a critical component of the LIF and BMP signaling pathways essential for maintenance of self-renewal and pluripotency. Brg knockdown effect on expression, Brg ChIP-Seq

2009-01-20 | E-GEOD-14344 | biostudies-arrayexpress

Liver tissue from the "Four Core Genotype" treated group C57BL/6J mice versus pool C57BL/6J mice of chow diet Liver

Project description:The purpose of this experiment was to determine the expression traits in Liver tissue from the Four Core Genotype treated group. Keywords: Sry transgene Four Core Genotype Mouse liver Tissue Liver tissue from the "Four Core Genotype" treated group consists of 20 female and male C57BL/6J mice fed a chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were gonadectomized at 8 weeks of life. In mice of the "four core genotypes" (FCG), the Y chromosome is deleted for the testis-determining gene Sry, producing the Y- chromosome. The Sry transgene is inserted onto an autosome, so that testis determination is independent of the complement of sex chromosomes. XY-Sry gonadal males are bred with XX gonadal females, producing progeny with four different genotypes: two types of gonadal males (XX.Sry and XY-Sry) and two types of gonadal females (XX and XY-). At 12 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80Â°C. All sample were compared to a common pool created from equal portions of RNA from each of the samples.

2010-06-24 | E-GEOD-13264 | biostudies-arrayexpress

CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (ChIP-Seq II)

2019-07-22 | GSE130509 | GEO

Core Binding Factor β Is Required For Group-2 Innate Lymphoid Cell Activation

Project description:Core Binding Factor β Is Required For Group-2 Innate Lymphoid Cell Activation

| PRJNA476938 | ENA