A cis-regulatory atlas of maize single cells
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ABSTRACT:
PROVIDER: PRJNA648930 | ENA |
REPOSITORIES: ENA
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Project description:Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. We describe 92 distinct patterns of chromatin accessibility across more than 165,913 putative CREs, greater than 56,575 cells, and 52 known cell-types using a novel regularized quasibinomial logistic model for estimating single cell accessibility. Cell-type specification could be largely explained by combinatorial accessibility of transcription factors (TFs) and their associated binding. Analysis of cell type-specific co-accessible chromatin recapitulated higher-order chromatin interactions, providing novel insight into cell type-specific regulatory dynamics. Integration of genetic diversity data revealed cell-type specific CREs contributed to specific morphological and molecular phenotypic traits indicative of their cellular functions, expanding our understanding of the molecular influence of complex traits in a eukaryotic species.
2020-09-30 | GSE155178 | GEO
Project description:Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution.
2014-11-06 | GSE61810 | GEO
Project description:Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem) followed by assessment of allele-specific gene expression.
2014-11-06 | E-GEOD-61810 | biostudies-arrayexpress
Project description:Widespread Long-range Cis-Regulatory Elements in the Maize Genome
| PRJNA492464 | ENA
Project description:Genetic mapping studies on crops suggest that agronomic traits can be controlled by loci within the gene-distal intergenic space. Despite the biological importance and the potential agronomic utility of these intergenic loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic chromatin features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate eQTL-gene interactions. Additionally, putative CREs display elevated transcriptional enhancer activities, as measured by STARR-seq. These results provide functional support for the widespread existence of CREs which act over large genomic distances to modulate gene expression.
2019-09-19 | GSE120304 | GEO
Project description:P1 is the major QTL for maysin and chlorogenic acid accumulation in silk. Both compounds were important for plant defenses. Silk is an important reproductive organ that is critical for good seed setting in corn ear and needs to be protected against various stresses, therefore, metabolics compounds (ex: phenolics) were highly enriched in silk. Here we characterize transcriptome changes in maize protoplast, and natural variants of P1 silks, and pericards to characterize the regulatory landscape. Also we evaluated profiles of silk in B73 x A632 hybrids in order to cis and trans specific effect driven by P1 in maize. Our study identifies new P1 targets in the silk and protoplast. Together with the RNA-seq data (P1-rr vs P1-ww in silk and pericarp and protoplast 35S:P1 vs empty vector control), we observed new P1 functions in silk that were not observed in pericarp. Also, Protoplast and silk ChIP-seq in F1 silk, as well as DAP-seq analysis of P1 - shows specific P1 targets with highlight cis and trans effect on the F1 hybrids.
2023-12-01 | GSE224196 | GEO
Project description:Naïve CD4+ T Cells are capable of differentiating into numerous T helper effector lineages depending on the provided local cytokines during activation. Cis-regulatory elements (CRE) are critical for cell differentiation, homeostasis, and function; however, CRE functional annotation (e.g. silencers, enhancers, and insulators) from existing genomic libraries remains an active need. Genome wide screens, including Transcribing Active Regulatory Region Sequencing (STARR-Seq) provides quantifies enhancer activity. However, these screens are mainly conducted in immortalized cell lines. Therefore, we have modified STARR-Seq using a non-integrating lentiviral transduction system (Lenti-STARR-seq) to investigate CRE in human CD4+ T cells. We identify and validate functional enhancers and negative regulatory elements (NRE). These elements differences stark differences in chromatin modification, TF binding, and nucleosome positioning. Additionally, STARR-Seq enhancers, but not NRE, exhibit transcription of enhancer RNA. Collectively these data suggest that Lenti-STARR-Seq may be a useful tool in the screening of primary human cell types for CRE function, and provides an atlas of functional CRE in human CD4+ T Cells.
2023-05-11 | GSE217535 | GEO
Project description:Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas for seed development of eight maize inbred lines based on 144 samples from the middle to late stages of grain development. A total of 26,747 genes with FPKM value more than 1 at least one sample were found to be involved in programming grain development. Global comparisons of genes expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with grain moisture content and grain dehydration rate of different developmental time points of eight maize inbred lines, we captured a large number of genes related to grain moisture content and grain dehydration rate, which should help elucidate key mechanisms and regulatory networks that underlie grain dehydration during maize grain development. These results provide a comprehensive understanding of which biological processes are involved in the regulation of moisture variety of maize grain, the general principles of which provide a new perspective on improving maize grain dehydration characteristics. Meanwhile, this study provides a valuable resource for understanding the genetic regulation of maize grain development.
2022-10-01 | GSE158816 | GEO
Project description:Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
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Project description:Single nucleus multi-omics regulatory atlas of the murine pituitary
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