Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1211828 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. We demonstrate a streamlined ATAC-seq protocol for maize in which nuclei purification can be achieved without cell sorting, and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, provides a precise and efficient assessment of the maize chromatin landscape.
2024-01-10 | GSE252638 | GEO
Project description:High-throughput discovery of post-transcriptional cis-regulatory elements
| PRJNA302654 | ENA
Project description:STARR-seq assay performed on uncharacterized cis-regulatory elements to find candidate silencer elements in K562 cells.
2019-12-18 | GSE142207 | 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: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:High-throughput discovery of post-transcriptional cis-regulatory elements (8-nt)
| PRJNA302651 | ENA
Project description:High-throughput discovery of post-transcriptional cis-regulatory elements (miRNA-seq)
| PRJNA302653 | ENA
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:Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis-regulatory activity remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 maize inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and how transposons rewired the regulatory landscape. We found widespread chromatin accessibility variation associated with >4.6 million genetic variants with largely cell-type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most prevalent determinants of chromatin accessibility. Finally, integration of genetic variants associated with chromatin accessibility, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular context to alter maize flowering phenotypes.
2024-11-19 | GSE273478 | GEO
Project description:To quantify functional enhancers, we performed STARR-seq (Self-Transcribing Active Regulatory Region sequencing) in the U2OS-GR and the U2OS-AR cell lines (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for rat GR or human AR, respectively). U2OS-GR cells were treated with dexamethasone (1 µM) or vehicle (ethanol) for 14 hours. U2OS-AR cells were treated with R1881 (5 nM) or vehicle (DMSO) for 14 hours. To limit the number of putative enhancers, the STARR library contained genomic regions isolated by FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) from dexamethasone-treated U2OS-GR cells to include regions that gain accessibility upon GR activation. We added unique molecular identifiers (UMIs) during the reverse transcription stage to facilitate quantitative measurements of enhancer activity for each fragment. The UMI for each read is present within the sequence identifier line (directly following the y coordinate and separated by a ':') of the fastq files.
2021-03-09 | E-MTAB-9614 | biostudies-arrayexpress