Diane E. Dickel
A5023809322- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Autism Spectrum Disorder Research
- Congenital heart defects research
- Genomic variations and chromosomal abnormalities
- Developmental Biology and Gene Regulation
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Biochemical Analysis and Sensing Techniques
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- melanin and skin pigmentation
- Genomics and Rare Diseases
- Receptor Mechanisms and Signaling
- Pluripotent Stem Cells Research
- Regulation of Appetite and Obesity
- Plant Molecular Biology Research
- Advanced biosensing and bioanalysis techniques
- Animal Genetics and Reproduction
- Gene expression and cancer classification
- Obsessive-Compulsive Spectrum Disorders
- Zebrafish Biomedical Research Applications
Lawrence Berkeley National Laboratory
2014-2024
University of California, Berkeley
2019-2022
Joint Genome Institute
2019-2022
Berkeley College
2022
University of Washington
2007-2011
Seattle University
2011
University of Illinois Chicago
2007
University of Chicago
2006
Abstract The human and mouse genomes contain instructions that specify RNAs proteins govern the timing, magnitude, cellular context of their production. To better delineate these elements, phase III Encyclopedia DNA Elements (ENCODE) Project has expanded analysis cell tissue repertoires RNA transcription, chromatin structure modification, methylation, looping, occupancy by transcription factors RNA-binding proteins. Here we summarize efforts, which have produced 5,992 new experimental...
Highlights•RNA expression profiling of >12,000 single Arabidopsis root cells by Drop-seq•Recovered major tissue types and cell stages identified specific marker genes•Sucrose alters type proportions but does not profoundly change identities•Identified ∼800 genes dynamically expressed across endodermis developmentSummarySingle-cell transcriptome heterogeneous tissues can provide high-resolution windows into developmental dynamics environmental responses, its application to plants has been...
The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling diverse panel mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state accessibility in developing fetus. In total performed 1,128 immunoprecipitation with sequencing (ChIP-seq) assays histone modifications 132 assay transposase-accessible using...
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal developing a comprehensive map functional elements human genome. These included genes, biochemical regions associated gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) transcript isoforms. marks serve as sites for candidate cis-regulatory (cCREs) that may roles regulating expression1. project has been extended to model organisms, particularly mouse. In...
Abstract During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 embryonic development to birth, sampling 17 tissues organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis cell-proliferation sets that were further characterized transcription factor motif codes their promoters. We...
Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1-3, but overall extent to which this occurs remains unknown. Here we demonstrate targeted deletions of TAD a range disruptions in vivo function organismal development. We used CRISPR editing mice individually delete eight (11-80 kb size) from genome. All examined...
<h3>Context</h3> The first 2 independent linkage studies for obsessive-compulsive disorder (OCD) identified a region on 9p24 with suggestive evidence linkage. glutamate transporter gene solute carrier family 1, member 1 (<i>SLC1A1</i>) is promising functional candidate in this because altered glutamatergic concentrations have been found the striatum and anterior cingulate neuroimaging of pediatric OCD. <h3>Objective</h3> To determine whether genotypes at polymorphisms the<i>SLC1A1</i>gene...
Non-coding mutations at the far end of a large gene desert surrounding SOX9 result in human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging stem cell differentiation model, we identify two clusters enhancers within PRS-associated region that regulate expression during restricted window facial progenitor development distances up to 1.45 Mb. Enhancers Mb cluster exhibit highly synergistic activity is dependent on Coordinator motif. Using mouse models, demonstrate PRS...
Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited
Abstract Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack accurate functional annotations prevents their interpretation. We describe genome-wide landscape distant-acting enhancers active developing and adult heart, an organ whose impairment a predominant cause mortality morbidity. Using integrative analysis >35 epigenomic data sets from mouse pre- postnatal hearts we created comprehensive reference >80,000 putative...
DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation Dlx1&2 alters expression genes that critical for development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), vivo vitro studies regulatory element (RE) function. This revealed DLX-organized gene network at genomic, cellular, spatial levels mouse embryonic basal ganglia. TFs perform dual...