Jennifer A. Akiyama
A5073570829- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Congenital heart defects research
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Autism Spectrum Disorder Research
- RNA modifications and cancer
- Neonatal Respiratory Health Research
- Developmental Biology and Gene Regulation
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- Advanced biosensing and bioanalysis techniques
- Single-cell and spatial transcriptomics
- Neuroscience of respiration and sleep
- Genomic variations and chromosomal abnormalities
- Lipid metabolism and disorders
- Cholesterol and Lipid Metabolism
- Animal Genetics and Reproduction
- Craniofacial Disorders and Treatments
- Chromatin Remodeling and Cancer
- Cellular transport and secretion
- Neurogenesis and neuroplasticity mechanisms
- Immune Response and Inflammation
- RNA regulation and disease
Lawrence Berkeley National Laboratory
2016-2025
Joint Genome Institute
2004-2015
United States Department of Energy
2004-2009
Western General Hospital
2008-2009
Institut Pasteur
2004
Institut Pasteur de Lille
2004
University of California, San Francisco
1996-2002
California Health and Human Services Agency
2002
Universidade de São Paulo
1995
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...
Significance Using high-throughput experiments, we determined the functional epigenomic landscape in pancreatic islet cells. Computational integration of these data along with similar from ENCODE project revealed presence large gene control elements across diverse cell types that refer to as “stretch enhancers.” Stretch enhancers are type specific and associated increased expression genes involved cell-specific processes. We find genetic variations common disease highly enriched stretch...
Surfactant protein D (SP-D) is one of two collectins found in the pulmonary alveolus. On basis homology with other collectins, potential functions for SP-D include roles innate immunity and surfactant metabolism. The gene was disrupted embryonic stem cells by homologous recombination to generate mice deficient SP-D. Mice heterozygous mutant allele had concentrations that were approximately 50% wild type but no obvious phenotypic abnormality. totally healthy 7 months a progressive...
Changes in gene regulation are thought to have contributed the evolution of human development. However, vivo evidence for uniquely developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence ( HACNS1 ) that evolved extremely rapidly humans acted as an enhancer expression gained strong limb domain relative orthologous elements from chimpanzee and rhesus macaque. This gain was consistent across two stages mouse included presumptive anterior wrist...
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...
Introduction The shape of the face is one most distinctive features among humans, and differences in facial morphology have substantial implications areas such as social interaction, psychology, forensics, clinical genetics. Craniofacial highly heritable, including normal spectrum morphological variation well susceptibility to major craniofacial birth defects. In this study, we explored role transcriptional enhancers development complex. Our study based on rationale that enhancers, which can...
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...
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...
Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such RNAs (eRNAs) within transcriptome, and association eRNA expression with tissue-specific activity in vivo remain poorly understood. Here, we investigated dynamics embryonic mouse tissues via deep RNA sequencing. Overall, approximately 80% validated enhancers show that correlates activity. Globally, identified thousands tissue-specifically regions (TSTRs) displaying...
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...