A5043475222- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- MicroRNA in disease regulation
- Muscle Physiology and Disorders
- Telomeres, Telomerase, and Senescence
- Acute Myeloid Leukemia Research
- Advanced biosensing and bioanalysis techniques
- Neuroinflammation and Neurodegeneration Mechanisms
- Adipose Tissue and Metabolism
- Single-cell and spatial transcriptomics
- Barrier Structure and Function Studies
- Cancer Genomics and Diagnostics
- Prenatal Screening and Diagnostics
- Proteoglycans and glycosaminoglycans research
Buck Institute for Research on Aging
2017-2021
University of California, Berkeley
2017
Pennsylvania State University
2011-2015
The laboratory mouse shares the majority of its protein-coding genes with humans, making it premier model organism in biomedical research, yet two mammals differ significant ways. To gain greater insights into both shared and species-specific transcriptional cellular regulatory programs mouse, Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications replication domains throughout genome diverse cell tissue types. By...
Summary Senescent cells play important roles in both physiological and pathological processes, including cancer aging. In all cases, however, senescent comprise only a small fraction of tissues. phenotypes have been studied largely relatively homogeneous populations cultured cells. vivo , are generally identified by number markers, but whether how these markers vary among individual is unknown. We therefore utilized combination single‐cell isolation nanofluidic PCR platform to determine the...
Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many factors dissociate from mitotic chromosomes, the observation that certain chromatin features remain associated individual loci during originated hypothesis such mitotically retained molecular signatures could provide memory mitosis. To understand role in...
Abstract Brain damage due to stroke or traumatic brain injury (TBI), both leading causes of serious long-term disability, often leads the development epilepsy. Patients who develop post-injury epilepsy tend have poor functional outcomes. Emerging evidence highlights a potential role for blood-brain barrier (BBB) dysfunction in However, common mechanisms underlying pathological hyperexcitability are largely unknown. Here, we show that comparative transcriptome analyses predict remodeling...
Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action coordination with transcriptional control are not fully understood. Alterations in structure appear to establish a permissive state for gene activation at some loci, they play an integral role other loci. To determine predominant roles states factor occupancy directing regulation during we mapped accessibility,...
Regulated gene expression controls organismal development, and variation in regulatory patterns has been implicated complex traits. Thus accurate prediction of enhancers is important for further understanding these processes. Genome-wide measurement epigenetic features, such as histone modifications occupancy by transcription factors, improving enhancer predictions, but the contribution features to accuracy not known. Given importance hematopoietic factor TAL1 erythroid activation, we...
Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures four master (GATA1, GATA2, TAL1, and FLI1) three diagnostic histone modification marks with gene expression changes that occur during development primary cultured megakaryocytes (MEG) erythroblasts (ERY) from murine fetal liver stem/progenitor cells. We identified a robust,...
We used mouse ENCODE data along with complementary from other laboratories to study the dynamics of occupancy and role in gene regulation transcription factor TAL1, a critical regulator hematopoiesis, at multiple stages hematopoietic differentiation. combined ChIP-seq RNA-seq six cell types representing progression multilineage precursors differentiated erythroblasts megakaryocytes. found that sites shift dramatically during commitment erythroid lineage, vary further terminal maturation, are...
During the maturation phase of mammalian erythroid differentiation, highly proliferative cells committed to lineage undergo dramatic changes in morphology and function produce circulating, enucleated erythrocytes. These are caused by equally alterations gene expression, which turn driven abundance binding patterns transcription factors such as GATA1. We have studied dynamics GATA1 ChIP-seq global expression responses RNA-seq a GATA1-dependent mouse cell line model for maturation, both cases...
Global views of biochemical mechanisms regulating gene expression during cell lineage commitment and maturation can be obtained by analyzing chromatin immunoprecipitation on a genome-wide scale, enabled massively parallel sequencing. We have conducted ChIP-seq RNA-seq assays cells from many informative stages mouse hematopoiesis, ranging multilineage progenitor to mature megakaryocytes erythroblasts. find that histone modification patterns characteristic repressed or active are established...