A5079674951- Genomics and Chromatin Dynamics
- Developmental Biology and Gene Regulation
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Acute Myeloid Leukemia Research
- Hematopoietic Stem Cell Transplantation
- Chromosomal and Genetic Variations
- Cancer-related gene regulation
- Histone Deacetylase Inhibitors Research
- Genetic Syndromes and Imprinting
- Sperm and Testicular Function
- Immune Cell Function and Interaction
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Marine Ecology and Invasive Species
- Reproductive Biology and Fertility
- T-cell and B-cell Immunology
- Marine Invertebrate Physiology and Ecology
- interferon and immune responses
- Plant Molecular Biology Research
- Genetics and Neurodevelopmental Disorders
- Hepatitis B Virus Studies
Stowers Institute for Medical Research
2014-2023
University of Kansas Medical Center
2018
University of Kansas
2018
To identify new molecular targets of rapamycin, an anticancer and immunosuppressive drug, we analyzed temporal changes in yeast over 6 h response to rapamycin at the transcriptome proteome levels integrated expression patterns with functional profiling. We show that integration transcriptomics, proteomics, data sets provides novel insights into mechanisms action. first observed a delay correlation mRNA protein where 1 2 correlated best after treatment. This was especially case for inhibition...
Summary Reproductive aging is characterized by a marked decline in oocyte quality that contributes to infertility, miscarriages, and birth defects. This multifactorial, the underlying mechanisms are under active investigation. Here, we performed RNA‐Seq on individual growing follicles from reproductively young old mice identify age‐dependent functions oocytes. unbiased approach revealed genes involved cellular processes known change with age, including mitochondrial function meiotic...
Poised RNA polymerase II (Pol II) is predominantly found at developmental control genes and thought to allow their rapid synchronous induction in response extracellular signals. How the recruitment of poised Pol regulated during development not known. By isolating muscle tissue from Drosophila embryos five stages differentiation, we show that occurs many de novo this makes them permissive for future gene expression. A comparison with other tissues shows these changes are stage specific...
The clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity along the body axis. Recent studies have underscored in addition to encoding homeotic clusters contain key noncoding RNA genes play central role development. In this study, we taken advantage of genome-wide approaches detailed analysis retinoic acid (RA)-induced transcriptional and epigenetic changes within mouse embryonic...
Although traditional genetic assays have characterized the pattern of crossing over across genome in Drosophila melanogaster, these could not precisely define location crossovers. Even less is known about frequency and distribution noncrossover gene conversion events. To assess specific number positions both meiotic crossover events, we sequenced genomes male progeny from females heterozygous for 93,538 X chromosomal single-nucleotide InDel polymorphisms. From analysis 30 F1 hemizygous...
Homeobox a1 ( Hoxa1 ) is one of the most rapidly induced genes in ES cell differentiation and it earliest expressed Hox gene mouse embryo. In this study, we used genomic approaches to identify Hoxa1-bound regions during early stages into neuro-ectoderm. Within 2 h retinoic acid treatment, recruited target sites that are associated with involved regulation pluripotency, these display changes expression. The pattern occupancy dynamic over time. At 12 differentiation, many bound at lost a new...
This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation technologies in whole-transcriptome analysis. Vendor-specific protocols used for library construction often require at least 100 ng total RNA. However, under certain conditions, much less is available construction. In these cases, effective transcriptome profiling requires amplification...
Evolution of the capacity to form secondary outgrowths from principal embryonic axes was a crucial innovation that potentiated diversification animal body plans. Precisely how such develop in early-branching metazoan species remains poorly understood. Here we demonstrate three fundamental processes contribute tentacle development cnidarian Nematostella vectensis. First, pseudostratified ectodermal placode forms at oral pole developing larvae and is transcriptionally patterned into four buds....
Hoxa1 has diverse functional roles in differentiation and development. We identify characterize properties of regions bound by HOXA1 on a genome-wide basis differentiating mouse ES cells. HOXA1-bound are enriched for clusters consensus binding motifs HOX, PBX, MEIS, many display co-occupancy PBX MEIS. MEIS members the TALE family analysis multiple (PBX, TGIF, PREP1, PREP2) shows that nearly all targets occupancy one or more members. The combinatorial patterns proteins define distinct classes...
KAT6 histone acetyltransferases (HATs) are highly conserved in eukaryotes and have been shown to play important roles transcriptional regulation. Here, we demonstrate that the Drosophila Enok acetylates H3 Lys 23 (H3K23) vitro vivo. Mutants lacking functional exhibited defects localization of Oskar (Osk) posterior end oocyte, resulting loss germline formation abdominal segments embryo. RNA sequencing (RNA-seq) analysis revealed spire ( spir ) maelstrom mael ), both required for Osk were...
The KDM4 subfamily of JmjC domain-containing demethylases mediates demethylation histone H3K36me3/me2 and H3K9me3/me2. Several studies have shown that human yeast proteins bind to specific gene promoters regulate expression. However, the genome-wide distribution mechanism genomic-targeting remain elusive. We previously identified Drosophila KDM4A (dKDM4A) as a H3K36me3 demethylase directly interacts with HP1a. Here, we performed ChIP-chip analysis in wild type dkdm4a mutant embryos identify...
The chemosensory system plays an important role in orchestrating sexual behaviors mammals. Pheromones trigger sexually dimorphic and different mouse strains exhibit differential responses to pheromone stimuli. It has been speculated that gene expression the sensory organs detect pheromones may underlie sexually-dimorphic strain-specific cues.We have performed transcriptome analyses of vomeronasal organ, a organ recognizing interspecies cues. We find little evidence dimorphism except for...
The liver is a vital organ with critical functions in metabolism, protein synthesis, and immune defense. Most of the are not mature at birth many changes happen during postnatal development. However, it unclear what occur after birth, developmental stages they occur, how processes regulated. Long non-coding RNAs (lncRNAs) involved development cell differentiation. Here, we analyzed transcriptome lncRNAs mouse from perinatal (day −2) to adult 60) by RNA-Sequencing, an attempt understand role...
Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations amino acid sequences lead to loss ancestral activity functional diversification proteins poorly understood. We used cross-species analysis Drosophila Labial its mouse HOX1 orthologs (HOXA1, HOXB1, HOXD1) as paradigm address this issue. Mouse display low (30%) sequence similarity with Labial. However, substituting endogenous revealed that HOXA1 has retained essential functions Labial,...
The transition of hematopoiesis from the fetal liver (FL) to bone marrow (BM) is incompletely characterized. We demonstrate that Wiskott-Aldrich syndrome verprolin-homologous protein (WAVE) complex 2 required for this transition, as degradation via deletion its scaffold Hem-1 causes premature exhaustion neonatal BM hematopoietic stem cells (HSCs). This HSC due failure engraftment Hem-1-/- FL HSCs, causing early death. defect not lack canonical function WAVE2 complex, regulation actin...
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in specification axial identity. Little is known about properties cis-regulatory elements and underlying transcriptional mechanisms integrate graded signaling inputs to coordinately control expression. Here, we optimized a single molecule fluorescent situ hybridization (smFISH) technique with probes spanning introns evaluate how three shared retinoic acid response element (RARE)-dependent enhancers...