A5115604209- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer-related gene regulation
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Genetic Syndromes and Imprinting
- Aquatic Invertebrate Ecology and Behavior
- RNA and protein synthesis mechanisms
- Pluripotent Stem Cells Research
- Genetics and Neurodevelopmental Disorders
- Chromosomal and Genetic Variations
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Marine Bivalve and Aquaculture Studies
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Myxozoan Parasites in Aquatic Species
- Bioinformatics and Genomic Networks
- Identity, Memory, and Therapy
- Machine Learning in Bioinformatics
- Marine Ecology and Invasive Species
- Atherosclerosis and Cardiovascular Diseases
Yangzhou University
2020-2024
Eunice Kennedy Shriver National Institute of Child Health and Human Development
2018-2020
National Institutes of Health
2018-2020
Virginia Tech
2014-2019
Biocom
2016-2019
University of Chinese Academy of Sciences
2009-2018
Chinese Academy of Sciences
2009-2011
Institute of Oceanology
2009
Beijing Institute of Genomics
2009
Abstract Life experience can leave lasting marks, such as epigenetic changes, in the brain. How life is translated into storable information remains largely unknown. With unbiased data-driven approaches, we predicted that Egr1 , a transcription factor important for memory formation, plays an essential role brain programming. We performed EGR1 ChIP-seq and validated thousands of binding sites with methylation patterns established during postnatal development. More specifically, these become...
The faithful transmission of DNA methylation patterns through cell divisions is essential for the daughter cells to retain a proper identity. To achieve comprehensive assessment fidelity, we implemented genome-scale hairpin bisulfite sequencing approach generate data double strands simultaneously. We show here that fidelity increases globally during differentiation mouse embryonic stem (mESCs), and particularly high in promoter regions actively expressed genes positively correlated with...
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these are recruited to specific regions genome is still poorly understood. In Drosophila, PcG response elements (PREs) that include combinations sites for sequence DNA binding "PcG recruiters," including Pho, Cg, and Spps. To understand their roles recruitment, we compared Pho-, Cg-, Spps-binding against H3K27me3 by ChIP-seq wild-type mutant third instar larvae. canonical domains...
Polycomb group (PcG) proteins mediate epigenetic silencing of important developmental genes by modifying histones and compacting chromatin through two major protein complexes, PRC1 PRC2. These complexes are recruited to DNA CpG islands (CGIs) in mammals response elements (PREs) Drosophila . When PcG target turned OFF, bind PREs or CGIs, serve as anchors that loop together stabilize gene silencing. Here, we address which whether looping when their targets the ON transcriptional state. While...
Nutrient sensing and adaptation in the placenta are essential for pregnancy viability proper fetal growth. Our recent study demonstrated that adapts to nutrient insufficiency through mechanistic target of rapamycin (mTOR) inhibition–mediated trophoblast differentiation toward syncytiotrophoblasts (STBs), a highly specialized multinucleated subtype mediating extensive maternal–fetal interactions. However, underlying mechanism remains elusive. Here, we unravel indispensable role mTORC1...
Background . Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states Cs in the genomes different tissues, cell types, developmental stages. Accurate characterization DNA is essential for understanding genotype phenotype association, gene environment interaction, diseases, cancer. Aligning to a reference genome has been challenging task. We compared five read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, BRAT-BW,...
Many Gram-negative bacteria infect hosts and cause diseases by translocating a variety of type III secreted effectors (T3SEs) into the host cell cytoplasm. However, despite dramatic increase in number available whole-genome sequences, it remains challenging for accurate prediction T3SEs. Traditional models have focused on atypical sequence features buried N-terminal peptides T3SEs, but unfortunately, these had high false-positive rates. In this research, we integrated promoter information...
Chromatin context influences Polycomb domain structure and function.
Veneridae is a diverse, commercially important, and cosmopolitan family. Here we present the complete mitochondrial genome of clam Meretrix petechialis (Bivalvia: Veneridae). The 19,567 bp in length, contains 36 genes including 12 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs (tRNAs). All are encoded on same strand. In contrast to typical animal genomes, it lacks gene atp8. other distinct features that has only one copy trnS duplication trnQ gene. Mitochondrial orders most...
HIRA is a histone chaperone that deposits the variant H3.3 in transcriptionally active genes. In DiGeorge syndromes, DNA stretch encompassing deleted. The syndromes manifest varied abnormalities, including immunodeficiency and thrombocytopenia. essential mice, as total knockout (KO) results early embryonic death. However, role of hematopoiesis poorly understood. We investigate hematopoietic cell-specific Hira deletion mice show it dramatically reduces bone marrow stem cells (HSCs), resulting...
Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles-usually by creating cis-elements (e.g. enhancers and promoters) bound distinct transcription factors (TFs). TE-derived have gained unprecedented attentions recently, one key step toward their understanding is to identify enriched genomic intervals a set or TF binding sites) as candidates for further study. Nevertheless, such analysis...
Abstract The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One open questions is defining mechanisms PcG recruitment to chromatin. In Drosophila, crucial role thought belong DNA-binding associated with response elements (PREs). However, current data suggests not all PRE-binding factors have been identified. Here, we report identification transcription factor Crooked legs (Crol) as a novel...
Human induced pluripotent stem cells (iPSCs) have a wide range of applications throughout the fields basic research, disease modeling and drug screening. Epigenetic instable iPSCs with aberrant DNA methylation may divide differentiate into cancer cells. Unfortunately, little effort has been taken to compare epigenetic variation in that differentiated Here, we developed an analytical procedure decipher heterogeneity mixed further exploited it quantitatively assess methylomes adipose-derived...
Embryonic stem cells (ESCs) consist of a population self-renewing displaying extensive phenotypic and functional heterogeneity. Research towards the understanding epigenetic mechanisms underlying heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci interpret biological meanings methylation variations remain largely unexplored. To fill research gap, we implemented computational pipeline analyze single-cell...
Abstract DNA methylation is an epigenetic mechanism critical for tissue development and cell specification. Mammalian brains consist of many different types cells with assumedly distinct profiles, thus some genomic loci may demonstrate bipolar pattern, i.e. hypermethylated in one subset but hypomethylated others. Currently, how extensive patterns vary among brain unknown methylated remain largely unexplored. In this study, we implemented a procedure to infer cell-subset specific (CSM) from...
DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach characterizing genome-wide using Next Generation Sequencing technology sequence bisulfite treated DNA. The short reads are mapped the reference genome determine statuses of Cs. However, despite intense effort, a much smaller proportion derived from (usually about 40-80%) can be than regular mapping (> 90%), it unclear what factors lead this low efficiency. To address issue,...
A comprehensive, multi-omic survey was performed to disclose the genetic backgrounds and differences between multidrug-resistant -susceptible C. haemulonii strains. Genes were identified with mutations or significant expression in compared multidrug-susceptible strains, which mainly involved multidrug resistance, stress fitness, morphology. The Cdr1-encoding gene, 2486 ( CH_2486 ), expressed at a significantly increased level Functional inhibition experiments further implicated potential...
Abstract Motivation In genome-wide rate comparison studies, there is a big challenge for effective identification of an appropriate number significant features objectively, since traditional statistical comparisons without multi-testing correction can generate large false positives while tremendously decreases the statistic power. Results this study, we proposed new exact test based on translation to two binomial distributions. With modeling and real datasets, (EBT) showed advantage in...
With recent development in sequencing technology, a large number of genome-wide DNA methylation studies have generated massive amounts bisulfite data. The analysis patterns helps researchers understand epigenetic regulatory mechanisms. Highly variable reflect stochastic fluctuations methylation, whereas well-structured imply deterministic events. Among these patterns, bipolar are important as they may originate from allele-specific (ASM) or cell-specific (CSM). Utilizing nonparametric...
Abstract Human genes form a large variety of isoforms after transcription, encoding distinct transcripts to exert different functions. Single-molecule RNA sequencing facilitates accurate identification the by extending nucleotide read length significantly. However, gene or isoform diversity is lowly represented mRNA molecules captured single-molecule sequencing. Here, we show that cDNA normalization procedure before library preparation for PacBio RS II captures 3.2–6.0 fold more full-length...