A5100715055- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Nuclear Structure and Function
- SARS-CoV-2 and COVID-19 Research
- Genomic variations and chromosomal abnormalities
- Viral gastroenteritis research and epidemiology
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Soybean genetics and cultivation
- SARS-CoV-2 detection and testing
- Photosynthetic Processes and Mechanisms
- Algal biology and biofuel production
- Plant Stress Responses and Tolerance
- MicroRNA in disease regulation
- Geomagnetism and Paleomagnetism Studies
- Cellular Mechanics and Interactions
- Hippo pathway signaling and YAP/TAZ
- Biocrusts and Microbial Ecology
- Plant Micronutrient Interactions and Effects
- Oral microbiology and periodontitis research
- Bone Metabolism and Diseases
- Biopolymer Synthesis and Applications
- Plant responses to water stress
University of Illinois Urbana-Champaign
1992-2025
Research Institute of Animal Husbandry
2025
Inner Mongolia People's Hospital
2025
The Netherlands Cancer Institute
2024
San Diego Biomedical Research Institute
2024
Carnegie Mellon University
2024
Oncode Institute
2024
Whitehead Institute for Biomedical Research
2012-2023
Massachusetts Institute of Technology
2023
Shanghai Micro Satellite Engineering Center
2022
While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined structures. In this study, we describe TSA-Seq, a new mapping capable providing “cytological ruler” estimating mean chromosomal from speckles genome-wide and predicting several Mbp trajectories between compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal clear lamina...
Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some these do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed integrated into DNA human cells culture transcription sequences might account for positive PCR seen patients. In support this hypothesis, we found copies genome infected...
TSA-seq mapping suggests that gene distance to nuclear speckles is more deterministic and predictive of expression levels than radial positioning. Gene correlates inversely with speckles, chromosome regions unusually high located at the apex loops protruding from periphery into interior. Genomic distances nearest lamina-associated domain are larger for loop apexes closest suggesting possibility conservation speckle-associated regions. To facilitate comparison genome organization by TSA-seq,...
Abstract We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative multiple structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN integrate compartment mapping (TSA-seq DamID) chromatin interaction data (Hi-C) from K562 cells identify 10 spatial states speckles, lamina, putative associations with nucleoli. These show novel patterns of organization their...
Baicalin is a natural flavonoid compound with wide range of biological activities, including anti-oxidant and anti-inflammatory properties. Previous we found that the abundance baicalin in bovine serum significantly higher than ovine at mid-lactation. It suggests may play role regulation lactation performance. Here, effects on proliferative, oxidative stress response, synthesis capacities major milk components mammary epithelial cells (OMECs) were investigated. And transcriptomic analysis...
In certain cyanobacteria and algae, cytochrome c553 or plastocyanin can serve to carry electrons from the bf complex photosystem I. The availability of copper in growth medium regulates which protein is present. To investigate induced control gene expression we isolated these proteins cyanobacterium Synechocystis 6803. Using immunodetection optical spectroscopy, steady state levels were measured cells grown at different concentrations. results show that 20-30 nM copper, was present, whereas...
Summary Prolonged SARS-CoV-2 RNA shedding and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these most commonly are non-infectious 1–14 . Here we investigated the possibility that RNAs can be reverse-transcribed integrated into human genome transcription sequences might account for tests. In support this hypothesis, found chimeric transcripts consisting viral fused to cellular published data sets infected cultured cells primary patients,...
Nuclear organization has an important role in determining genome function; however, it is not clear how spatiotemporal of the relates to functionality. To elucidate this relationship, a method for tracking any locus interest desirable. Recently clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or transcription activator-like effectors were adapted imaging endogenous loci; they are mostly limited visualization repetitive regions. Here, we...
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook bodies. Here we integrated analysis sequencing and image-based data to compare in four human cell types relative three different locales: the lamina, speckles, nucleoli. Whereas gene expression correlates mostly with speckle proximity, DNA replication timing proximity multiple locales. Speckle attachment regions emerge as initiation zones whose composition vary...
Abstract The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to function. Here, we integrate a wide variety genomic data generated by 4D Nucleome Project provide detailed view 3D in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We extensive benchmarking mapping assays these diverse datasets annotate spatial features across scales. reveal rich complexity chromatin domains their sub-nuclear positions,...
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook bodies. Here we integrated analysis sequencing and image-based data to compare in four human cell types relative three different locales: the lamina, speckles, nucleoli. Whereas gene expression correlates mostly with speckle proximity, DNA replication timing proximity multiple locales. Speckle attachment regions emerge as initiation zones whose composition...
Abstract Background The study of ovine lactation and mastitis is limited by the lack physiologically relevant in vitro models. Compared to mammary epithelial cells, gland organoids (MaOs) offer a better model for studying lactation, as they more accurately replicate tissue structure interactions cells vivo. Here, we optimize protocol isolation, culture, characterization, transfection MaOs derived from ewe tissue. Results: We compared different enzymatic digestion methods found that type IV...
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook bodies. Here we integrated analysis sequencing and image-based data to compare in four human cell types relative three different locales: the lamina, speckles, nucleoli. Whereas gene expression correlates mostly with speckle proximity, DNA replication timing proximity multiple locales. Speckle attachment regions emerge as initiation zones whose composition...
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook bodies. Here we integrated analysis sequencing and image-based data to compare in four human cell types relative three different locales: the lamina, speckles, nucleoli. Whereas gene expression correlates mostly with speckle proximity, DNA replication timing proximity multiple locales. Speckle attachment regions emerge as initiation zones whose composition vary...
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook bodies. Here we integrated analysis sequencing and image-based data to compare in four human cell types relative three different locales: the lamina, speckles, nucleoli. Whereas gene expression correlates mostly with speckle proximity, DNA replication timing proximity multiple locales. Speckle attachment regions emerge as initiation zones whose composition vary...
Non-receptor tyrosine kinase activated cdc42 was reported to participate in several types of cancers mammals. It is also believed have an anti-apoptotic function Drosophila. Here, we report the identification Drosophila as a growth promoter and novel Hippo signaling pathway regulator. We find that promotes tissue through modulating Yorkie activity. Furthermore, demonstrate interacts with Expanded induces phosphorylation on multiple sites. propose model negatively regulates by changing its...
Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology transcriptome assembly R. under normal cold conditions evaluate how it responds stress.After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from assembled transcripts. Based on similarity search analysis with seven...
Abstract Chromosomes segregate differentially relative to distinct subnuclear structures, but this genome-wide compartmentalization, pivotal for modulating genome function, remains poorly understood. New genomic mapping methods can reveal chromosome positioning specific nuclear structures. However, computational that integrate their results identify overall intranuclear chromo-some have not yet been developed. We report SPIN, a new method spatial localization patterns. As proof-of-principle,...
Abstract Genome-wide mapping of chromosomal distances relative to nuclear compartments using TSA-Seq suggests a more deterministic relationship between intranuclear gene position and expression as function speckle distance than radial position. Gene activity increases overall with decreasing speckles, active regions forming the apex chromosome loops protruding from periphery into interior. Interestingly, genomic nearest lamina-associated domain are larger for loop apexes very close...