scholarly journals Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1478
Author(s):  
Ezgi Süheyla Karaaslan ◽  
Natalie Faiß ◽  
Chang Liu ◽  
Kenneth Wayne Berendzen
Keyword(s):  
High Efficiency ◽  
Cell Lineage ◽  
Light Response ◽  
Chromatin Accessibility ◽  
Tissue Layer ◽  
Great Precision ◽  
Ploidy Levels ◽  
Epidermal Tissue ◽  
Transcriptional Changes ◽  
Accessible Chromatin

The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response.

scholarly journals Conserved cell-lineage controlled epigenetic regulation in human and mouse glioblastoma stem cells determines functionally distinct subgroups

2021 ◽  
Author(s):  
Xi Lu ◽  
Naga Prathyusha Maturi ◽  
Malin Jarvius ◽  
Linxuan Zhao ◽  
Yuan Xie ◽  
...  
Keyword(s):  
Stem Cells ◽  
Epigenetic Regulation ◽  
Developmental Regulation ◽  
Regulatory Element ◽  
Cell Lineage ◽  
Mouse Cell ◽  
Chromatin Accessibility ◽  
Cell Of Origin ◽  
Glioblastoma Stem Cells ◽  
Accessible Chromatin

AbstractThere is ample support for developmental regulation of glioblastoma stem cells (GSCs). To examine how cell lineage controls GSC function we have performed a cross-species epigenome analysis of mouse and human GSC cultures. We have analyzed and compared the chromatin-accessibility landscape of nine mouse GSC cultures of defined cell of origin and 60 patient-derived GSC cultures by assay for transposase-accessible chromatin using sequencing (ATAC-seq). This uncovered a variability of both mouse and human GSC cultures that was different from transcriptome analysis and better at predicting functional subgroups. In both species the chromatin accessibility-guided clusters were predominantly determined by distal regulatory element (DRE) regions, displayed contrasting sets of transcription factor binding motifs, and exhibited different functional and drug-response properties. Cross-species analysis of DRE regions in accessible chromatin revealed conserved epigenetic regulation of mouse and human GSCs. Human ATAC-seq data produced three distinct clusters with significant overlap to our previous mouse cell of origin- based stratification, where two of the clusters displayed significantly different patient survival. We conclude that epigenetic regulation of GSCs primarily is dictated by developmental origin which controls key GSC properties and affects therapeutic response.

scholarly journals ECOA-7. Conserved cell-lineage controlled chromatin accessibility in human and mouse glioblastoma stem cells predicts functionally distinct subgroups

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii2-ii2
Author(s):  
Xi Lu ◽  
Naga Prathyusha Maturi ◽  
Malin Jarvius ◽  
Linxuan Zhao ◽  
Yuan Xie ◽  
...  
Keyword(s):  
Stem Cells ◽  
Epigenetic Regulation ◽  
Regulatory Element ◽  
Cell Lineage ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cell Of Origin ◽  
Glioblastoma Stem Cells ◽  
Transcription Factor Motif ◽  
Accessible Chromatin

Abstract There is ample support for developmental control of glioblastoma stem cells (GSCs), and a deeper knowledge of their epigenetic regulation could be central to more efficient glioblastoma (GBM) therapies. For this purpose, we analyzed the chromatin-accessibility landscape of nine mouse GSC cultures of defined cell of origin and 60 patient-derived GSC cultures by assay for transposase-accessible chromatin using sequencing (ATAC-seq). This uncovered an epigenetic variability of both mouse and human GSC cultures that differed from transcriptome clusters. Both mouse and human chromatin accessibility-guided clusters were predominantly determined by distal regulatory elements, displayed unique sets of transcription factor motif enrichment, and exhibited different functional and drug-response properties. Cross-species analysis of distal regulatory element regions in accessible chromatin of mouse and human cultures revealed conserved epigenetic regulation of GSCs.

scholarly journals Analysis of accessible chromatin landscape in the inner cell mass and trophectoderm of human blastocysts

2020 ◽  
Vol 26 (9) ◽  
pp. 702-711
Author(s):  
Min Yang ◽  
Xin Tao ◽  
Shiny Titus ◽  
Tianhua Zhao ◽  
Richard T Scott ◽  
...  
Keyword(s):  
Epigenetic Regulation ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Lineage ◽  
Distal Region ◽  
Chromatin Accessibility ◽  
Early Embryo ◽  
Preimplantation Embryos ◽  
Accessible Chromatin ◽  
Human Preimplantation Embryos

Abstract Early embryonic development is characterized by drastic changes in chromatin structure that affects the accessibility of the chromatin. In human, the chromosome reorganization and its involvement in the first linage segregation are poorly characterized due to the difficulties in obtaining human embryonic material and limitation on low input technologies. In this study, we aimed to explore the chromatin remodeling pattern in human preimplantation embryos and gain insight into the epigenetic regulation of inner cell mass (ICM) and trophectoderm (TE) differentiation. We optimized ATAC-seq (an assay for transposase-accessible chromatin using sequencing) to analyze the chromatin accessibility landscape for low DNA input. Sixteen preimplantation human blastocysts frozen on Day 6 were used. Our data showed that ATAC peak distributions of the promoter regions (<1 kb) and distal regions versus other regions were significantly different between ICM versus TE samples (P < 0.01). We detected that a higher percentage of accessible binding loci were located within 1 kb of the transcription start site in ICM compared to TE (P < 0.01). However, a higher percentage of accessible regions was detected in the distal region of TE compared to ICM (P < 0.01). In addition, eight differential peaks with a false discovery rate <0.05 between ICM and TE were detected. This is the first study to compare the landscape of the accessible chromatin between ICM and TE of human preimplantation embryos, which unveiled chromatin-level epigenetic regulation of cell lineage specification in early embryo development.

scholarly journals GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yapeng Li ◽  
Junfeng Gao ◽  
Mohammad Kamran ◽  
Laura Harmacek ◽  
Thomas Danhorn ◽  
...  
Keyword(s):  
Mast Cell ◽  
Binding Sites ◽  
Cell Lineage ◽  
Allergic Inflammation ◽  
Chromatin Accessibility ◽  
Antigenic Stimulation ◽  
Parasitic Infections ◽  
Cell Identity ◽  
Super Enhancer ◽  
Determining Factors

AbstractMast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage-determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes.

scholarly journals Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Genetics ◽  
2020 ◽  
Vol 217 (1) ◽  
Author(s):  
Jaclyn M Noshay ◽  
Alexandre P Marand ◽  
Sarah N Anderson ◽  
Peng Zhou ◽  
Maria Katherine Mejia Guerra ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Allelic Variation ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Responses ◽  
Maize Genotypes ◽  
Show Evidence ◽  
Regulatory Potential ◽  
Dna Regulatory Elements ◽  
Accessible Chromatin

Abstract Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.

scholarly journals Lineage Switching in Acute Leukemias: A Consequence of Stem Cell Plasticity?

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Elisa Dorantes-Acosta ◽  
Rosana Pelayo
Keyword(s):  
Cell Fate ◽  
High Efficiency ◽  
Current Knowledge ◽  
Lymphoblastic Leukemia ◽  
Survival Rates ◽  
Cell Lineage ◽  
Leukemic Cells ◽  
Acute Leukemias ◽  
Cell Fate Decisions ◽  
Lineage Switch

Acute leukemias are the most common cancer in childhood and characterized by the uncontrolled production of hematopoietic precursor cells of the lymphoid or myeloid series within the bone marrow. Even when a relatively high efficiency of therapeutic agents has increased the overall survival rates in the last years, factors such as cell lineage switching and the rise of mixed lineages at relapses often change the prognosis of the illness. During lineage switching, conversions from lymphoblastic leukemia to myeloid leukemia, or vice versa, are recorded. The central mechanisms involved in these phenomena remain undefined, but recent studies suggest that lineage commitment of plastic hematopoietic progenitors may be multidirectional and reversible upon specific signals provided by both intrinsic and environmental cues. In this paper, we focus on the current knowledge about cell heterogeneity and the lineage switch resulting from leukemic cells plasticity. A number of hypothetical mechanisms that may inspire changes in cell fate decisions are highlighted. Understanding the plasticity of leukemia initiating cells might be fundamental to unravel the pathogenesis of lineage switch in acute leukemias and will illuminate the importance of a flexible hematopoietic development.

scholarly journals Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing

2020 ◽  
Vol 6 (37) ◽  
pp. eaba1190
Author(s):  
Q. R. Xing ◽  
C. A. El Farran ◽  
P. Gautam ◽  
Y. S. Chuah ◽  
T. Warrier ◽  
...  
Keyword(s):  
Single Cell ◽  
Chromatin Accessibility ◽  
Human Cells ◽  
Cellular Reprogramming ◽  
Surface Markers ◽  
Low Efficiency ◽  
Cell Transcriptome ◽  
Intermediate Cells ◽  
Single Cell Transcriptome ◽  
Accessible Chromatin

Cellular reprogramming suffers from low efficiency especially for the human cells. To deconstruct the heterogeneity and unravel the mechanisms for successful reprogramming, we adopted single-cell RNA sequencing (scRNA-Seq) and single-cell assay for transposase-accessible chromatin (scATAC-Seq) to profile reprogramming cells across various time points. Our analysis revealed that reprogramming cells proceed in an asynchronous trajectory and diversify into heterogeneous subpopulations. We identified fluorescent probes and surface markers to enrich for the early reprogrammed human cells. Furthermore, combinatory usage of the surface markers enabled the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 and a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Together, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part list of the reprogramming machinery.

scholarly journals ATAC-seq with unique molecular identifiers improves quantification and footprinting

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Tao Zhu ◽  
Keyan Liao ◽  
Rongfang Zhou ◽  
Chunjiao Xia ◽  
Weibo Xie
Keyword(s):  
Transcription Factor ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Chromatin Accessibility ◽  
Link Type ◽  
Pcr Duplicates ◽  
Identify Transcription Factor ◽  
Accessible Chromatin ◽  
Accurate Quantification

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq in our study. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.

scholarly journals Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhe Cui ◽  
Ya Cui ◽  
Yan Gao ◽  
Tao Jiang ◽  
Tianyi Zang ◽  
...  
Keyword(s):  
Single Cell ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Support Vector ◽  
Cell Type ◽  
Peripheral Blood Mononuclear ◽  
Copy Numbers ◽  
Genome Wide ◽  
Accessible Chromatin

Single-cell Assay Transposase Accessible Chromatin sequencing (scATAC-seq) has been widely used in profiling genome-wide chromatin accessibility in thousands of individual cells. However, compared with single-cell RNA-seq, the peaks of scATAC-seq are much sparser due to the lower copy numbers (diploid in humans) and the inherent missing signals, which makes it more challenging to classify cell type based on specific expressed gene or other canonical markers. Here, we present svmATAC, a support vector machine (SVM)-based method for accurately identifying cell types in scATAC-seq datasets by enhancing peak signal strength and imputing signals through patterns of co-accessibility. We applied svmATAC to several scATAC-seq data from human immune cells, human hematopoietic system cells, and peripheral blood mononuclear cells. The benchmark results showed that svmATAC is free of literature-based markers and robust across datasets in different libraries and platforms. The source code of svmATAC is available at https://github.com/mrcuizhe/svmATAC under the MIT license.

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