scholarly journals Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos

Cell Genomics ◽  
2022 ◽  
Vol 2 (1) ◽  
pp. 100083 ◽  
Author(s):  
Alison C. McGarvey ◽  
Wolfgang Kopp ◽  
Dubravka Vučićević ◽  
Kenny Mattonet ◽  
Rieke Kempfer ◽  
...  
MethodsX ◽  
2018 ◽  
Vol 5 ◽  
pp. 1287-1290 ◽  
Author(s):  
Erica Bresciani ◽  
Elizabeth Broadbridge ◽  
Paul P. Liu

2020 ◽  
Author(s):  
Miao Yu ◽  
Armen Abnousi ◽  
Yanxiao Zhang ◽  
Guoqiang Li ◽  
Lindsay Lee ◽  
...  

Single cell Hi-C (scHi-C) analysis has been increasingly used to map the chromatin architecture in diverse tissue contexts, but computational tools to define chromatin contacts at high resolution from scHi-C data are still lacking. Here, we describe SnapHiC, a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. We benchmark SnapHiC against HiCCUPS, a common tool for mapping chromatin contacts in bulk Hi-C data, using scHi-C data from 742 mouse embryonic stem cells. We further demonstrate its utility by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells. We uncover cell-type-specific chromatin loops and predict putative target genes for non-coding sequence variants associated with neuropsychiatric disorders. Our results suggest that SnapHiC could facilitate the analysis of cell-type-specific chromatin architecture and gene regulatory programs in complex tissues.


2020 ◽  
Author(s):  
Alison C. McGarvey ◽  
Wolfgang Kopp ◽  
Dubravka Vučićević ◽  
Rieke Kempfer ◽  
Kenny Mattonet ◽  
...  

DNA accessibility of cis regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many of the genes that regulate embryonic development have been described, the underlying CRE dynamics controlling their expression remain largely unknown. To address this, we applied single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq) to whole 24 hours post fertilization (hpf) stage zebrafish embryos and developed a new computational tool, ScregSeg, that selects informative genome segments and classifies complex accessibility dynamics. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization, expanding knowledge of regulatory principles between chromatin modalities. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos revealed novel cellular roles for this hemato-vascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work constitutes a valuable resource for future studies in developmental, molecular, and computational biology.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 527-527
Author(s):  
Donn L Calkins ◽  
Jami L Shaffer ◽  
Emily M Teets ◽  
Alex M Belardo ◽  
Serine Avagyan ◽  
...  

We currently have little understanding of the mechanisms by which hematopoietic stem and progenitor cells (HSPCs) gain a selective advantage in patients with clonal hematopoiesis and other myeloid neoplasms. The chemokine CXCL8 is elevated in a subset of patients with myeloid neoplasms. Our previous work in zebrafish has discovered a novel role for cxcl8 and its receptor, cxcr1, in supporting colonization of HSPCs within the sinusoidal endothelial cell niche of the embryonic zebrafish known as the caudal hematopoietic tissue (CHT). We hypothesized that mosaic overexpression of cxcl8 in a population of HSPCs during development would alter HSPC-niche interactions, selectively favor HSPCs expressing cxcl8 and lead to their expansion in adults. To test this hypothesis, we microinjected DNA constructs encoding cxcl8-2A-GFP or GFP alone under the control of the HSPC-specific Runx1+23 enhancer into zebrafish embryos at the single-cell stage. Time lapse fluorescence video microscopy and single-cell tracking was performed on HSPCs within the CHT. Overexpression of cxcl8 nearly doubled the amount of time HSPCs resided within the CHT when compared to expression of GFP alone as a control (cxcl8: 4.94 ± 0.86 h vs GFP: 2.54 ± 0.18 h, p=0.01, N=142 tracked cells). Substitution of WT cxcl8 with a mutant cxcl8 construct lacking the ELRCXC motif required for receptor binding reduced these effects (WT cxcl8: 6.6 ± 0.48 h vs ELRCXC-cxcl8: 5.3 ± 0.33 h, p=0.02, N=355 tracked cells). To observe HSPC-niche interactions, kdrl:mCherry endothelial cell reporter zebrafish were microinjected with Runx1+23:cxcl8-2A-GFP or Runx1+23:GFP DNA constructs. The percent of time individual HSPCs spent closely interacting with a single group of CHT endothelial cells (endothelial cell cuddling) was quantified over the period from 52 to 72 hours post-fertilization. Overexpression of cxcl8 by HSPCs increased HSPC-endothelial cell cuddling time by 30% (cxcl8: 87% vs GFP: 57%, p=0.001). To directly test competition between wild type and cxcl8 overexpressing HSPCs, zebrafish embryos were microinjected with a 1:1 molar ratio of Runx1+23:cxcl8-2A-mCherry and Runx1+23:clover DNA. Single cxcl8-2A-mCherry+ and clover+ competitor cells were tracked by time-lapse fluorescence confocal microscopy. HSPCs expressing cxcl8 resided longer within the CHT than competitor HSPCs when quantified over the period from 72 to 96 hours post-fertilization (cxcl8: 4.0 ± 0.20 h vs competitor: 2.5 ± 0.25 h, p=2.0 x 10-6, n=426 tracked cells). Single cell RNA-sequencing (scRNA-seq) of zebrafish embryos with mosaic expression of cxcl8 in HSPCs showed upregulation of cxcl12a in endothelial cells compared to endothelial cells from control embryos (p=5.19 x 10-3), suggesting a possible mechanism to explain the increased CHT residency time. Zebrafish with mosaic expression of Runx1+23:cxcl8 were raised to adulthood and the kidney marrow cells were analyzed by flow cytometry. Compared to clutchmate controls, Runx1+23:cxcl8 mosaic transgenics had a higher hematopoietic progenitor/precursor to lymphocyte ratio, suggesting a mild differentiation block and possible lineage skewing (cxcl8: 2.0 ± 0.15 vs control: 1.6 ± 0.10, p=0.048, N=25 animals). Taken together, these data support a model in which pre-malignant HSPC clones aberrantly express cxcl8 and acquire a selective advantage over normal clones through enhanced interactions with the endothelial cell niche. Disclosures Zon: Fate Therapeutics: Equity Ownership; Scholar Rock: Equity Ownership; CAMP4: Equity Ownership.


2021 ◽  
Vol 55 (3) ◽  
pp. 1885-1896
Author(s):  
Yuxuan Liu ◽  
Yonghua Wang ◽  
Xin Ling ◽  
Zhenhua Yan ◽  
Donghai Wu ◽  
...  

2021 ◽  
Author(s):  
Benjamin K Johnson ◽  
Jean-Philippe Fortin ◽  
Kasper D. Hansen ◽  
Hui Shen ◽  
Timothy J. Triche

Single-cell profiling of chromatin structure remains a challenge due to cost, throughput, and resolution. We introduce compartmap to reconstruct higher-order chromatin domains in individual cells from transcriptomic (RNAseq) and epigenomic (ATACseq) assays. In cell lines and primary human samples, compartmap infers higher-order chromatin structure comparable to specialized chromatin capture methods, and identifies clinically relevant structural alterations in single cells. This provides a common lens to integrate transcriptional and epigenomic results, linking higher-order chromatin architecture to gene regulation and to clinically relevant phenotypes in individual cells.


2021 ◽  
Vol 18 (9) ◽  
pp. 1056-1059
Author(s):  
Miao Yu ◽  
Armen Abnousi ◽  
Yanxiao Zhang ◽  
Guoqiang Li ◽  
Lindsay Lee ◽  
...  

AbstractSingle-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for Hi-C (SnapHiC), a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. Using scHi-C data from 742 mouse embryonic stem cells, we benchmark SnapHiC against a number of computational tools developed for mapping chromatin loops and interactions from bulk Hi-C. We further demonstrate its use by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells, which uncovers cell type-specific chromatin loops and predicts putative target genes for noncoding sequence variants associated with neuropsychiatric disorders. Our results indicate that SnapHiC could facilitate the analysis of cell type-specific chromatin architecture and gene regulatory programs in complex tissues.


2000 ◽  
Vol 42 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Christina F. Leung ◽  
Sarah E. Webb ◽  
Andrew L. Miller

2021 ◽  
Author(s):  
Yuki Kitanishi ◽  
Hiroki Sugishita ◽  
Yukiko Gotoh ◽  
Yoshito Hirata

The chromatin conformation capture-related methods such as Hi-C have improved our understanding of nuclear architecture and organization in recent years. However, reconstruction of nuclear architecture of individual cells from single cell Hi-C (scHi-C) data has been challenging due to limited information of DNA contacts owing to the low efficiency of DNA recovery from a single cell. We have previously developed an algorithm named as “recurrence plot- based reconstruction (RPR) method” for reconstructing three dimensional (3D) genomic structure from Hi-C data of single haploid cells and diploid cells. This mathematical method is based on a recurrence plot, a tool of nonlinear time series analysis for visualizing temporal patterns within a time series and enables the reconstruction of a unique 3D chromosome architecture even from sparse (low-coverage) DNA contact information. Here we applied the RPR method to analyzing published scHi-C data of diploid cells derived from early-stage F1 hybrid embryos. We found that paternal and maternal chromosomes become gradually intermingled from 1 cell to 64 cell stage and that discrete chromosome territories (CTs) are largely established between 8 cell and 64 cell stages. We also observed Rabl-like polarized distribution of chromosomes from 2 cell to 8 cell stage but this polarization becomes mostly dissolved by 64 cell stage. The formation of Rabl-like configuration precedes rod-like extension of the chromosomal shape and their parallel alignment, implicating a role of Rabl-like configuration in avoiding entanglement and promoting effective mixing of chromosomes before establishment of CTs. We also found a cell-to-cell variability in chromatin configuration. Combination of scHi-C and RPR analyses thus can characterize distinct 3D chromatin architecture of individual cells at different developmental stages during early embryogenesis.


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