Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos

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.

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C3D: A tool to predict 3D genomic interactions between cis-regulatory elements

10.1101/197301 ◽

2017 ◽

Cited By ~ 1

Author(s):

Tahmid Mehdi ◽

Swneke D. Bailey ◽

Paul Guilhamon ◽

Mathieu Lupien

Keyword(s):

Regulatory Elements ◽

Gene Promoters ◽

Cell Type ◽

Computational Tool ◽

3D Genome ◽

Dna Accessibility ◽

Chromatin Interactions ◽

Hypersensitive Sites ◽

R Packages ◽

Mcf 7

ABSTRACTMotivationThe 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a highly customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.ResultsC3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.AvailabilitySource code is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (≥4.0), R (≥3.1.1) and BEDTools (≥2.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.

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EGR1 Transcription Factor is a Multifaceted Regulator of Matrix Production in Tendons and Other Connective Tissues

International Journal of Molecular Sciences ◽

10.3390/ijms21051664 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1664 ◽

Cited By ~ 21

Author(s):

Emmanuelle Havis ◽

Delphine Duprez

Keyword(s):

Extracellular Matrix ◽

Transcription Factor ◽

Connective Tissue ◽

Transcriptional Activity ◽

Tendon Repair ◽

Regulatory Elements ◽

Biological Functions ◽

Connective Tissues ◽

Post Translational Modifications ◽

Matrix Production

Although the transcription factor EGR1 is known as NGF1-A, TIS8, Krox24, zif/268, and ZENK, it still has many fewer names than biological functions. A broad range of signals induce Egr1 gene expression via numerous regulatory elements identified in the Egr1 promoter. EGR1 is also the target of multiple post-translational modifications, which modulate EGR1 transcriptional activity. Despite the myriad regulators of Egr1 transcription and translation, and the numerous biological functions identified for EGR1, the literature reveals a recurring theme of EGR1 transcriptional activity in connective tissues, regulating genes related to the extracellular matrix. Egr1 is expressed in different connective tissues, such as tendon (a dense connective tissue), cartilage and bone (supportive connective tissues), and adipose tissue (a loose connective tissue). Egr1 is involved in the development, homeostasis, and healing processes of these tissues, mainly via the regulation of extracellular matrix. In addition, Egr1 is often involved in the abnormal production of extracellular matrix in fibrotic conditions, and Egr1 deletion is seen as a target for therapeutic strategies to fight fibrotic conditions. This generic EGR1 function in matrix regulation has little-explored implications but is potentially important for tendon repair.

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Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽

10.1186/s12864-020-07324-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Stéphane Deschamps ◽

John A. Crow ◽

Nadia Chaidir ◽

Brooke Peterson-Burch ◽

Sunil Kumar ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Transcriptional Activity ◽

Spatial Organization ◽

Regulatory Elements ◽

Open Chromatin ◽

Maize Genome ◽

Chromatin Loop ◽

Structural Components ◽

Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

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Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Nature Communications ◽

10.1038/s41467-021-21583-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Rongxin Fang ◽

Sebastian Preissl ◽

Yang Li ◽

Xiaomeng Hou ◽

Jacinta Lucero ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Expression Patterns ◽

Regulatory Elements ◽

Cellular Heterogeneity ◽

Specific Gene ◽

Open Chromatin ◽

Cell Type ◽

Process Data ◽

Cell Type Specific

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

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Transcriptional Analysis of the Adeno-Associated Virus Integration Site

Journal of Virology ◽

10.1128/jvi.01754-09 ◽

2009 ◽

Vol 83 (23) ◽

pp. 12512-12525 ◽

Cited By ~ 5

Author(s):

Nathalie Dutheil ◽

Els Henckaerts ◽

Erik Kohlbrenner ◽

R. Michael Linden

Keyword(s):

Transcriptional Activity ◽

Integration Site ◽

Regulatory Elements ◽

Transcriptional Analysis ◽

Start Codon ◽

Adeno Associated Virus ◽

Site Specific ◽

Complex Interactions ◽

Site Specific Integration ◽

Virus Integration

ABSTRACT The nonpathogenic human adeno-associated virus type 2 (AAV-2) has adopted a unique mechanism to site-specifically integrate its genome into the human MBS85 gene, which is embedded in AAVS1 on chromosome 19. The fact that AAV has evolved to integrate into this ubiquitously transcribed region and that the chromosomal motifs required for integration are located a few nucleotides upstream of the translation initiation start codon of MBS85 suggests that the transcriptional activity of MBS85 might influence site-specific integration and thus might be involved in the evolution of this mechanism. In order to begin addressing this question, we initiated the characterization of the human MBS85 promoter region and compared its transcriptional activity to that of the AAV-2 p5 promoter. Our results clearly indicate that AAVS1 is defined by a complex transcriptional environment and that the MBS85 promoter shares key regulatory elements with the viral p5 promoter. Furthermore, we provide evidence for bidirectional MBS85 promoter activity and demonstrate that the minimal motifs required for AAV site-specific integration are present in the 5′ untranslated region of the gene and play a posttranscriptional role in the regulation of MBS85 expression. These findings should provide a framework to further elucidate the complex interactions between the virus and its cellular host in this unique pathway to latency.

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Fluorescent protein expression driven by her4 regulatory elements reveals the spatiotemporal pattern of Notch signaling in the nervous system of zebrafish embryos

Developmental Biology ◽

10.1016/j.ydbio.2006.10.020 ◽

2007 ◽

Vol 301 (2) ◽

pp. 555-567 ◽

Cited By ~ 92

Author(s):

Sang-Yeob Yeo ◽

MinJung Kim ◽

Hyung-Seok Kim ◽

Tae-Lin Huh ◽

Ajay B. Chitnis

Keyword(s):

Nervous System ◽

Protein Expression ◽

Notch Signaling ◽

Fluorescent Protein ◽

Regulatory Elements ◽

Spatiotemporal Pattern ◽

Zebrafish Embryos

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The 3D Genome Structure of Single Cells

Annual Review of Biomedical Data Science ◽

10.1146/annurev-biodatasci-020121-084709 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Tianming Zhou ◽

Ruochi Zhang ◽

Jian Ma

Keyword(s):

Single Cell ◽

Data Science ◽

Spatial Organization ◽

Method Development ◽

Single Cells ◽

Genome Structure ◽

Computational Method ◽

Publication Date ◽

3D Genome ◽

Genome Features

The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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