Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos

Doğanlı, Canan; Sandoval, Melissa; Thomas, Sean; Hart, Daniel J.

doi:10.1007/978-1-4939-6518-2_5

Cited by 19 publications

(13 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genome-wide analysis of THSs distribution over functional genomic elements revealed that the promoter-TSS, introns and intergenic regions were preferentially (more than 90%) accessible to Tn5 transposase (Figure 2B). Moreover, our results conform to the pattern reported in previous studies in multiple organisms by showing that ATAC-seq signal was significantly enriched at ±1 Kb region surrounding TSS (Figure 2C), which suggests that the majority of cis-regulatory regions were located in the vicinity of gene core promoters and that open chromatin at THSs is predictive of active transcription (Buenrostro et al, 2013;Doganli et al, 2017;Lu et al, 2017;Bozek et al, 2019).…”

Section: Genome-wide Changes In Chromatin Accessibilitysupporting

confidence: 91%

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells

Wang

Yan

Shen

et al. 2021

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

BackgroundDoxorubicin is one of the most effective chemotherapeutic drugs for breast cancer while its common drug resistance leads to poor patient prognosis and survival. Growing evidence indicate dynamically reorganized chromatin allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression through direct transcription factor (TF) activation and regulatory element binding.MethodsTo better understand the regulatory network underlying doxorubicin resistance in breast cancer cells, we explored the systematic alterations of chromatin accessibility and gene expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with RNA sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in doxorubicin-resistant MCF7 (MCF7-DR) cells.ResultsA total of 3,963 differentially expressed genes (DEGs) related to doxorubicin resistance were identified, including dramatically up-regulated MT1E, GSTP1, LDHB, significantly down-regulated TFF1, UBB, DSCAM-AS1, and histone-modifying enzyme coding genes HDAC2, EZH2, PRMT5, etc. By integrating with transcriptomic datasets, we identified 18,228 DARs in MCF7-DR cells compared to control, which were positively correlated with their nearest DEGs (r = 0.6). There were 11,686 increased chromatin-accessible regions, which were enriched in up-regulated genes related to diverse KEGG pathways, such as the cell cycle, regulation of actin cytoskeleton, signaling pathways of MAPK, PI3K/Akt and Hippo, which play essential roles in regulating cell apoptosis, proliferation, metabolism, and inflammatory responses. The 6,542 decreased chromatin-accessible regions were identified for the declined doxorubicin-associated biological processes, for instance, endocrine and insulin resistance, central carbon metabolism, signaling pathways of TGF-beta and P53. Combining data from TCGA, analyses of the DAR sequences associated with the DNA-binding motifs of significantly enriched TF families including AP-1, TEAD and FOX, indicated that the loss-function of FOXA1 might play a critical role in doxorubicin-resistant breast cancer cells (DOX-R BCCs).ConclusionThese data exhibit the non-genetic landscape of chromatin accessibility and transcript levels in the DOX-R BCCs, and provide clear insights and resources for the detection of critical TFs and potential cis-regulatory elements-based putative therapeutic targets.

show abstract

Section: Genome-wide Changes In Chromatin Accessibilitysupporting

confidence: 91%

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells

Wang

Yan

Shen

et al. 2021

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

“…Pioneer transcription factors bind to condensed chromatin and have the ability to increase accessibility, enabling other factors to access their target sites (Iwafuchi-Doi and Zaret, 2014). To investigate whether Npas4l acts as a pioneer factor, we assessed chromatin accessibility in npas4l mutants, using the assay for transposase-accessible chromatin coupled to next-generation sequencing (ATAC-seq) (Buenrostro et al, 2015;Doganli et al, 2017). We incrossed npas4l +/− fish and genotyped single embryos at the one-somite stage.…”

Section: Transcriptomic and Epigenomic Analyses Of Npas4l Mutantsmentioning

confidence: 99%

“…After removing the supernatant, we added 51 μl of ice-cold PBS (one microliter was used for genotyping) and we centrifuged the samples again at 500 g for 10 min at 4°C. The supernatant was removed and 50 μl of cold lysis buffer, prepared as described previously (Doganli et al, 2017), was added. Samples were centrifuged at 500 g at 4°C for 10 min.…”

Section: Atac-sequencingmentioning

confidence: 99%

Genome-wide strategies reveal target genes of Npas4l associated with vascular development in zebrafish

et al. 2019

View full text Add to dashboard Cite

The development of a vascular network is essential to nourish tissues and sustain organ function throughout life. Endothelial cells (ECs) are the building blocks of blood vessels, yet our understanding of EC specification remains incomplete. Zebrafish cloche/npas4l mutants have been used broadly as an avascular model, but little is known about the molecular mechanisms of action of the Npas4l transcription factor. Here, to identify its direct and indirect target genes, we have combined complementary genome-wide approaches, including transcriptome analyses and chromatin immunoprecipitation. The cross-analysis of these datasets indicates that Npas4l functions as a master regulator by directly inducing a group of transcription factor genes that are crucial for hematoendothelial specification, such as etv2, tal1 and lmo2. We also identified new targets of Npas4l and investigated the function of a subset of them using the CRISPR/Cas9 technology. Phenotypic characterization of tspan18b mutants reveals a novel player in developmental angiogenesis, confirming the reliability of the datasets generated. Collectively, these data represent a useful resource for future studies aimed to better understand EC fate determination and vascular development.

show abstract

“…Other techniques for identifying gene regulatory elements are based on the detection of open chromatin, for instance, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). ATAC-seq requires much less input material than ChIP-seq, and has even been used successfully with single cells ( Fernandez-Minan et al, 2016 ; Doganli et al, 2017 ). This method allowed the identification of endothelial enhancers ( Quillien et al, 2017 ) and revealed the role of cohesin in rearranging the genomic architecture during the transition of maternal to zygotic transcription in early embryos ( Meier et al, 2018 ).…”

Section: Identification Of Novel Regulatory Mechanisms Of Normal and mentioning

confidence: 99%

Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis

Pater

Trompouki

2018

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

Hematopoiesis is an optimal system for studying stem cell maintenance and lineage differentiation under physiological and pathological conditions. In vertebrate organisms, billions of differentiated hematopoietic cells need to be continuously produced to replenish the blood cell pool. Disruptions in this process have immediate consequences for oxygen transport, responses against pathogens, maintenance of hemostasis and vascular integrity. Zebrafish is a widely used and well-established model for studying the hematopoietic system. Several new hematopoietic regulators were identified in genetic and chemical screens using the zebrafish model. Moreover, zebrafish enables in vivo imaging of hematopoietic stem cell generation and differentiation during embryogenesis, and adulthood. Finally, zebrafish has been used to model hematopoietic diseases. Recent technological advances in single-cell transcriptome analysis, epigenetic regulation, proteomics, metabolomics, and processing of large data sets promise to transform the current understanding of normal, abnormal, and malignant hematopoiesis. In this perspective, we discuss how the zebrafish model has proven beneficial for studying physiological and pathological hematopoiesis and how these novel technologies are transforming the field.

show abstract

Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos

Cited by 19 publications

References 6 publications

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells

Genome-wide strategies reveal target genes of Npas4l associated with vascular development in zebrafish

Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis

Contact Info

Product

Resources

About