An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Corces, M. Ryan; Trevino, Alexandro E.; Hamilton, Emily G.; Greenside, Peyton G.; Sinnott‐Armstrong, Nicholas A.; Vesuna, Sam; Satpathy, Ansuman T.; Rubin, Adam J.; Montine, Kathleen S.; Wu, Beijing; Kathiria, Arwa S.; Cho, Seung Woo; Mumbach, Maxwell R.; Carter, Ava C.; Kasowski, Maya; Orloff, Lisa A.; Risca, Viviana I.; Kundaje, Anshul; Khavari, Paul A.; Montine, Thomas J.; Greenleaf, William J.; Chang, Howard Y.

doi:10.1101/181206

Cited by 185 publications

(271 citation statements)

References 25 publications

Supporting

Mentioning

269

Contrasting

Order By: Relevance

“…Emerging novel technologies including CUT&Tag, low cell input protocols for ChIPseq and ATACseq, and using isolated nuclei from frozen tissues as containers of chemistry could overcome some of the technical obstacles and allow future examination on larger cohorts of specimens. 84,85 Our data document the molecular profiles at two ends of the physiological spectrum of myometrial tissues. Aside from the different functional and structural states, the NP specimens were at a low serum progesterone environment while the TP samples were exposed to high levels of serum progesterone.…”

Section: Limitation and Future Directionmentioning

confidence: 62%

Dynamic transcriptome, accessible genome, and PGR cistrome profiles in the human myometrium

Anderson

Wang

et al. 2019

FASEB j.

View full text Add to dashboard Cite

The myometrium undergoes structural and functional remodeling during pregnancy.We hypothesize that myometrial genomic elements alter correspondingly in preparation for parturition. Human myometrial tissues from nonpregnant (NP) and term pregnant (TP) human subjects were examined by RNAseq, ATACseq, and PGR ChIPseq assays to profile transcriptome, assessible genome, and PGR occupancy.NP and TP specimens exhibit 2890 differentially expressed genes, reflecting an increase of metabolic, inflammatory, and PDGF signaling, among others, in adaptation to pregnancy. At the epigenome level, patterns of accessible genome change between NP and TP myometrium, leading to the altered enrichment of binding motifs for hormone and muscle regulators such as the progesterone receptor (PGR), Krüppellike factors, and MEF2A transcription factors. PGR genome occupancy exhibits a significant difference between the two stages of the myometrium, concomitant with distinct transcriptomic profiles including genes such as ENO1, LHDA, and PLCL1 in the glycolytic and calcium signaling pathways. Over-representation of SRF, MYOD, and STAT binding motifs in PGR occupying sites further suggests interactions between PGR and major muscle regulators for myometrial gene expression. In conclusion, changes in accessible genome and PGR occupancy are part of the myometrial remodeling process and may serve as mechanisms to formulate the state-specific transcriptome profiles.

show abstract

Section: Limitation and Future Directionmentioning

confidence: 62%

Dynamic transcriptome, accessible genome, and PGR cistrome profiles in the human myometrium

Anderson

Wang

et al. 2019

FASEB j.

View full text Add to dashboard Cite

show abstract

“…Nuclei from frozen liver tissue were isolated as described . A total of 50,000 isolated nuclei in each sample (Ctrl n = 6; LKO n = 6) were used in transposase reaction (Illumina).…”

Section: Methodsmentioning

confidence: 99%

“…Nuclei from frozen liver tissue were isolated as described. (24) A total of 50,000 isolated nuclei in each sample (Ctrl n = 6; LKO n = 6) were used in transposase reaction (Illumina). The libraries were sequenced on NovaSeq-6000 instrument with 50-bp paired-end reads after 2-step PCR amplification.…”

Section: Liver Atac Sequencingmentioning

confidence: 99%

hnRNPU/TrkB Defines a Chromatin Accessibility Checkpoint for Liver Injury and Nonalcoholic Steatohepatitis Pathogenesis

et al. 2020

View full text Add to dashboard Cite

Background and Aims Nonalcoholic steatohepatitis (NASH) is a progressive liver disease that is characterized by liver injury, inflammation, and fibrosis. NASH pathogenesis is linked to reprogramming of chromatin landscape in the liver that predisposes hepatocytes to stress‐induced tissue injury. However, the molecular nature of the putative checkpoint that maintains chromatin architecture and preserves hepatocyte health remains elusive. Approach and Results Here we show that heterogeneous nuclear ribonucleoprotein U (hnRNPU), a nuclear matrix protein that governs chromatin architecture and gene transcription, is a critical factor that couples chromatin disruption to NASH pathogenesis. RNA‐seq and chromatin immunoprecipitation‐seq studies revealed an extensive overlap between hnRNPU occupancy and altered gene expression during NASH. Hepatocyte‐specific inactivation of hnRNPU disrupted liver chromatin accessibility, activated molecular signature of NASH, and sensitized mice to diet‐induced NASH pathogenesis. Mechanistically, hnRNPU deficiency stimulated the expression of a truncated isoform of TrkB (TRKB‐T1) that promotes inflammatory signaling in hepatocytes and stress‐induced cell death. Brain‐derived neurotrophic factor treatment reduced membrane TRKB‐T1 protein and protected mice from diet‐induced NASH. Conclusions These findings illustrate a mechanism through which disruptions of chromatin architecture drive the emergence of disease‐specific signaling patterns that promote liver injury and exacerbate NASH pathogenesis.

show abstract

“…ATAC-seq was carried out using the Omni-ATAC protocol (Corces et al, 2017) with minor modifications. Briefly, 5 × 10 4 cells were pelleted by centrifugation and re-suspended in 50 ll of cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl 2 , 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin).…”

Section: Atac-seqmentioning

confidence: 99%

FOXA 2 controls the cis ‐regulatory networks of pancreatic cancer cells in a differentiation grade‐specific manner

et al. 2019

View full text Add to dashboard Cite

Differentiation of normal and tumor cells is controlled by regulatory networks enforced by lineage‐determining transcription factors (TFs). Among them, TFs such as FOXA1/2 bind naïve chromatin and induce its accessibility, thus establishing new gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the coexistence of well‐ and poorly differentiated cells at all stages of disease. How the transcriptional networks determining such massive cellular heterogeneity are established remains to be determined. We found that FOXA2, a TF controlling pancreas specification, broadly contributed to the cis‐regulatory networks of PDACs. Despite being expressed in both well‐ and poorly differentiated PDAC cells, FOXA2 displayed extensively different genomic distributions and controlled distinct gene expression programs. Grade‐specific functions of FOXA2 depended on its partnership with TFs whose expression varied depending on the differentiation grade. These data suggest that FOXA2 contributes to the regulatory networks of heterogeneous PDAC cells via interactions with alternative partner TFs.

show abstract

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Cited by 185 publications

References 25 publications

Dynamic transcriptome, accessible genome, and PGR cistrome profiles in the human myometrium

Dynamic transcriptome, accessible genome, and PGR cistrome profiles in the human myometrium

hnRNPU/TrkB Defines a Chromatin Accessibility Checkpoint for Liver Injury and Nonalcoholic Steatohepatitis Pathogenesis

FOXA 2 controls the cis ‐regulatory networks of pancreatic cancer cells in a differentiation grade‐specific manner

Contact Info

Product

Resources

About