bims-ectoca 2022-07-24 papers

Methods Mol Biol. 2022 ;2535 171-185

Dissecting the Epigenome Driving Drug Resistance by ATAC-Seq.

Francesca de Nicola, Giacomo Corleone, Frauke Goeman.

The transcription of each gene is tightly regulated by elements like promoters, enhancers, silencers and insulators. These elements determine the temporal and tissue-specific expression in development and disease. Drug resistance is the major obstacle in successfully treating cancer patients. In the recent years, it became evident that epigenetic changes represent one of the mechanisms that contribute to the onset and progression of cancer but also to the development of therapy resistance. The assay for transposase-accessible chromatin coupled with next generation sequencing (ATAC-seq) is a fast and easy technique to track epigenetic changes that result in different opening of the chromatin in regulatory regions genome-wide. The transposase cuts DNA in regions that are open and therefore accessible for transcription factors, regulatory RNAs and proteins that alter the architectural structure of the DNA and drive or inhibit transcription through the RNA polymerase. Here we describe a detailed protocol to perform an ATAC-seq of cells from culture or tissue.

Keywords: ATAC-seq; Chromatin; Cis-acting elements; Enhancer; Epigenome; Epigenomic; Insulator; Promoter; Silencer; Transcription factors

DOI: https://doi.org/10.1007/978-1-0716-2513-2_14

Curr Opin Plant Biol. 2022 Jul 13. pii: S1369-5266(22)00090-5. [Epub ahead of print]69 102261

Linking transcriptional silencing with chromatin remodeling, folding, and positioning in the nucleus.

Zhang-Wei Liu, Carl H Simmons, Xuehua Zhong.

Chromatin organization is important for many DNA-templated processes in eukaryotic cells such as replication and transcription. Recent studies have uncovered the capacity of epigenetic modifications, phase separation, and nuclear architecture and spatial positioning to regulate chromatin organization in both plants and animals. Here, we provide an overview of the recent progress made in understanding how chromatin is organized within the nucleus at both the local and global levels with respect to the regulation of transcriptional silencing in plants. To be concise while covering important mechanisms across a range of scales, we focus on how epigenetic modifications and chromatin remodelers alter local chromatin structure, how liquid-liquid phase separation physically separates broader chromatin domains into distinct droplets, and how nuclear positioning affects global chromatin organization.

Keywords: Chromatin organization; Epigenetic modifications; Transcriptional regulation

DOI: https://doi.org/10.1016/j.pbi.2022.102261

Mol Syst Biol. 2022 Jul;18(7): e11168

Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard-to-kill persister cells.

Yaara Oren.

Similar to persister bacterial cells that survive antibiotic treatments, some cancer cells can evade drug treatments. This Commentary discusses the different classes of persister cells and their implications for developing more efficient cancer treatments.

DOI: https://doi.org/10.15252/msb.202211168

Nat Commun. 2022 Jul 20. 13(1): 4199

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery.

Allison P Siegenfeld, Shelby A Roseman, Heejin Roh, Nicholas Z Lue, Corin C Wagen, Eric Zhou, Sarah E Johnstone, Martin J Aryee, Brian B Liau.

The genome can be divided into two spatially segregated compartments, A and B, which partition active and inactive chromatin states. While constitutive heterochromatin is predominantly located within the B compartment near the nuclear lamina, facultative heterochromatin marked by H3K27me3 spans both compartments. How epigenetic modifications, compartmentalization, and lamina association collectively maintain heterochromatin architecture remains unclear. Here we develop Lamina-Inducible Methylation and Hi-C (LIMe-Hi-C) to jointly measure chromosome conformation, DNA methylation, and lamina positioning. Through LIMe-Hi-C, we identify topologically distinct sub-compartments with high levels of H3K27me3 and differing degrees of lamina association. Inhibition of Polycomb repressive complex 2 (PRC2) reveals that H3K27me3 is essential for sub-compartment segregation. Unexpectedly, PRC2 inhibition promotes lamina association and constitutive heterochromatin spreading into H3K27me3-marked B sub-compartment regions. Consistent with this repositioning, genes originally marked with H3K27me3 in the B compartment, but not the A compartment, remain largely repressed, suggesting that constitutive heterochromatin spreading can compensate for H3K27me3 loss at a transcriptional level. These findings demonstrate that Polycomb sub-compartments and their antagonism with lamina association are fundamental features of genome structure. More broadly, by jointly measuring nuclear position and Hi-C contacts, our study demonstrates how compartmentalization and lamina association represent distinct but interdependent modes of heterochromatin regulation.

DOI: https://doi.org/10.1038/s41467-022-31857-5

Exp Biol Med (Maywood). 2022 Jul 21. 15353702221110645

YAP signaling is involved in WDR1-regulated proliferation and migration of non-small-cell lung cancer cells.

Ran An, Junyan Wang, Xuan Chen, Ruifeng Xu, Jisheng Hu, Zhongying Liu, Chanjuan Wei, Chenxi Zhang, Baiyin Yuan.

As a major co-factor of F-actin depolymerization, WD-repeat domain 1 (WDR1) affects the cellular microenvironment by cytoskeleton remodeling, thereby influencing cell molecular behavior. Our previous study showed that WDR1 activates YAP (Yes-associated protein) signaling in non-small-cell lung cancer (NSCLC) cells, but the mechanism remains unclear. We discovered that knockdown WDR1 in NSCLC cells decreased the expression of YAP and the nucleus-to-cytoplasm ratio. Disruption of cortical stress by drugs significantly inhibited YAP nuclear trafficking and enhanced YAP phosphorylation. In WDR1-knockdown NSCLC cells, inhibition of Hippo pathway reduced the nuclear exclusion of YAP and phosphorylated YAP. Our data suggest that WDR1-mediated cortical stress might be involved in regulating YAP signaling, thereby affecting the proliferation and migration of NSCLC cells.

Keywords: WDR1; YAP; cytoskeleton; non-small-cell lung cancer

DOI: https://doi.org/10.1177/15353702221110645

Int J Biol Sci. 2022 ;18(11): 4497-4512

Smoke-induced SAV1 Gene Promoter Hypermethylation Disrupts YAP Negative Feedback and Promotes Malignant Progression of Non-small Cell Lung Cancer.

YAP (gene symbol YAP1) as a potential oncoprotein, is positively correlated with the malignancy of various tumors. However, overexpression of YAP alone in multiple normal tissue cells has failed to induce tumor formation and the underlying mechanism is poorly understood. Herein, we show that YAP activation directly induces transcription of its negative regulator, SAV1, to constitute a negative feedback loop, which plays a vital role in maintaining lung epithelial cell homeostasis and was dysregulated in non-small cell lung cancer (NSCLC). Notably, smoking promotes the hypermethylation of the SAV1 promoter region, which disrupts YAP negative feedback by inactivating the Hippo pathway. Besides, exogenous overexpression of SAV1 can act as a traffic protein, activating the Hippo signaling and concurrently inhibiting the WNT pathway to decrease cancer cell growth. Furthermore, using the lung cancer organoids, we found that lentivirus-mediated SAV1 gene transfer combined with methylation inhibitor and YAP-TEAD inhibitor is a potential feasible clinical medication regimen for the lung cancer patient, especially among the smoking population. Thus, this SAV1 mediated feedback loop provides an efficient mechanism to establish the robustness and homeostasis of YAP regulation and as a potential target of gene therapy for the smoking NSCLC population.

Keywords: Lung Cancer; Methylation; SAV1; Tobacco smoking; YAP

DOI: https://doi.org/10.7150/ijbs.73428