一周快讯：本周表观文献精选（2018.4.21）

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

Hong Sook Kim, Yuliang Tan, Wubin Ma, Daria Merkurjev, Eugin Destici, Qi Ma, Tom Suter, Kenneth Ohgi, Meyer Friedman, Dorota Skowronska-Krawczyk & Michael G. Rosenfeld

原文链接：

https://www.nature.com/articles/s41586-018-0048-8

原文摘要： Enhancers for embryonic stem (ES) cell-expressed genes and lineage-determining factors are characterized by conventional marks of enhancer activation in ES cells1,2,3, but it remains unclear whether enhancers destined to regulate cell-type-restricted transcription units might also have distinct signatures in ES cells. Here we show that cell-type-restricted enhancers are ‘premarked’ and activated as transcription units by the binding of one or two ES cell transcription factors, although they do not exhibit traditional enhancer epigenetic marks in ES cells, thus uncovering the initial temporal origins of cell-type-restricted enhancers. This premarking is required for future cell-type-restricted enhancer activity in the differentiated cells, with the strength of the ES cell signature being functionally important for the subsequent robustness of cell-type-restricted enhancer activation. We have experimentally validated this model in macrophage-restricted enhancers and neural precursor cell (NPC)-restricted enhancers using ES cell-derived macrophages or NPCs, edited to contain specific ES cell transcription factor motif deletions. DNA hydroxyl-methylation of enhancers in ES cells, determined by ES cell transcription factors, may serve as a potential molecular memory for subsequent enhancer activation in mature macrophages. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily premarked by binding of a defining ES cell transcription factor in ES cells, dictating the robustness of enhancer activation in mature cells.

Defining essential genes for human pluripotent stem cells by CRISPR–Cas9 screening in haploid cells

Atilgan Yilmaz, Mordecai Peretz, Aviram Aharony, Ido Sagi& Nissim Benvenisty

原文链接：

https://www.nature.com/articles/s41556-018-0088-1

原文摘要： The maintenance of pluripotency requires coordinated expression of a set of essential genes. Using our recently established haploid human pluripotent stem cells (hPSCs), we generated a genome-wide loss-of-function library targeting 18,166 protein-coding genes to define the essential genes in hPSCs. With this we could allude to an intrinsic bias of essentiality across cellular compartments, uncover two opposing roles for tumour suppressor genes and link autosomal-recessive disorders with growth-retardation phenotypes to early embryogenesis. hPSC-enriched essential genes mainly encode transcription factors and proteins related to cell-cycle and DNA-repair, revealing that a quarter of the nuclear factors are essential for normal growth. Our screen also led to the identification of growth-restricting genes whose loss of function provides a growth advantage to hPSCs, highlighting the role of the P53–mTOR pathway in this context. Overall, we have constructed an atlas of essential and growth-restricting genes in hPSCs, revealing key aspects of cellular essentiality and providing a reference for future studies on human pluripotency.

Pluripotency transcription factors and Tet1/2 maintain Brd4-independent stem cell identity

Lydia W. S. Finley ， Santosha A. Vardhana, Bryce W. Carey, Direna Alonso-Curbelo, Richard Koche, Yanyang Chen, Duancheng Wen, Bryan King, Megan R. Radler, Shahin Rafii, Scott W. Lowe, C. David Allis  & Craig B. Thompson

原文链接：

https://www.nature.com/articles/s41556-018-0086-3

原文摘要： A robust network of transcription factors and an open chromatin landscape are hallmarks of the naive pluripotent state. Recently, the acetyllysine reader Brd4 has been implicated in stem cell maintenance, but the relative contribution of Brd4 to pluripotency remains unclear. Here, we show that Brd4 is dispensable for self-renewal and pluripotency of embryonic stem cells (ESCs). When maintained in their ground state, ESCs retain transcription factor binding and chromatin accessibility independent of Brd4 function or expression. In metastable ESCs, Brd4 independence can be achieved by increased expression of pluripotency transcription factors, including STAT3, Nanog or Klf4, so long as the DNA methylcytosine oxidases Tet1 and Tet2 are present. These data reveal that Brd4 is not essential for ESC self-renewal. Rather, the levels of pluripotency transcription factor abundance and Tet1/2 function determine the extent to which bromodomain recognition of protein acetylation contributes to the maintenance of gene expression and cell identity.

Deconvolution of seed and RNA-binding protein crosstalk in RNAi-based functional genomics

Hiroshi I. Suzuki  , Ryan M. Spengler, Giedre Grigelioniene, Tatsuya Kobayashi& Phillip A. Sharp

原文链接：

https://www.nature.com/articles/s41588-018-0104-1

原文摘要： RNA interference (RNAi) is a major, powerful platform for gene perturbations, but is restricted by off-target mechanisms. Communication between RNAs, small RNAs, and RNA-binding proteins (RBPs) is a pervasive feature of cellular RNA networks. We present a crosstalk scenario, designated as crosstalk with endogenous RBPs’ (ceRBP), in which small interfering RNAs or microRNAs with seed sequences that overlap RBP motifs have extended biological effects by perturbing endogenous RBP activity. Systematic analysis of small interfering RNA (siRNA) off-target data and genome-wide RNAi cancer lethality screens using 501 human cancer cell lines, a cancer dependency map, identified that seed-to-RBP crosstalk is widespread, contributes to off-target activity, and affects RNAi performance. Specifically, deconvolution of the interactions between gene knockdown and seed-mediated silencing effects in the cancer dependency map showed widespread contributions of seed-to-RBP crosstalk to growth-phenotype modulation. These findings suggest a novel aspect of microRNA biology and offer a basis for improvement of RNAi agents and RNAi-based functional genomics.

Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target

Olli Dufva1, Matti Kankainen, Tiina Kelkka  , Nodoka Sekiguchi  , Shady Adnan  Samuli Eldfors  , Bhagwan Yadav, Heikki Kuusanmäki, Disha Malani, Emma I Andersson , Paavo Pietarinen, Leena Saikko, Panu E. Kovanen, Teija Ojala, Dean A. Lee, Thomas P. Loughran Jr., Hideyuki Nakazawa, Junji Suzumiya, Ritsuro Suzuki, Young Hyeh Ko , Won Seog Kim, Shih-Sung Chuang, Tero Aittokallio , Wing C. Chan, Koichi Ohshima, Fumihiro Ishida & Satu Mustjoki

原文链接：

http://www.nature.com/articles/s41467-018-03987-2

原文摘要： Aggressive natural killer-cell (NK-cell) leukemia (ANKL) is an extremely aggressive malignancy with dismal prognosis and lack of targeted therapies. Here, we elucidate the molecular pathogenesis of ANKL using a combination of genomic and drug sensitivity profiling. We study 14 ANKL patients using whole-exome sequencing (WES) and identify mutations in STAT3 (21%) and RAS-MAPK pathway genes (21%) as well as in DDX3X (29%) and epigenetic modifiers (50%). Additional alterations include JAK-STAT copy gains and tyrosine phosphatase mutations, which we show recurrent also in extranodal NK/T-cell lymphoma, nasal type (NKTCL) through integration of public genomic data. Drug sensitivity profiling further demonstrates the role of the JAK-STAT pathway in the pathogenesis of NK-cell malignancies, identifying NK cells to be highly sensitive to JAK and BCL2 inhibition compared to other hematopoietic cell lineages. Our results provide insight into ANKL genetics and a framework for application of targeted therapies in NK-cell malignancies.

The miR-106b-25 cluster mediates breast tumor initiation through activation of NOTCH1 via direct repression of NEDD4L

A. L. Guarnieri, C. G. Towers1, D. J. Drasin, M. U. J. Oliphant, Z. Andrysik, T. J. Hotz, R. L. Vartuli, E. S. Linklater, A. Pandey, S. Khanal, J. M. Espinosa& H. L. Ford

原文链接：

http://www.nature.com/articles/s41388-018-0239-7

原文摘要： Tumor-initiating cells (TIC) represent a subset of tumor cells with increased self-renewal capability. TICs display resistance to frontline cancer treatment and retain the ability to repopulate a tumor after therapy, leading to cancer relapse. NOTCH signaling has been identified as an important driver of the TIC population, yet mechanisms governing regulation of this pathway in cancer remain to be fully elucidated. Here we identify a novel mechanism of NOTCH regulation and TIC induction in breast cancer via the miR-106b-25 miRNA cluster. We show that the miR-106b-25 cluster upregulates NOTCH1 in multiple breast cancer cell lines, representing both estrogen receptor (ER+) and triple negative breast cancer (TNBC) through direct repression of the E3 ubiquitin ligase, NEDD4L. We further show that upregulation of NOTCH1 is necessary for TIC induction downstream of miR-106b-25 in both ER + and TNBC breast cancer cells, and that re-expression of NEDD4L is sufficient to reverse miR106b-25-mediated NOTCH1 upregulation and TIC induction. Importantly, we demonstrate a significant positive correlation between miR-106b-25 and NOTCH1 protein, yet a significant inverse correlation between miR-106b-25 and NEDD4L mRNA in human breast cancer, suggesting a critical role for the miR106b-25/NEDD4L/NOTCH1 axis in the disease. Further, we show for the first time that NEDD4L expression alone is significantly associated with a better relapse-free prognosis for breast cancer patients. These data expand our knowledge of the mechanisms underlying NOTCH activation and TIC induction in breast cancer, and may provide new avenues for the development of therapies targeting this resistant subset of tumor cells.

NGR (Asn-Gly-Arg)-targeted delivery of coagulase to tumor vasculature arrests cancer cell growth

Khaled Seidi, Rana Jahanban-Esfahlan, Hassan Monhemi, Peyman Zare, Babak Minofar, Amir Daei Farshchi Adli, Davoud Farajzadeh, Ramezan Behzadi, Mehran Mesgari Abbasi, Heidi A. Neubauer, Richard Morigg, Nosratollah Zarghami& Tahereh Javaheri

原文链接：

http://www.nature.com/articles/s41388-018-0213-4

原文摘要： Induction of selective thrombosis and infarction in tumor-feeding vessels represents an attractive strategy to combat cancer. Here we took advantage of the unique coagulation properties of staphylocoagulase and genetically engineered it to generate a new fusion protein with novel anti-cancer properties. This novel bi-functional protein consists of truncated coagulase (tCoa) and an NGR (GNGRAHA) motif that recognizes CD13 and αvβ3integrin receptors, targeting it to tumor endothelial cells. Herein, we report that tCoa coupled by its C-terminus to an NGR sequence retained its normal binding activity with prothrombin and avβ3integrins, as confirmed in silico and in vitro. Moreover, in vivo biodistribution studies demonstratedselective accumulation of FITC-labeled tCoa-NGR fusion proteins at the site of subcutaneously implanted PC3 tumor xenografts in nude mice. Notably, systemic administration of tCoa-NGR to mice bearing 4T1 mouse mammary xenografts or PC3 human prostate tumors resulted in a significant reduction in tumor growth. These anti-tumor effects were accompanied by massive thrombotic occlusion of small and large tumor vessels, tumor infarction and tumor cell death. From these findings, we propose tCoa-NGR mediated tumor infarction as a novel and promising anti-cancer strategy targeting both CD13 and integrin αvβ3positive tumor neovasculature.

Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin

Chul-Hwan Lee，Jia-Ray Yu，Sunil Kumar，Ying Jin，Gary LeRoy，Natarajan Bhanu，Syuzo Kaneko，Benjamin A. Garcia，Andrew D. Hamilton，Danny Reinberg