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Molecular Cell

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https://www.readbyqxmd.com/read/29033323/mtorc1-phosphorylates-acetyltransferase-p300-to-regulate-autophagy-and-lipogenesis
#1
Wei Wan, Zhiyuan You, Yinfeng Xu, Li Zhou, Zhunlv Guan, Chao Peng, Catherine C L Wong, Hua Su, Tianhua Zhou, Hongguang Xia, Wei Liu
Acetylation is increasingly recognized as one of the major post-translational mechanisms for the regulation of multiple cellular functions in mammalian cells. Acetyltransferase p300, which acetylates histone and non-histone proteins, has been intensively studied in its role in cell growth and metabolism. However, the mechanism underlying the activation of p300 in cells remains largely unknown. Here, we identify the homeostatic sensor mTORC1 as a direct activator of p300. Activated mTORC1 interacts with p300 and phosphorylates p300 at 4 serine residues in the C-terminal domain...
October 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033322/structural-basis-of-mec1-ddc2-rpa-assembly-and-activation-on-single-stranded-dna-at-sites-of-damage
#2
Ishan Deshpande, Andrew Seeber, Kenji Shimada, Jeremy J Keusch, Heinz Gut, Susan M Gasser
Mec1-Ddc2 (ATR-ATRIP) is a key DNA-damage-sensing kinase that is recruited through the single-stranded (ss) DNA-binding replication protein A (RPA) to initiate the DNA damage checkpoint response. Activation of ATR-ATRIP in the absence of DNA damage is lethal. Therefore, it is important that damage-specific recruitment precedes kinase activation, which is achieved at least in part by Mec1-Ddc2 homodimerization. Here, we report a structural, biochemical, and functional characterization of the yeast Mec1-Ddc2-RPA assembly...
October 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033321/regulation-of-m-6-a-transcripts-by-the-3-%C3%A2-5-rna-helicase-ythdc2-is-essential-for-a-successful-meiotic-program-in-the-mammalian-germline
#3
Magdalena Natalia Wojtas, Radha Raman Pandey, Mateusz Mendel, David Homolka, Ravi Sachidanandam, Ramesh S Pillai
N(6)-methyladenosine (m(6)A) is an essential internal RNA modification that is critical for gene expression control in most organisms. Proteins with a YTH domain recognize m(6)A marks and are mediators of molecular functions like RNA splicing, mRNA decay, and translation control. Here we demonstrate that YTH domain-containing 2 (YTHDC2) is an m(6)A reader that is essential for male and female fertility in mice. High-throughput mapping of the m(6)A transcriptome and expression analysis in the Yhtdc2 mutant testes reveal an upregulation of m(6)A-enriched transcripts...
October 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033324/the-elongation-factor-spt6-maintains-esc-pluripotency-by-controlling-super-enhancers-and-counteracting-polycomb-proteins
#4
A Hongjun Wang, Aster H Juan, Kyung Dae Ko, Pei-Fang Tsai, Hossein Zare, Stefania Dell'Orso, Vittorio Sartorelli
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription...
October 10, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033320/mitophagy-controls-the-activities-of-tumor-suppressor-p53-to-regulate-hepatic-cancer-stem-cells
#5
Kai Liu, Jiyoung Lee, Ja Yeon Kim, Linya Wang, Yongjun Tian, Stephanie T Chan, Cecilia Cho, Keigo Machida, Dexi Chen, Jing-Hsiung James Ou
Autophagy is required for benign hepatic tumors to progress into malignant hepatocellular carcinoma. However, the mechanism is unclear. Here, we report that mitophagy, the selective removal of mitochondria by autophagy, positively regulates hepatic cancer stem cells (CSCs) by suppressing the tumor suppressor p53. When mitophagy is enhanced, p53 co-localizes with mitochondria and is removed by a mitophagy-dependent manner. However, when mitophagy is inhibited, p53 is phosphorylated at serine-392 by PINK1, a kinase associated with mitophagy, on mitochondria and translocated into the nucleus, where it binds to the NANOG promoter to prevent OCT4 and SOX2 transcription factors from activating the expression of NANOG, a transcription factor critical for maintaining the stemness and the self-renewal ability of CSCs, resulting in the reduction of hepatic CSC populations...
October 10, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033319/checkpoint-kinase-rad53-couples-leading-and-lagging-strand-dna-synthesis-under-replication-stress
#6
Haiyun Gan, Chuanhe Yu, Sujan Devbhandari, Sushma Sharma, Junhong Han, Andrei Chabes, Dirk Remus, Zhiguo Zhang
The checkpoint kinase Rad53 is activated during replication stress to prevent fork collapse, an essential but poorly understood process. Here we show that Rad53 couples leading- and lagging-strand synthesis under replication stress. In rad53-1 cells stressed by dNTP depletion, the replicative DNA helicase, MCM, and the leading-strand DNA polymerase, Pol ε, move beyond the site of DNA synthesis, likely unwinding template DNA. Remarkably, DNA synthesis progresses further along the lagging strand than the leading strand, resulting in the exposure of long stretches of single-stranded leading-strand template...
October 10, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28988932/6s-rna-mimics-b-form-dna-to-regulate-escherichia-coli-rna-polymerase
#7
James Chen, Karen M Wassarman, Shili Feng, Katherine Leon, Andrey Feklistov, Jared T Winkelman, Zongli Li, Thomas Walz, Elizabeth A Campbell, Seth A Darst
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ(70)-holoenzyme (Eσ(70)) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ(70) determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches...
October 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28965816/tetherin-suppresses-type-i-interferon-signaling-by-targeting-mavs-for-ndp52-mediated-selective-autophagic-degradation-in-human-cells
#8
Shouheng Jin, Shuo Tian, Man Luo, Weihong Xie, Tao Liu, Tianhao Duan, Yaoxing Wu, Jun Cui
Tetherin (BST2/CD317) is an interferon-inducible antiviral factor known for its ability to block the release of enveloped viruses from infected cells. Yet its role in type I interferon (IFN) signaling remains poorly defined. Here, we demonstrate that Tetherin is a negative regulator of RIG-I like receptor (RLR)-mediated type I IFN signaling by targeting MAVS. The induction of Tetherin by type I IFN accelerates MAVS degradation via ubiquitin-dependent selective autophagy in human cells. Moreover, Tetherin recruits E3 ubiquitin ligase MARCH8 to catalyze K27-linked ubiquitin chains on MAVS at lysine 7, which serves as a recognition signal for NDP52-dependent autophagic degradation...
September 27, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28943311/ribosome-collision-is-critical-for-quality-control-during-no-go-decay
#9
Carrie L Simms, Liewei L Yan, Hani S Zaher
No-go decay (NGD) is a eukaryotic quality control mechanism that evolved to cope with translational arrests. The process is characterized by an endonucleolytic cleavage near the stall sequence, but the mechanistic details are unclear. Our analysis of cleavage sites indicates that cleavage requires multiple ribosomes on the mRNA. We also show that reporters harboring stall sequences near the initiation codon, which cannot accommodate multiple ribosomes, are not subject to NGD. Consistent with our model, we uncover an inverse correlation between ribosome density per mRNA and cleavage efficiency...
September 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985512/the-anti-crispr-story-a-battle-for-survival
#10
REVIEW
Karen L Maxwell
The last decade has seen the fields of molecular biology and genetics transformed by the development of CRISPR-based gene editing technologies. These technologies were derived from bacterial defense systems that protect against viral invasion. Elegant studies focused on the evolutionary battle between CRISPR-encoding bacteria and the viruses that infect and kill them revealed the next step in this arms race, the anti-CRISPR proteins. Investigation of these proteins has provided important new insight into how CRISPR-Cas systems work and how bacterial genomes evolve...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985511/epigenetic-control-of-nrf2-directed-cellular-antioxidant-status-in-dictating-life-death-decisions
#11
John D Hayes, Albena T Dinkova-Kostova
In this issue of Molecular Cell, Chen et al. (2017) demonstrate that the tumor suppressor protein ARF sensitizes cancer cells to programmed death through a surprising mechanism: ARF physically interacts with and antagonizes activation by acetylation of the master redox regulator NRF2, providing an unusual mode of posttranslational NRF2 regulation.
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985510/high-throughput-approaches-to-pinpoint-function-within-the-noncoding-genome
#12
REVIEW
Antonino Montalbano, Matthew C Canver, Neville E Sanjana
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas nuclease system is a powerful tool for genome editing, and its simple programmability has enabled high-throughput genetic and epigenetic studies. These high-throughput approaches offer investigators a toolkit for functional interrogation of not only protein-coding genes but also noncoding DNA. Historically, noncoding DNA has lacked the detailed characterization that has been applied to protein-coding genes in large part because there has not been a robust set of methodologies for perturbing these regions...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985509/untangling-p-bodies-dissecting-the-complex-web-of-interactions-that-enable-tiered-control-of-gene-expression
#13
Christopher J Kershaw, Mark P Ashe
In this issue of Molecular Cell, Hubstenberger et al. (2017) define the molecular composition of P-bodies isolated from human epithelial cells to propose that these foci act as mRNA storage depots rather than mRNA decay facilities.
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985508/methods-and-applications-of-crispr-mediated-base-editing-in-eukaryotic-genomes
#14
REVIEW
Gaelen T Hess, Josh Tycko, David Yao, Michael C Bassik
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985507/randomized-crispr-cas-transcriptional-perturbation-screening-reveals-protective-genes-against-alpha-synuclein-toxicity
#15
Ying-Chou Chen, Fahim Farzadfard, Nava Gharaei, William C W Chen, Jicong Cao, Timothy K Lu
The genome-wide perturbation of transcriptional networks with CRISPR-Cas technology has primarily involved systematic and targeted gene modulation. Here, we developed PRISM (Perturbing Regulatory Interactions by Synthetic Modulators), a screening platform that uses randomized CRISPR-Cas transcription factors (crisprTFs) to globally perturb transcriptional networks. By applying PRISM to a yeast model of Parkinson's disease (PD), we identified guide RNAs (gRNAs) that modulate transcriptional networks and protect cells from alpha-synuclein (αSyn) toxicity...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985506/nrf2-is-a-major-target-of-arf-in-p53-independent-tumor-suppression
#16
Delin Chen, Omid Tavana, Bo Chu, Luke Erber, Yue Chen, Richard Baer, Wei Gu
Although ARF can suppress tumor growth by activating p53 function, the mechanisms by which it suppresses tumor growth independently of p53 are not well understood. Here, we identified ARF as a key regulator of nuclear factor E2-related factor 2 (NRF2) through complex purification. ARF inhibits the ability of NRF2 to transcriptionally activate its target genes, including SLC7A11, a component of the cystine/glutamate antiporter that regulates reactive oxygen species (ROS)-induced ferroptosis. As a consequence, ARF expression sensitizes cells to ferroptosis in a p53-independent manner while ARF depletion induces NRF2 activation and promotes cancer cell survival in response to oxidative stress...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985505/combined-crispri-a-based-chemical-genetic-screens-reveal-that-rigosertib-is-a-microtubule-destabilizing-agent
#17
Marco Jost, Yuwen Chen, Luke A Gilbert, Max A Horlbeck, Lenno Krenning, Grégory Menchon, Ankit Rai, Min Y Cho, Jacob J Stern, Andrea E Prota, Martin Kampmann, Anna Akhmanova, Michel O Steinmetz, Marvin E Tanenbaum, Jonathan S Weissman
Chemical libraries paired with phenotypic screens can now readily identify compounds with therapeutic potential. A central limitation to exploiting these compounds, however, has been in identifying their relevant cellular targets. Here, we present a two-tiered CRISPR-mediated chemical-genetic strategy for target identification: combined genome-wide knockdown and overexpression screening as well as focused, comparative chemical-genetic profiling. Application of these strategies to rigosertib, a drug in phase 3 clinical trials for high-risk myelodysplastic syndrome whose molecular target had remained controversial, pointed singularly to microtubules as rigosertib's target...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985504/clock-acetylates-ass1-to-drive-circadian-rhythm-of-ureagenesis
#18
Ran Lin, Yan Mo, Haihong Zha, Zhipeng Qu, Pancheng Xie, Zheng-Jiang Zhu, Ying Xu, Yue Xiong, Kun-Liang Guan
In addition to responding to environmental entrainment with diurnal variation, metabolism is also tightly controlled by cell-autonomous circadian clock. Extensive studies have revealed key roles of transcription in circadian control. Post-transcriptional regulation for the rhythmic gating of metabolic enzymes remains elusive. Here, we show that arginine biosynthesis and subsequent ureagenesis are collectively regulated by CLOCK (circadian locomotor output cycles kaput) in circadian rhythms. Facilitated by BMAL1 (brain and muscle Arnt-like protein), CLOCK directly acetylates K165 and K176 of argininosuccinate synthase (ASS1) to inactivate ASS1, which catalyzes the rate-limiting step of arginine biosynthesis...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985503/a-peptide-encoded-by-a-putative-lncrna-hoxb-as3-suppresses-colon-cancer-growth
#19
Jin-Zhou Huang, Min Chen, De Chen, Xing-Cheng Gao, Song Zhu, Hongyang Huang, Min Hu, Huifang Zhu, Guang-Rong Yan
A substantial fraction of eukaryotic transcripts are considered long non-coding RNAs (lncRNAs), which regulate various hallmarks of cancer. Here, we discovered that the lncRNA HOXB-AS3 encodes a conserved 53-aa peptide. The HOXB-AS3 peptide, not lncRNA, suppresses colon cancer (CRC) growth. Mechanistically, the HOXB-AS3 peptide competitively binds to the ariginine residues in RGG motif of hnRNP A1 and antagonizes the hnRNP A1-mediated regulation of pyruvate kinase M (PKM) splicing by blocking the binding of the ariginine residues in RGG motif of hnRNP A1 to the sequences flanking PKM exon 9, ensuring the formation of lower PKM2 and suppressing glucose metabolism reprogramming...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28985502/the-revolution-continues-newly-discovered-systems-expand-the-crispr-cas-toolkit
#20
REVIEW
Karthik Murugan, Kesavan Babu, Ramya Sundaresan, Rakhi Rajan, Dipali G Sashital
CRISPR-Cas systems defend prokaryotes against bacteriophages and mobile genetic elements and serve as the basis for revolutionary tools for genetic engineering. Class 2 CRISPR-Cas systems use single Cas endonucleases paired with guide RNAs to cleave complementary nucleic acid targets, enabling programmable sequence-specific targeting with minimal machinery. Recent discoveries of previously unidentified CRISPR-Cas systems have uncovered a deep reservoir of potential biotechnological tools beyond the well-characterized Type II Cas9 systems...
October 5, 2017: Molecular Cell
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