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Reactive oxygen species signalling in plant stress responses Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-27 Ron Mittler, Sara I. Zandalinas, Yosef Fichman, Frank Van Breusegem
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Signalling mechanisms and cellular functions of SUMO Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-24 Alfred C. O. Vertegaal
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ncRNA regulation of mitochondrial transcription Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-21 Eytan Zlotorynski
The non-coding RNA 7S inhibits transcription initiation in mitochondria by preventing the RNA polymerase from interacting with promoter DNA and transcription factors.
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The Mediator complex as a master regulator of transcription by RNA polymerase II Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-20 William F. Richter, Shraddha Nayak, Janet Iwasa, Dylan J. Taatjes
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Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-16 Sara Lopez-Gomollon, David C. Baulcombe
RNA silencing is a well-established antiviral immunity system in plants, in which small RNAs guide Argonaute proteins to targets in viral RNA or DNA, resulting in virus repression. Virus-encoded suppressors of silencing counteract this defence system. In this Review, we discuss recent findings about antiviral RNA silencing, including the movement of RNA through plasmodesmata and the differentiation
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Mining the mitochondrial proteome Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-08 Paulina Strzyz
Rensvold et al. provide a resource to characterize the function of mitochondrial proteins and to facilitate the discovery of disease-relevant mutations.
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End of the road: from the ER to the proteasome Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-07 James A. Olzmann
James Olzmann discusses the groundbreaking work of Ron Kopito and colleagues, which demonstrated that a CFTR mutant is ubiquitinated and degraded by the cytosolic 26S proteasome. This discovery contributed to our understanding of ERAD and had important implications for the development of therapeutic agents for cystic fibrosis.
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Mediat(or)ing adult stem cells by XIST Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-06 Eytan Zlotorynski
XIST loss causes partial gene reactivation at the inactive X chromosome, resulting in Mediator-dependent expansion of adult mammary stem cells and tumorigenesis.
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Selective motor activation in organelle transport along axons Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-30 Sydney E. Cason, Erika L. F. Holzbaur
The active transport of organelles and other cargos along the axon is required to maintain neuronal health and function, but we are just beginning to understand the complex regulatory mechanisms involved. The molecular motors, cytoplasmic dynein and kinesins, transport cargos along microtubules; this transport is tightly regulated by adaptors and effectors. Here we review our current understanding
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Publisher Correction: Plant hormone regulation of abiotic stress responses. Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-30 Rainer Waadt,Charles A Seller,Po-Kai Hsu,Yohei Takahashi,Shintaro Munemasa,Julian I Schroeder
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Phosphoinositides as membrane organizers Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-19 York Posor, Wonyul Jang, Volker Haucke
Phosphoinositides are signalling lipids derived from phosphatidylinositol, a ubiquitous phospholipid in the cytoplasmic leaflet of eukaryotic membranes. Initially discovered for their roles in cell signalling, phosphoinositides are now widely recognized as key integrators of membrane dynamics that broadly impact on all aspects of cell physiology and on disease. The past decade has witnessed a vast
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Curvature-mediated endocytosis Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-16 Paulina Strzyz
Cail et al. introduce a platform to study the role of plasma membrane curvature during clathrin-mediated endocytosis.
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Transcriptional control of energy metabolism by nuclear receptors Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-16 Charlotte Scholtes, Vincent Giguère
Transcriptional regulation of catabolic pathways is a central mechanism by which cells respond to physiological cues to generate the energy required for anabolic pathways, transport of molecules and mechanical work. Nuclear receptors are members of a superfamily of transcription factors that transduce hormonal, nutrient, metabolite and redox signals into specific metabolic gene programmes, and thus
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-13 Jan Padeken, Stephen P. Methot, Susan M. Gasser
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1)
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Plant hormone regulation of abiotic stress responses Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-05 Rainer Waadt, Charles A. Seller, Po-Kai Hsu, Yohei Takahashi, Shintaro Munemasa, Julian I. Schroeder
Plant hormones are signalling compounds that regulate crucial aspects of growth, development and environmental stress responses. Abiotic stresses, such as drought, salinity, heat, cold and flooding, have profound effects on plant growth and survival. Adaptation and tolerance to such stresses require sophisticated sensing, signalling and stress response mechanisms. In this Review, we discuss recent
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Mechanics and functional consequences of nuclear deformations Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-05 Yohalie Kalukula, Andrew D. Stephens, Jan Lammerding, Sylvain Gabriele
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus
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Author Correction: Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-06-01 Eva Petermann,Li Lan,Lee Zou
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How m6A makes its mark Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-04 Kate D. Meyer
Kate Meyer reminds us of a study of mRNA N6-methyladenosine that predated the epitranscriptomics era by decades.
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New imprinting control-like regions Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-03 Eytan Zlotorynski
H3K9me3 promotes imprinting in mouse embryos, including in a newly discovered type of imprinting control-like regions.
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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-05-03 Mathias Girbig, Agata D. Misiaszek, Christoph W. Müller
The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces
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The prospects and opportunities of protein structure prediction with AI Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-27 Kathryn Tunyasuvunakool
A Comment on the impact of improved protein structure prediction by Kathryn Tunyasuvunakool from DeepMind — the company behind AlphaFold. The 2020 Critical Assessment of protein Structure Prediction (CASP) marked a significant advance. The machine learning method AlphaFold predicted the structure of most target proteins to an accuracy assessors called “competitive with experiment”. Here, I discuss
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Sources, resolution and physiological relevance of R-loops and RNA–DNA hybrids Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-22 Eva Petermann, Li Lan, Lee Zou
RNA–DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA–DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating
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From trans-splicing discovery and onwards, trypanosomes lead the way Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-20 Idálio J. Viegas, Luisa M. Figueiredo
Viegas and Figueiredo tell us how, among several molecular and biochemical discoveries, RNA trans-splicing was discovered in trypanosomes.
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Apical–basal polarity and the control of epithelial form and function Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-19 Clare E. Buckley, Daniel St Johnston
Epithelial cells are the most common cell type in all animals, forming the sheets and tubes that compose most organs and tissues. Apical–basal polarity is essential for epithelial cell form and function, as it determines the localization of the adhesion molecules that hold the cells together laterally and the occluding junctions that act as barriers to paracellular diffusion. Polarity must also target
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ATP and ROS signal cell extrusion Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-14 Paulina Strzyz
Mori et al. identify ATP and reactive oxygen species as key upstream cues for cell extrusion.
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Why novel mRNA modifications are so challenging and what we can do about it Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-14 Audrey Penning, Jana Jeschke, François Fuks
The discovery of diverse chemical modifications of mRNA has spurred efforts to identify, map and characterize them. Yet aside from N6-methyladenosine (m6A), progress in epitranscriptomics has been stymied by discrepant data. Here we discuss the main obstacles in studying novel mRNA modifications and offer insights into how to surmount them. Progress in the characterization of new mRNA modifications
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Reaching the inaccessible DNA Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-06 Olivier Mathieu
Heterochromatin DNA is heavily methylated yet also inaccessible. Olivier Mathieu describes the work that revealed how DNA methyltransferases access heterochromatin.
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Endothelial cell diversity in the liver Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-05 Kim Baumann
The transcription factor c-Maf is required for the specification of liver sinusoids and for the maintenance of a specialized sinusoidal network necessary for sustaining hepatocyte function.
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Chaperoning solid aggregates for autophagy Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-05 Paulina Strzyz
Ma et al. show the role of CCT2, a chaperonin TRiC subunit, in aggrephagy, specifically in the removal of mature, solid-like protein aggregates.
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Mechanisms of microtubule organization in differentiated animal cells Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-05 Anna Akhmanova, Lukas C. Kapitein
Microtubules are polarized cytoskeletal filaments that serve as tracks for intracellular transport and form a scaffold that positions organelles and other cellular components and modulates cell shape and mechanics. In animal cells, the geometry, density and directionality of microtubule networks are major determinants of cellular architecture, polarity and proliferation. In dividing cells, microtubules
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Interplay between mechanics and signalling in regulating cell fate Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-04-01 Henry De Belly, Ewa K. Paluch, Kevin J. Chalut
Mechanical signalling affects multiple biological processes during development and in adult organisms, including cell fate transitions, cell migration, morphogenesis and immune responses. Here, we review recent insights into the mechanisms and functions of two main routes of mechanical signalling: outside-in mechanical signalling, such as mechanosensing of substrate properties or shear stresses; and
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Returning to the lab after a career break Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-29 Jane A. Skok
Returning to the lab after a career break can be a daunting prospect even if you have only been away for a year. My time away lasted 12 years, which meant I was returning to a whole new era in science. Jane Skok recounts her journey back to academia after a 12-year-long career break.
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oskar stands on solid ground for translation Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-25 Eytan Zlotorynski
The solid phase of oskar mRNA granules is required for proper Oskar protein synthesis and fruit fly development.
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Alternative cycle for citrate Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-16 Paulina Strzyz
Arnold et al. document an alternative tricarboxylic acid cycle that takes place between the mitochondria and the cytosol and that can be adopted in specific cell states.
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Transposons: catch them if you can Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-09 Tuğçe Aktaş
Transposons and their host genomes are entangled in an evolutionary arms race, recounts Tuğçe Aktaş.
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Pioneer factors as master regulators of the epigenome and cell fate Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-09 Aurelio Balsalobre, Jacques Drouin
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin
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Phase separation in stress resistance Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-08 Kim Baumann
The RNA-binding proteins RBGD2 and RBGD4 improve resistance to heat stress in plants by phase separating into heat-induced stress granules.
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Challenges and directions in studying cell–cell communication by extracellular vesicles Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-03-08 Guillaume van Niel, David R. F. Carter, Aled Clayton, Daniel W. Lambert, Graça Raposo, Pieter Vader
Extracellular vesicles (EVs) are increasingly recognized as important mediators of intercellular communication. They have important roles in numerous physiological and pathological processes, and show considerable promise as novel biomarkers of disease, as therapeutic agents and as drug delivery vehicles. Intriguingly, however, understanding of the cellular and molecular mechanisms that govern the
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Human topoisomerases and their roles in genome stability and organization Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-28 Yves Pommier, André Nussenzweig, Shunichi Takeda, Caroline Austin
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent
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Roles of transposable elements in the regulation of mammalian transcription Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-28 Raquel Fueyo, Julius Judd, Cedric Feschotte, Joanna Wysocka
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and
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Metabolic regulation of somatic stem cells in vivo Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-28 Corbin E. Meacham, Andrew W. DeVilbiss, Sean J. Morrison
Metabolism has been studied mainly in cultured cells or at the level of whole tissues or whole organisms in vivo. Consequently, our understanding of metabolic heterogeneity among cells within tissues is limited, particularly when it comes to rare cells with biologically distinct properties, such as stem cells. Stem cell function, tissue regeneration and cancer suppression are all metabolically regulated
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5mC: what goes on must come off Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-25 Angela H. Ting, Byron H. Lee
Ting and Lee describe how the trypanosome base J ‘inspired’ the discovery of the mechanism of active DNA demethylation.
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Transcripts in the loop Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-23 Eytan Zlotorynski
Highly transcribed long genes ‘stiffen’ and form loops extending from the harbouring chromosomes.
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Deep learning shapes single-cell data analysis Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-23 Qin Ma, Dong Xu
Deep learning has tremendous potential in single-cell data analyses, but numerous challenges and possible new developments remain to be explored. In this commentary, we consider the progress, limitations, best practices and outlook of adapting deep learning methods for analysing single-cell data. Ma and Xu discuss the status, best practices and future of using deep learning methods to analyse single-cell
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Let’s talk about (biological) sex Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-23 Irene Miguel-Aliaga
You spent years investigating your beloved protein. You generated mouse models, found a phenotype and fixed it with a drug. You even used human cells to reveal a conserved mechanism. But a prestigious journal has rejected your manuscript because you did not include females. Here is why you should not be mad at them. Irene Miguel-Aliaga comments on the importance of considering biological sex as an
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Defining roles of specific reactive oxygen species (ROS) in cell biology and physiology Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-21 Helmut Sies, Vsevolod V. Belousov, Navdeep S. Chandel, Michael J. Davies, Dean P. Jones, Giovanni E. Mann, Michael P. Murphy, Masayuki Yamamoto, Christine Winterbourn
‘Reactive oxygen species’ (ROS) is a generic term that defines a wide variety of oxidant molecules with vastly different properties and biological functions that range from signalling to causing cell damage. Consequently, the description of oxidants needs to be chemically precise to translate research on their biological effects into therapeutic benefit in redox medicine. This Expert Recommendation
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New tool for MAPping microtubule dynamics Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-10 Paulina Strzyz
Jijumon et al. introduce a straightforward, cell-free assay to unravel the functions of microtubule-associated proteins.
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Mesoscale organization in bacteria Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-04 Keren Lasker
Keren Lasker discusses early work of Lucy Shapiro, which provided first evidence that bacterial cells spatially regulate their cellular processes, akin to their eukaryotic counterparts.
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A lncRNA builds a glycolytic metabolon Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-02-03 Kim Baumann
A long non-coding RNA is found to enable the assembly of a glycolytic metabolon that contributes to cell adaptation to metabolic stress and cell survival.
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Pseudouridylation alters splicing Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-27 Eytan Zlotorynski
Pseudouridylation of pre-mRNA can broadly modulate alternative splicing in human cells.
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Revisiting small RNA movement in plants Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-27 Olivier Voinnet
Regulation of intercellular small RNA (sRNA)-mediated gene silencing in plants is commonly ascribed to hypothetical mechanisms involving movement channels. In this commentary, I present a complementary, perhaps counter-intuitive view, in which sRNA movement is also crucially regulated by the cell-autonomous silencing machinery found in silencing-emitting, traversed and recipient cells. Olivier Voinnet
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Ubiquitin ligases: guardians of mammalian development Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-25 David A. Cruz Walma, Zhuoyao Chen, Alex N. Bullock, Kenneth M. Yamada
Mammalian development demands precision. Millions of molecules must be properly located in temporal order, and their function regulated, to orchestrate important steps in cell cycle progression, apoptosis, migration and differentiation, to shape developing embryos. Ubiquitin and its associated enzymes act as cellular guardians to ensure precise spatio-temporal control of key molecules during each of
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Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-25 Takayuki Nojima, Nick J. Proudfoot
Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some
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Seeing the smallest rotary biomotor Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-24 Valeria Levi
Valeria Levi recounts how a clever way to visualize the function of H+-ATP synthase pioneered single-molecule technologies.
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How the α-helix got its name Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-24 Martin Egli, Shuguang Zhang
‘Alpha helix’ was not Linus Pauling’s first choice of a name for the protein structural motif. Egli and Zhang recount what the original name was, why it was changed and what is between the alpha helix and the DNA double helix.
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Karyopherin-mediated nucleocytoplasmic transport Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-20 Casey E. Wing, Ho Yee Joyce Fung, Yuh Min Chook
Efficient and regulated nucleocytoplasmic trafficking of macromolecules to the correct subcellular compartment is critical for proper functions of the eukaryotic cell. The majority of the macromolecular traffic across the nuclear pores is mediated by the Karyopherin-β (or Kap) family of nuclear transport receptors. Work over more than two decades has shed considerable light on how the different Kap
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Modulation of cellular processes by histone and non-histone protein acetylation Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-18 Maria Shvedunova, Asifa Akhtar
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to
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The healing role of gasdermin B in IBD Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-17 Paulina Strzyz
Rana et al. show that in the gut epithelium, gasdermin B has an inherent, non-pyroptotic function, supporting the maintenance of the epithelial barrier when challenged with inflammatory damage.
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Mapping organelle supply chains Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-13 W. Mike Henne
Mike Henne discusses the pioneering work of Jean Vance, which revealed that mitochonodria-associated membranes (MAMs) are sites for inter-organelle phospholipid exchange and step-wise synthesis reactions.
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First prediction of sequence-specific recognition of double-helix nucleic acids by proteins Nat. Rev. Mol. Cell Biol. (IF 94.444) Pub Date : 2022-01-12 Martin Egli, Shuguang Zhang
Prior to introduction of the first DNA–protein structure, Ned Seeman et al. correctly conceived how proteins recognize specific sequences in double-helix nucleic acids.