Advertisement
Cell
This journal offers authors two options (open access or subscription) to publish research

Oct 05, 2017

Volume 171Issue 2p259-496
Open Archive
On the cover: In this issue, Rao et al. (305–320) investigated the impact of cohesin loss on the formation and maintenance of chromatin 3D configuration. On the cover, an art piece entitled “Unraveling” is presented and inspired by the knowledge on chromatin folding inside the nucleus. The meandering, unbroken linear theme is informed by the intricate packaging of the two-meter-long contour of the human genome into a nucleus only a few microns wide. Arwork by Mary Ellen Scherl....
On the cover: In this issue, Rao et al. (305–320) investigated the impact of cohesin loss on the formation and maintenance of chromatin 3D configuration. On the cover, an art piece entitled “Unraveling” is presented and inspired by the knowledge on chromatin folding inside the nucleus. The meandering, unbroken linear theme is informed by the intricate packaging of the two-meter-long contour of the human genome into a nucleus only a few microns wide. Arwork by Mary Ellen Scherl.

Leading Edge

Voices

  • Human Genetics: Questions, Challenges, and the Future

    Since the studies of “mitochondrial Eve” in the 1980s indicating that all modern humans originated in Africa, new and less expensive technologies have been developed, giving us the potential to sequence millions of genomes from individuals across the globe as well as genomes of ancient hominids as old as 400,000 years. Integration of fossil, archeological, and genetic data elucidates the evolutionary processes resulting in uniquely human traits as well as traits that vary across individuals, including risk for disease.

Commentary

  • Gene Discovery for Complex Traits: Lessons from Africa

    • Jon M. McClellan,
    • Thomas Lehner,
    • Mary-Claire King
    The genetics of African populations reveal an otherwise “missing layer” of human variation that arose between 100,000 and 5 million years ago. Both the vast number of these ancient variants and the selective pressures they survived yield insights into genes responsible for complex traits in all populations.

Previews

  • Land Plant Model Systems Branch Out

    • Charles F. Delwiche,
    • Charles A. Goodman,
    • Caren Chang
    The genome of the liverwort Marchantia polymorpha is an important step toward development of a new plant model system (Bowman et al., 2017). Liverworts may be the sister taxon to all other land plants, and the genome shows features that illuminate the ancestor of all land plants and give insights into how plant systems function and evolved.
  • Guardians of the ERAD Galaxy

    • Zhihao Sun,
    • Jeffrey L. Brodsky
    The endoplasmic reticulum-associated degradation (ERAD) pathway facilitates the disposal of terminally misfolded proteins in the early secretory pathway yet spares folding intermediates from being destroyed. Zhang et al. report on a protein complex that acts as a guardian to protect these folding intermediates from being targeted for ERAD.
  • Editing the Phenotype: A Revolution for Quantitative Genetics

    • James A. Birchler
    Quantitative trait genes have been difficult to analyze because of the subtle effects of their natural variation. Rodríguez-Leal et al. now develop a promoter-editing approach to generate a range of effective alleles for analysis, providing an avenue to investigate complex interactions among such genes.
  • Untangling the Web of Lymphoma Somatic Mutations

    • Matt Teater,
    • Ari Melnick
    In this issue of Cell, Reddy et al. report integrative genetic characterization of diffuse large B cell lymphomas (DLBCL), including large-scale exome capture, transcriptomes, CRISPR screens, and integrative clinical biomarker studies. This provides the first comprehensive overview of DLBCL biology and the basis for future precision medicine approaches to this disease.

Primer

  • Ferroptosis: A Regulated Cell Death Nexus Linking Metabolism, Redox Biology, and Disease

    • Brent R. Stockwell,
    • José Pedro Friedmann Angeli,
    • Hülya Bayir,
    • Ashley I. Bush,
    • Marcus Conrad,
    • Scott J. Dixon,
    • Simone Fulda,
    • Sergio Gascón,
    • Stavroula K. Hatzios,
    • Valerian E. Kagan,
    • Kay Noel,
    • Xuejun Jiang,
    • Andreas Linkermann,
    • Maureen E. Murphy,
    • Michael Overholtzer,
    • Atsushi Oyagi,
    • Gabriela C. Pagnussat,
    • Jason Park,
    • Qitao Ran,
    • Craig S. Rosenfeld,
    • Konstantin Salnikow,
    • Daolin Tang,
    • Frank M. Torti,
    • Suzy V. Torti,
    • Shinya Toyokuni,
    • K.A. Woerpel,
    • Donna D. Zhang
    This Primer reviews the mechanisms, tools, and guidelines to study ferroptosis, a form of cell death that is emerging as a central player in several degenerative diseases.

Articles

  • Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

    • John L. Bowman,
    • Takayuki Kohchi,
    • Katsuyuki T. Yamato,
    • Jerry Jenkins,
    • Shengqiang Shu,
    • Kimitsune Ishizaki,
    • Shohei Yamaoka,
    • Ryuichi Nishihama,
    • Yasukazu Nakamura,
    • Frédéric Berger,
    • Catherine Adam,
    • Shiori Sugamata Aki,
    • Felix Althoff,
    • Takashi Araki,
    • Mario A. Arteaga-Vazquez,
    • Sureshkumar Balasubrmanian,
    • Kerrie Barry,
    • Diane Bauer,
    • Christian R. Boehm,
    • Liam Briginshaw,
    • Juan Caballero-Perez,
    • Bruno Catarino,
    • Feng Chen,
    • Shota Chiyoda,
    • Mansi Chovatia,
    • Kevin M. Davies,
    • Mihails Delmans,
    • Taku Demura,
    • Tom Dierschke,
    • Liam Dolan,
    • Ana E. Dorantes-Acosta,
    • D. Magnus Eklund,
    • Stevie N. Florent,
    • Eduardo Flores-Sandoval,
    • Asao Fujiyama,
    • Hideya Fukuzawa,
    • Bence Galik,
    • Daniel Grimanelli,
    • Jane Grimwood,
    • Ueli Grossniklaus,
    • Takahiro Hamada,
    • Jim Haseloff,
    • Alexander J. Hetherington,
    • Asuka Higo,
    • Yuki Hirakawa,
    • Hope N. Hundley,
    • Yoko Ikeda,
    • Keisuke Inoue,
    • Shin-ichiro Inoue,
    • Sakiko Ishida,
    • Qidong Jia,
    • Mitsuru Kakita,
    • Takehiko Kanazawa,
    • Yosuke Kawai,
    • Tomokazu Kawashima,
    • Megan Kennedy,
    • Keita Kinose,
    • Toshinori Kinoshita,
    • Yuji Kohara,
    • Eri Koide,
    • Kenji Komatsu,
    • Sarah Kopischke,
    • Minoru Kubo,
    • Junko Kyozuka,
    • Ulf Lagercrantz,
    • Shih-Shun Lin,
    • Erika Lindquist,
    • Anna M. Lipzen,
    • Chia-Wei Lu,
    • Efraín De Luna,
    • Robert A. Martienssen,
    • Naoki Minamino,
    • Masaharu Mizutani,
    • Miya Mizutani,
    • Nobuyoshi Mochizuki,
    • Isabel Monte,
    • Rebecca Mosher,
    • Hideki Nagasaki,
    • Hirofumi Nakagami,
    • Satoshi Naramoto,
    • Kazuhiko Nishitani,
    • Misato Ohtani,
    • Takashi Okamoto,
    • Masaki Okumura,
    • Jeremy Phillips,
    • Bernardo Pollak,
    • Anke Reinders,
    • Moritz Rövekamp,
    • Ryosuke Sano,
    • Shinichiro Sawa,
    • Marc W. Schmid,
    • Makoto Shirakawa,
    • Roberto Solano,
    • Alexander Spunde,
    • Noriyuki Suetsugu,
    • Sumio Sugano,
    • Akifumi Sugiyama,
    • Rui Sun,
    • Yutaka Suzuki,
    • Mizuki Takenaka,
    • Daisuke Takezawa,
    • Hirokazu Tomogane,
    • Masayuki Tsuzuki,
    • Takashi Ueda,
    • Masaaki Umeda,
    • John M. Ward,
    • Yuichiro Watanabe,
    • Kazufumi Yazaki,
    • Ryusuke Yokoyama,
    • Yoshihiro Yoshitake,
    • Izumi Yotsui,
    • Sabine Zachgo,
    • Jeremy Schmutz
    The genome of the liverwort Marchantia polymorpha sheds light on the evolution of land plants.
  • Cohesin Loss Eliminates All Loop Domains

    • Suhas S.P. Rao,
    • Su-Chen Huang,
    • Brian Glenn St Hilaire,
    • Jesse M. Engreitz,
    • Elizabeth M. Perez,
    • Kyong-Rim Kieffer-Kwon,
    • Adrian L. Sanborn,
    • Sarah E. Johnstone,
    • Gavin D. Bascom,
    • Ivan D. Bochkov,
    • Xingfan Huang,
    • Muhammad S. Shamim,
    • Jaeweon Shin,
    • Douglass Turner,
    • Ziyi Ye,
    • Arina D. Omer,
    • James T. Robinson,
    • Tamar Schlick,
    • Bradley E. Bernstein,
    • Rafael Casellas,
    • Eric S. Lander,
    • Erez Lieberman Aiden
    Mapping the nucleome in 4D during cohesin loss and recovery reveals that cohesin degradation eliminates loop domains but has only modest transcriptional consequences.
  • Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns

    • Martin Enge,
    • H. Efsun Arda,
    • Marco Mignardi,
    • John Beausang,
    • Rita Bottino,
    • Seung K. Kim,
    • Stephen R. Quake
    Aging is associated with increased transcriptional dysregulation and loss of identity at the single-cell level
  • Mitochondrial Fission Promotes the Continued Clearance of Apoptotic Cells by Macrophages

    • Ying Wang,
    • Manikandan Subramanian,
    • Arif Yurdagul Jr.,
    • Valéria C. Barbosa-Lorenzi,
    • Bishuang Cai,
    • Jaime de Juan-Sanz,
    • Timothy A. Ryan,
    • Masatoshi Nomura,
    • Frederick R. Maxfield,
    • Ira Tabas
    How are dead cells in our bodies rapidly cleared by phagocytes in order to avoid inflammation and necrosis?
  • Slp1-Emp65: A Guardian Factor that Protects Folding Polypeptides from Promiscuous Degradation

    • Shan Zhang,
    • Chengchao Xu,
    • Katherine E. Larrimore,
    • Davis T.W. Ng
    A dedicated cellular mechanism protects folding polypeptides from degradation.
  • Lactate Metabolism in Human Lung Tumors

    • Brandon Faubert,
    • Kevin Y. Li,
    • Ling Cai,
    • Christopher T. Hensley,
    • Jiyeon Kim,
    • Lauren G. Zacharias,
    • Chendong Yang,
    • Quyen N. Do,
    • Sarah Doucette,
    • Daniel Burguete,
    • Hong Li,
    • Giselle Huet,
    • Qing Yuan,
    • Trevor Wigal,
    • Yasmeen Butt,
    • Min Ni,
    • Jose Torrealba,
    • Dwight Oliver,
    • Robert E. Lenkinski,
    • Craig R. Malloy,
    • Jason W. Wachsmann,
    • Jamey D. Young,
    • Kemp Kernstine,
    • Ralph J. DeBerardinis
    Human non-small cell lung cancer preferentially utilizes lactate over glucose to fuel TCA cycle and sustain tumor metabolism in vivo.
  • Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity

    • Wei Ying,
    • Matthew Riopel,
    • Gautam Bandyopadhyay,
    • Yi Dong,
    • Amanda Birmingham,
    • Jong Bae Seo,
    • Jachelle M. Ofrecio,
    • Joshua Wollam,
    • Angelina Hernandez-Carretero,
    • Wenxian Fu,
    • Pingping Li,
    • Jerrold M. Olefsky
    Macrophages residing in adipose tissue use exosomes to modulate systemic insulin responses.
  • Mitochondrial Priming by CD28

    • Ramon I. Klein Geltink,
    • David O’Sullivan,
    • Mauro Corrado,
    • Anna Bremser,
    • Michael D. Buck,
    • Joerg M. Buescher,
    • Elke Firat,
    • Xuekai Zhu,
    • Gabriele Niedermann,
    • George Caputa,
    • Beth Kelly,
    • Ursula Warthorst,
    • Anne Rensing-Ehl,
    • Ryan L. Kyle,
    • Lana Vandersarren,
    • Jonathan D. Curtis,
    • Annette E. Patterson,
    • Simon Lawless,
    • Katarzyna Grzes,
    • Jing Qiu,
    • David E. Sanin,
    • Oliver Kretz,
    • Tobias B. Huber,
    • Sophie Janssens,
    • Bart N. Lambrecht,
    • Angelika S. Rambold,
    • Edward J. Pearce,
    • Erika L. Pearce
    Costimulatory signals during the initial phase of T cell activation prime mitochondria with latent metabolic capacity essential for future T cell responses.
  • Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues

    • Motohiko Kadoki,
    • Ashwini Patil,
    • Cornelius C. Thaiss,
    • Donald J. Brooks,
    • Surya Pandey,
    • Deeksha Deep,
    • David Alvarez,
    • Ulrich H. von Andrian,
    • Amy J. Wagers,
    • Kenta Nakai,
    • Tarjei S. Mikkelsen,
    • Magali Soumillon,
    • Nicolas Chevrier
    Tissue-resident memory T cells establish a multi-organ web of communication to stop viral particles from progressing from one tissue to the next.
  • Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex

    • Tai Wei Guo,
    • Alberto Bartesaghi,
    • Hui Yang,
    • Veronica Falconieri,
    • Prashant Rao,
    • Alan Merk,
    • Edward T. Eng,
    • Ashleigh M. Raczkowski,
    • Tara Fox,
    • Lesley A. Earl,
    • Dinshaw J. Patel,
    • Sriram Subramaniam
    Single-particle cryo-EM structures of a type I-F CRISPR surveillance complex before and after target dsDNA binding, as well as after inhibitor binding, demonstrate unique structural features for dsDNA recognition and a large global elongation of the complex, which may facilitate nuclease recruitment and subsequent target degradation.
  • Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars

    • Thomas F. Cooke,
    • Curt R. Fischer,
    • Ping Wu,
    • Ting-Xin Jiang,
    • Kathleen T. Xie,
    • James Kuo,
    • Elizabeth Doctorov,
    • Ashley Zehnder,
    • Chaitan Khosla,
    • Cheng-Ming Chuong,
    • Carlos D. Bustamante
    An enzyme required for yellow pigmentation in a popular variety of pet parrots is discovered through genome-wide mapping and biochemical studies.
  • Deconstruction of Corticospinal Circuits for Goal-Directed Motor Skills

    • Xuhua Wang,
    • Yuanyuan Liu,
    • Xinjian Li,
    • Zicong Zhang,
    • Hengfu Yang,
    • Yu Zhang,
    • Philip R. Williams,
    • Noaf S.A. Alwahab,
    • Kush Kapur,
    • Bin Yu,
    • Yiming Zhang,
    • Mengying Chen,
    • Haixia Ding,
    • Charles R. Gerfen,
    • Kuan Hong Wang,
    • Zhigang He
    What are the neuronal circuits underlying goal-directed motor skills, and how are they organized and spatiotemporally activated?

Resource

  • Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism

    • Yongsoo Kim,
    • Guangyu Robert Yang,
    • Kith Pradhan,
    • Kannan Umadevi Venkataraju,
    • Mihail Bota,
    • Luis Carlos García del Molino,
    • Greg Fitzgerald,
    • Keerthi Ram,
    • Miao He,
    • Jesse Maurica Levine,
    • Partha Mitra,
    • Z. Josh Huang,
    • Xiao-Jing Wang,
    • Pavel Osten
    A quantitative cell-type-based whole-brain anatomical resource reveals new principles of structural organization of the brain
  • Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing

    • Daniel Rodríguez-Leal,
    • Zachary H. Lemmon,
    • Jarrett Man,
    • Madelaine E. Bartlett,
    • Zachary B. Lippman
    In this article, we discuss how to use the CRISPR/Cas9 genome editing approach to dissect the biology of quantitative trait loci.
  • Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma

    • Anupama Reddy,
    • Jenny Zhang,
    • Nicholas S. Davis,
    • Andrea B. Moffitt,
    • Cassandra L. Love,
    • Alexander Waldrop,
    • Sirpa Leppa,
    • Annika Pasanen,
    • Leo Meriranta,
    • Marja-Liisa Karjalainen-Lindsberg,
    • Peter Nørgaard,
    • Mette Pedersen,
    • Anne O. Gang,
    • Estrid Høgdall,
    • Tayla B. Heavican,
    • Waseem Lone,
    • Javeed Iqbal,
    • Qiu Qin,
    • Guojie Li,
    • So Young Kim,
    • Jane Healy,
    • Kristy L. Richards,
    • Yuri Fedoriw,
    • Leon Bernal-Mizrachi,
    • Jean L. Koff,
    • Ashley D. Staton,
    • Christopher R. Flowers,
    • Ora Paltiel,
    • Neta Goldschmidt,
    • Maria Calaminici,
    • Andrew Clear,
    • John Gribben,
    • Evelyn Nguyen,
    • Magdalena B. Czader,
    • Sarah L. Ondrejka,
    • Angela Collie,
    • Eric D. Hsi,
    • Eric Tse,
    • Rex K.H. Au-Yeung,
    • Yok-Lam Kwong,
    • Gopesh Srivastava,
    • William W.L. Choi,
    • Andrew M. Evens,
    • Monika Pilichowska,
    • Manju Sengar,
    • Nishitha Reddy,
    • Shaoying Li,
    • Amy Chadburn,
    • Leo I. Gordon,
    • Elaine S. Jaffe,
    • Shawn Levy,
    • Rachel Rempel,
    • Tiffany Tzeng,
    • Lanie E. Happ,
    • Tushar Dave,
    • Deepthi Rajagopalan,
    • Jyotishka Datta,
    • David B. Dunson,
    • Sandeep S. Dave
    An integrative analysis in 1,001 newly diagnosed DLBCL patients identifies 150 genetic drivers with functional characterization using an unbiased CRISPR screen in DLBCL cell lines and connects with clinical outcome.

Correction

Snapshot

  • SnapShot: Tissue Clearing

    • Douglas S. Richardson,
    • Jeff W. Lichtman
    Tissue clearing has become an important tool for the investigation of biological systems in three dimensions. However, many pioneering techniques were based on serendipitous discoveries. Next-generation clearing methods have been (re)designed with a better understanding of the chemistry and physics required to equalize the refractive index throughout a sample which prevents the random bending of light that clouds biological tissues.
Advertisement
Advertisement