Resources

  • Resource |

    Xia and colleagues provided a map for transcriptome-wide distribution of m6A RNA methylation in eight human fetal tissue types.

    • Shan Xiao
    • , Shuo Cao
    • , Qitao Huang
    • , Linjian Xia
    • , Mingqiang Deng
    • , Mengtian Yang
    • , Guiru Jia
    • , Xiaona Liu
    • , Junfang Shi
    • , Weishi Wang
    • , Yuan Li
    • , Sun Liu
    • , Haoran Zhu
    • , Kaifen Tan
    • , Qizhi Luo
    • , Mei Zhong
    • , Chunjiang He
    •  & Laixin Xia
  • Resource |

    Using scCOOL-seq, Li et al. simultaneously characterize the DNA methylation and chromatin accessibility of the same cell during human preimplantation development.

    • Lin Li
    • , Fan Guo
    • , Yun Gao
    • , Yixin Ren
    • , Peng Yuan
    • , Liying Yan
    • , Rong Li
    • , Ying Lian
    • , Jingyun Li
    • , Boqiang Hu
    • , Junpeng Gao
    • , Lu Wen
    • , Fuchou Tang
    •  & Jie Qiao
  • Resource |

    Using a multi-tier scRNA-seq and CRISP-seq approach, Giladi et al. define a transcriptional signature for the naive haematopoietic stem cell state, and follow progenitor plasticity and fate commitment under the influence of cytokines and growth factors.

    • Amir Giladi
    • , Franziska Paul
    • , Yoni Herzog
    • , Yaniv Lubling
    • , Assaf Weiner
    • , Ido Yofe
    • , Diego Jaitin
    • , Nina Cabezas-Wallscheid
    • , Regine Dress
    • , Florent Ginhoux
    • , Andreas Trumpp
    • , Amos Tanay
    •  & Ido Amit
  • Resource |

    Knapp et al. analyse the heterogeneous molecular profiles and functions of CD49f human cord blood haematopoietic stem cells and report that a subset with CD33 expression has improved regenerative activity.

    • David J. H. F. Knapp
    • , Colin A. Hammond
    • , Tony Hui
    • , Marijn T. J. van Loenhout
    • , Fangwu Wang
    • , Nima Aghaeepour
    • , Paul H. Miller
    • , Michelle Moksa
    • , Gabrielle M. Rabu
    • , Philip A. Beer
    • , Davide Pellacani
    • , R. Keith Humphries
    • , Carl Hansen
    • , Martin Hirst
    •  & Connie J. Eaves
  • Resource |

    Gao et al. provide a comprehensive single-cell transcriptomic resource of four organs from the human fetal gastrointestinal tract and adult large intestine.

    • Shuai Gao
    • , Liying Yan
    • , Rui Wang
    • , Jingyun Li
    • , Jun Yong
    • , Xin Zhou
    • , Yuan Wei
    • , Xinglong Wu
    • , Xiaoye Wang
    • , Xiaoying Fan
    • , Jie Yan
    • , Xu Zhi
    • , Yun Gao
    • , Hongshan Guo
    • , Xiao Jin
    • , Wendong Wang
    • , Yunuo Mao
    • , Fengchao Wang
    • , Lu Wen
    • , Wei Fu
    • , Hao Ge
    • , Jie Qiao
    •  & Fuchou Tang
  • Resource |

    Gao and colleagues characterize genome-wide H3K9me3 distributions in pre- and post-implantation mouse embryos, providing a resource to further our understanding of epigenomic dynamics during mammalian embryogenesis.

    • Chenfei Wang
    • , Xiaoyu Liu
    • , Yawei Gao
    • , Lei Yang
    • , Chong Li
    • , Wenqiang Liu
    • , Chuan Chen
    • , Xiaochen Kou
    • , Yanhong Zhao
    • , Jiayu Chen
    • , Yixuan Wang
    • , Rongrong Le
    • , Hong Wang
    • , Tao Duan
    • , Yong Zhang
    •  & Shaorong Gao
  • Resource |

    Lyden and colleagues use asymmetric flow field-flow fractionation to classify nanoparticles derived from cell lines and human samples, including previously uncharacterized large, Exo-L and small, Exo-S, exosome subsets.

    • Haiying Zhang
    • , Daniela Freitas
    • , Han Sang Kim
    • , Kristina Fabijanic
    • , Zhong Li
    • , Haiyan Chen
    • , Milica Tesic Mark
    • , Henrik Molina
    • , Alberto Benito Martin
    • , Linda Bojmar
    • , Justin Fang
    • , Sham Rampersaud
    • , Ayuko Hoshino
    • , Irina Matei
    • , Candia M. Kenific
    • , Miho Nakajima
    • , Anders Peter Mutvei
    • , Pasquale Sansone
    • , Weston Buehring
    • , Huajuan Wang
    • , Juan Pablo Jimenez
    • , Leona Cohen-Gould
    • , Navid Paknejad
    • , Matthew Brendel
    • , Katia Manova-Todorova
    • , Ana Magalhães
    • , José Alexandre Ferreira
    • , Hugo Osório
    • , André M. Silva
    • , Ashish Massey
    • , Juan R. Cubillos-Ruiz
    • , Giuseppe Galletti
    • , Paraskevi Giannakakou
    • , Ana Maria Cuervo
    • , John Blenis
    • , Robert Schwartz
    • , Mary Sue Brady
    • , Héctor Peinado
    • , Jacqueline Bromberg
    • , Hiroshi Matsui
    • , Celso A. Reis
    •  & David Lyden
  • Resource |

    Porpiglia et al. use single-cell mass cytometry to analyse surface markers and key myogenic transcription factors of skeletal muscle stem cells during homeostasis and repair, and identify previously unrecognized myogenic progenitor cell populations.

    • Ermelinda Porpiglia
    • , Nikolay Samusik
    • , Andrew Tri Van Ho
    • , Benjamin D. Cosgrove
    • , Thach Mai
    • , Kara L. Davis
    • , Astraea Jager
    • , Garry P. Nolan
    • , Sean C. Bendall
    • , Wendy J. Fantl
    •  & Helen M. Blau
  • Resource |

    Boxem and colleagues perform a yeast two-hybrid screen to identify interactions between C. elegans polarity genes, followed by an RNAi screen to identify the functions of interaction pairs in the establishment and maintenance of cell polarity in various tissues.

    • Thijs Koorman
    • , Diana Klompstra
    • , Monique van der Voet
    • , Irma Lemmens
    • , João J. Ramalho
    • , Susan Nieuwenhuize
    • , Sander van den Heuvel
    • , Jan Tavernier
    • , Jeremy Nance
    •  & Mike Boxem
  • Resource |

    Humphries and colleagues analyse proteomic data of integrin adhesion complexes to derive a consensus integrin adhesome and characterize the temporal dynamics of adhesome component recruitment during adhesion complex assembly and disassembly.

    • Edward R. Horton
    • , Adam Byron
    • , Janet A. Askari
    • , Daniel H. J. Ng
    • , Angélique Millon-Frémillon
    • , Joseph Robertson
    • , Ewa J. Koper
    • , Nikki R. Paul
    • , Stacey Warwood
    • , David Knight
    • , Jonathan D. Humphries
    •  & Martin J. Humphries
  • Resource |

    Piccolo and colleagues report that the YAP/TAZ factors form ternary complexes with TEAD and AP-1 factors to drive a transcriptional program that promotes cell proliferation and tumour growth.

    • Francesca Zanconato
    • , Mattia Forcato
    • , Giusy Battilana
    • , Luca Azzolin
    • , Erika Quaranta
    • , Beatrice Bodega
    • , Antonio Rosato
    • , Silvio Bicciato
    • , Michelangelo Cordenonsi
    •  & Stefano Piccolo
  • Resource |

    In an effort by several research groups, a genome-wide RNAi-based screen presents a list of validated genes involved in cilia assembly and maintenance, and reveals previously unidentified ciliopathy factors.

    • Gabrielle Wheway
    • , Miriam Schmidts
    • , Dorus A. Mans
    • , Katarzyna Szymanska
    • , Thanh-Minh T. Nguyen
    • , Hilary Racher
    • , Ian G. Phelps
    • , Grischa Toedt
    • , Julie Kennedy
    • , Kirsten A. Wunderlich
    • , Nasrin Sorusch
    • , Zakia A. Abdelhamed
    • , Subaashini Natarajan
    • , Warren Herridge
    • , Jeroen van Reeuwijk
    • , Nicola Horn
    • , Karsten Boldt
    • , David A. Parry
    • , Stef J. F. Letteboer
    • , Susanne Roosing
    • , Matthew Adams
    • , Sandra M. Bell
    • , Jacquelyn Bond
    • , Julie Higgins
    • , Ewan E. Morrison
    • , Darren C. Tomlinson
    • , Gisela G. Slaats
    • , Teunis J. P. van Dam
    • , Lijia Huang
    • , Kristin Kessler
    • , Andreas Giessl
    • , Clare V. Logan
    • , Evan A. Boyle
    • , Jay Shendure
    • , Shamsa Anazi
    • , Mohammed Aldahmesh
    • , Selwa Al Hazzaa
    • , Robert A. Hegele
    • , Carole Ober
    • , Patrick Frosk
    • , Aizeddin A. Mhanni
    • , Bernard N. Chodirker
    • , Albert E. Chudley
    • , Ryan Lamont
    • , Francois P. Bernier
    • , Chandree L. Beaulieu
    • , Paul Gordon
    • , Richard T. Pon
    • , Clem Donahue
    • , A. James Barkovich
    • , Louis Wolf
    • , Carmel Toomes
    • , Christian T. Thiel
    • , Kym M. Boycott
    • , Martin McKibbin
    • , Chris F. Inglehearn
    • , UK10K Consortium
    • , University of Washington Center for Mendelian Genomics
    • , Fiona Stewart
    • , Heymut Omran
    • , Martijn A. Huynen
    • , Panagiotis I. Sergouniotis
    • , Fowzan S. Alkuraya
    • , Jillian S. Parboosingh
    • , A. Micheil Innes
    • , Colin E. Willoughby
    • , Rachel H. Giles
    • , Andrew R. Webster
    • , Marius Ueffing
    • , Oliver Blacque
    • , Joseph G. Gleeson
    • , Uwe Wolfrum
    • , Philip L. Beales
    • , Toby Gibson
    • , Dan Doherty
    • , Hannah M. Mitchison
    • , Ronald Roepman
    •  & Colin A. Johnson
  • Resource |

    Groth and colleagues identify proteins associated with newly synthesized DNA — isolated by nascent chromatin capture — as well as proteins associated with mature DNA, and find factors not previously linked to replication or nascent chromatin.

    • Constance Alabert
    • , Jimi-Carlo Bukowski-Wills
    • , Sung-Bau Lee
    • , Georg Kustatscher
    • , Kyosuke Nakamura
    • , Flavia de Lima Alves
    • , Patrice Menard
    • , Jakob Mejlvang
    • , Juri Rappsilber
    •  & Anja Groth
  • Resource |

    Zon and colleagues have performed a reverse genetic screen to target orthologues of 425 human chromatin factors in zebrafish. This allowed them to delineate chromatin regulators that function at distinct stages of primitive and definitive blood formation.

    • Hsuan-Ting Huang
    • , Katie L. Kathrein
    • , Abby Barton
    • , Zachary Gitlin
    • , Yue-Hua Huang
    • , Thomas P. Ward
    • , Oliver Hofmann
    • , Anthony Dibiase
    • , Anhua Song
    • , Svitlana Tyekucheva
    • , Winston Hide
    • , Yi Zhou
    •  & Leonard I. Zon
  • Resource |

    Bakal, Wong and colleagues performed an RNAi screen in Drosophila cells, as well as imaging and systems-level analyses, to identify genes regulating morphological complexity in heterogeneous cell populations. They report that rather than generating novel shapes, most genes control a switch-like transition between distinct morphologies. The authors also extend their findings to mouse and human melanoma cells.

    • Zheng Yin
    • , Amine Sadok
    • , Heba Sailem
    • , Afshan McCarthy
    • , Xiaofeng Xia
    • , Fuhai Li
    • , Mar Arias Garcia
    • , Louise Evans
    • , Alexis R. Barr
    • , Norbert Perrimon
    • , Christopher J. Marshall
    • , Stephen T. C. Wong
    •  & Chris Bakal
  • Resource |

    Plath and colleagues survey the global histone modification changes linked to reprogramming. They delineate that the H3K9-methylation-associated protein Cbx3 restricts late events of reprogramming and, in particular, prevents the expression of the pluripotent gene Nanog.

    • Rupa Sridharan
    • , Michelle Gonzales-Cope
    • , Constantinos Chronis
    • , Giancarlo Bonora
    • , Robin McKee
    • , Chengyang Huang
    • , Sanjeet Patel
    • , David Lopez
    • , Nilamadhab Mishra
    • , Matteo Pellegrini
    • , Michael Carey
    • , Benjamin A. Garcia
    •  & Kathrin Plath
  • Resource |

    Human embryonic stem cells contain 5-hydroxymethylcytosine (5hmC) generated by the TET enzyme. Jin and colleagues show that TET1 increases 5hmC levels during reprogramming to human inducible pluripotent stem cells, and although this change is critical for optimal epigenetic reprogramming, it does not compromise primed pluripotency.

    • Tao Wang
    • , Hao Wu
    • , Yujing Li
    • , Keith E. Szulwach
    • , Li Lin
    • , Xuekun Li
    • , I-Ping Chen
    • , Ian S. Goldlust
    • , Stormy J. Chamberlain
    • , Ann Dodd
    • , He Gong
    • , Gene Ananiev
    • , Ji Woong Han
    • , Young-sup Yoon
    • , M. Katharine Rudd
    • , Miao Yu
    • , Chun-Xiao Song
    • , Chuan He
    • , Qiang Chang
    • , Stephen T. Warren
    •  & Peng Jin
  • Resource |

    Maliga and colleagues have produced a library of bacterial artificial chromosome (BAC) transgenes encoding tagged human kinesin and myosin motors, and have generated a collection of BAC-expressing human and mouse cell lines for the study of motor function.

    • Zoltan Maliga
    • , Magno Junqueira
    • , Yusuke Toyoda
    • , Andreas Ettinger
    • , Felipe Mora-Bermúdez
    • , Robin W. Klemm
    • , Andrej Vasilj
    • , Elaine Guhr
    • , Itziar Ibarlucea-Benitez
    • , Ina Poser
    • , Ezio Bonifacio
    • , Wieland B. Huttner
    • , Andrej Shevchenko
    •  & Anthony A. Hyman
  • Resource |

    Cell polarity is important for the function of many animal cells, and several aspects of its establishment are conserved across species, from worm to human. Ahringer and colleagues have performed large-scale genetic interaction screens in Caenorhabditis elegans to identify a network of polarity regulators that includes genes not previously associated with polarity, such as the nuclear pore protein NPP-2.

    • Bruno Thomas Fievet
    • , Josana Rodriguez
    • , Sundar Naganathan
    • , Christine Lee
    • , Eva Zeiser
    • , Takao Ishidate
    • , Masaki Shirayama
    • , Stephan Grill
    •  & Julie Ahringer
  • Resource |

    Clark and colleagues have characterized the stages during which global epigenetic reprogramming occurs in human primordial germ cells, and delineate the appearance of these changes at 16 days of differentiation.

    • Sofia Gkountela
    • , Ziwei Li
    • , John J. Vincent
    • , Kelvin X. Zhang
    • , Angela Chen
    • , Matteo Pellegrini
    •  & Amander T. Clark
  • Resource |

    Brown and colleagues take a systems-level approach to the DNA damage response by analysing the changes in localization and abundance of proteins in response to replication stress, using a budding yeast GFP fusion library and high-throughput microscopy.

    • Johnny M. Tkach
    • , Askar Yimit
    • , Anna Y. Lee
    • , Michael Riffle
    • , Michael Costanzo
    • , Daniel Jaschob
    • , Jason A. Hendry
    • , Jiongwen Ou
    • , Jason Moffat
    • , Charles Boone
    • , Trisha N. Davis
    • , Corey Nislow
    •  & Grant W. Brown
  • Resource |

    Watt and colleagues carried out an RNAi screen to identify epigenetic modifiers involved in the control of epidermal differentiation. They delineate a network of genetic interactions using a Bayesian mixture model approach, and uncover two complexes of modifiers that differentially affect self-renewal and differentiation of epidermal stem cells.

    • Klaas W. Mulder
    • , Xin Wang
    • , Carles Escriu
    • , Yoko Ito
    • , Roland F. Schwarz
    • , Jesse Gillis
    • , Gábor Sirokmány
    • , Giacomo Donati
    • , Santiago Uribe-Lewis
    • , Paul Pavlidis
    • , Adele Murrell
    • , Florian Markowetz
    •  & Fiona M. Watt
  • Resource |

    Pepperkok, Simpson and colleagues performed genome-wide RNAi screens in human cells to uncover regulators of the secretory pathway. They also identify protein networks with previously unappreciated roles in secretory pathway regulation.

    • Jeremy C. Simpson
    • , Brigitte Joggerst
    • , Vibor Laketa
    • , Fatima Verissimo
    • , Cihan Cetin
    • , Holger Erfle
    • , Mariana G. Bexiga
    • , Vasanth R. Singan
    • , Jean-Karim Hériché
    • , Beate Neumann
    • , Alvaro Mateos
    • , Jonathon Blake
    • , Stephanie Bechtel
    • , Vladimir Benes
    • , Stefan Wiemann
    • , Jan Ellenberg
    •  & Rainer Pepperkok
  • Resource |

    Wedlich-Söldner and colleagues characterize the localization of plasma membrane proteins in Saccharomyces cerevisiae by total internal reflection microscopy and deconvolution. Their data reveal a self-organization of proteins into patterns and demonstrate that association of the arginine transporter Can1 with its membrane domain is important for its function.

    • Felix Spira
    • , Nikola S. Mueller
    • , Gisela Beck
    • , Philipp von Olshausen
    • , Joachim Beig
    •  & Roland Wedlich-Söldner
  • Resource |

    Elledge and colleagues performed siRNA (short interfering RNA) screens in human cells to identify regulators of homologous recombination (HR), a mechanism for the repair of double-strand breaks in DNA. Validation of screen data reveals the susceptibility of HR siRNA screens to off-target effects but defines the heterogeneous ribonucloprotein RBMX as a regulator of HR.

    • Britt Adamson
    • , Agata Smogorzewska
    • , Frederic D. Sigoillot
    • , Randall W. King
    •  & Stephen J. Elledge
  • Resource |

    Cowan and colleagues have developed a method to efficiently differentiate human pluripotent stem cells into functional white or brown adipocytes, through the transient expression of PPARG2 alone or in combination with CEBP and PRDM16. The programmed cells are able to give rise to ectopic fat pads with white or brown adipose tissue characteristics.

    • Tim Ahfeldt
    • , Robert T. Schinzel
    • , Youn-Kyoung Lee
    • , David Hendrickson
    • , Adam Kaplan
    • , David H. Lum
    • , Raymond Camahort
    • , Fang Xia
    • , Jennifer Shay
    • , Eugene P. Rhee
    • , Clary B. Clish
    • , Rahul C. Deo
    • , Tony Shen
    • , Frank H. Lau
    • , Alicia Cowley
    • , Greg Mowrer
    • , Heba Al-Siddiqi
    • , Matthias Nahrendorf
    • , Kiran Musunuru
    • , Robert E. Gerszten
    • , John L. Rinn
    •  & Chad A. Cowan
  • Resource |

    Improperly folded proteins are targeted for destruction through the endoplasmic-reticulum-associated degradation pathway (ERAD). Kopito and colleagues present a high-resolution interaction analysis of the ERAD system in combination with functional genomics, and identify new ERAD components.

    • John C. Christianson
    • , James A. Olzmann
    • , Thomas A. Shaler
    • , Mathew E. Sowa
    • , Eric J. Bennett
    • , Caleb M. Richter
    • , Ryan E. Tyler
    • , Ethan J. Greenblatt
    • , J. Wade Harper
    •  & Ron R. Kopito
  • Resource |

    Bershadsky and colleagues show that fibroblast polarization depends on matrix rigidity and focal adhesion mechanosensing. They target protein tyrosine kinases through RNAi to identify signalling molecules that regulate traction force generation, focal adhesion assembly and mechanosensitivity.

    • Masha Prager-Khoutorsky
    • , Alexandra Lichtenstein
    • , Ramaswamy Krishnan
    • , Kavitha Rajendran
    • , Avi Mayo
    • , Zvi Kam
    • , Benjamin Geiger
    •  & Alexander D. Bershadsky