Resources

  • Resource |

    The authors show that a coordinated epigenetic priming event during memory encoding and consolidation facilitates promoter–enhancer interactions that are vital for the unique transcriptional output of reactivated engram neurons.

    • Asaf Marco
    • , Hiruy S. Meharena
    • , Vishnu Dileep
    • , Ravikiran M. Raju
    • , Jose Davila-Velderrain
    • , Amy Letao Zhang
    • , Chinnakkaruppan Adaikkan
    • , Jennie Z. Young
    • , Fan Gao
    • , Manolis Kellis
    •  & Li-Huei Tsai
  • Resource |

    By analyzing hundreds of mice treated with a library of neuro- and psychoactive drugs, Wiltschko et al. show that Motion Sequencing can effectively discriminate and categorize drug effects and link molecular targets to behavioral syllables.

    • Alexander B. Wiltschko
    • , Tatsuya Tsukahara
    • , Ayman Zeine
    • , Rockwell Anyoha
    • , Winthrop F. Gillis
    • , Jeffrey E. Markowitz
    • , Ralph E. Peterson
    • , Jesse Katon
    • , Matthew J. Johnson
    •  & Sandeep Robert Datta
  • Resource |

    The ventral hippocampus is central in the processing of emotional information. Here, a combination of viral and sequencing approaches defines the organizational logic of the extended ventral CA1 circuit.

    • Mark M. Gergues
    • , Kasey J. Han
    • , Hye Sun Choi
    • , Brandon Brown
    • , Kelsey J. Clausing
    • , Victoria S. Turner
    • , Ilia D. Vainchtein
    • , Anna V. Molofsky
    •  & Mazen A. Kheirbek
  • Resource |

    Chen et al. define previously unreported zebrafish astrocytes, provide new insights into vertebrate astrocyte development and lay the foundation for studying astrocyte function in the entire nervous system of an intact and behaving animal.

    • Jiakun Chen
    • , Kira E. Poskanzer
    • , Marc R. Freeman
    •  & Kelly R. Monk
  • Resource |

    Single-nucleus transcriptomics reveal brain alterations associated with major depression. Deep layer excitatory cells and immature oligodendrocytes showed most changes, involving synaptic plasticity, immune function and steroid hormones.

    • Corina Nagy
    • , Malosree Maitra
    • , Arnaud Tanti
    • , Matthew Suderman
    • , Jean-Francois Théroux
    • , Maria Antonietta Davoli
    • , Kelly Perlman
    • , Volodymyr Yerko
    • , Yu Chang Wang
    • , Shreejoy J. Tripathy
    • , Paul Pavlidis
    • , Naguib Mechawar
    • , Jiannis Ragoussis
    •  & Gustavo Turecki
  • Resource |

    The authors identify two subsets of peripheral nerve macrophages residing in the endoneurium and the epineurium and displaying a distinct transcriptome and response to injury. These cells lack the main microglia identity and have a distinct origin.

    • Elke Ydens
    • , Lukas Amann
    • , Bob Asselbergh
    • , Charlotte L. Scott
    • , Liesbet Martens
    • , Dorine Sichien
    • , Omar Mossad
    • , Thomas Blank
    • , Sofie De Prijck
    • , Donovan Low
    • , Takahiro Masuda
    • , Yvan Saeys
    • , Vincent Timmerman
    • , Ralf Stumm
    • , Florent Ginhoux
    • , Marco Prinz
    • , Sophie Janssens
    •  & Martin Guilliams
  • Resource |

    Wen et al. combined single-cell RNA-seq and spatiotemporal analysis techniques to characterize the basic cell types in the mouse SCN, identifying their spatial distributions and circadian and light-induced gene expression patterns.

    • Shao’ang Wen
    • , Danyi Ma
    • , Meng Zhao
    • , Lucheng Xie
    • , Qingqin Wu
    • , Lingfeng Gou
    • , Chuanzhen Zhu
    • , Yuqi Fan
    • , Haifang Wang
    •  & Jun Yan
  • Resource |

    This resource comprises ultra-high-resolution MRI datasets and corresponding gray and white matter atlases of the marmoset brain to facilitate brain connectivity studies and the development of tractography algorithms in the primate brain.

    • Cirong Liu
    • , Frank Q. Ye
    • , John D. Newman
    • , Diego Szczupak
    • , Xiaoguang Tian
    • , Cecil Chern-Chyi Yen
    • , Piotr Majka
    • , Daniel Glen
    • , Marcello G. P. Rosa
    • , David A. Leopold
    •  & Afonso C. Silva
  • Resource |

    By comparing neural responses to diverse visual stimuli measured with a standardized two-photon imaging pipeline, the authors reveal response specializations within the mouse visual cortex.

    • Saskia E. J. de Vries
    • , Jerome A. Lecoq
    • , Michael A. Buice
    • , Peter A. Groblewski
    • , Gabriel K. Ocker
    • , Michael Oliver
    • , David Feng
    • , Nicholas Cain
    • , Peter Ledochowitsch
    • , Daniel Millman
    • , Kate Roll
    • , Marina Garrett
    • , Tom Keenan
    • , Leonard Kuan
    • , Stefan Mihalas
    • , Shawn Olsen
    • , Carol Thompson
    • , Wayne Wakeman
    • , Jack Waters
    • , Derric Williams
    • , Chris Barber
    • , Nathan Berbesque
    • , Brandon Blanchard
    • , Nicholas Bowles
    • , Shiella D. Caldejon
    • , Linzy Casal
    • , Andrew Cho
    • , Sissy Cross
    • , Chinh Dang
    • , Tim Dolbeare
    • , Melise Edwards
    • , John Galbraith
    • , Nathalie Gaudreault
    • , Terri L. Gilbert
    • , Fiona Griffin
    • , Perry Hargrave
    • , Robert Howard
    • , Lawrence Huang
    • , Sean Jewell
    • , Nika Keller
    • , Ulf Knoblich
    • , Josh D. Larkin
    • , Rachael Larsen
    • , Chris Lau
    • , Eric Lee
    • , Felix Lee
    • , Arielle Leon
    • , Lu Li
    • , Fuhui Long
    • , Jennifer Luviano
    • , Kyla Mace
    • , Thuyanh Nguyen
    • , Jed Perkins
    • , Miranda Robertson
    • , Sam Seid
    • , Eric Shea-Brown
    • , Jianghong Shi
    • , Nathan Sjoquist
    • , Cliff Slaughterbeck
    • , David Sullivan
    • , Ryan Valenza
    • , Casey White
    • , Ali Williford
    • , Daniela M. Witten
    • , Jun Zhuang
    • , Hongkui Zeng
    • , Colin Farrell
    • , Lydia Ng
    • , Amy Bernard
    • , John W. Phillips
    • , R. Clay Reid
    •  & Christof Koch
  • Resource |

    Grubman et al. generated a single-cell transcriptomic atlas of the entorhinal cortex from patients with Alzheimer’s disease and identified transcription factor networks predicted to control disease progression in a cell-subtype-specific way.

    • Alexandra Grubman
    • , Gabriel Chew
    • , John F. Ouyang
    • , Guizhi Sun
    • , Xin Yi Choo
    • , Catriona McLean
    • , Rebecca K. Simmons
    • , Sam Buckberry
    • , Dulce B. Vargas-Landin
    • , Daniel Poppe
    • , Jahnvi Pflueger
    • , Ryan Lister
    • , Owen J. L. Rackham
    • , Enrico Petretto
    •  & Jose M. Polo
  • Resource |

    Sankowski et al. have combined high-throughput techniques to characterize human microglia, identifying a spectrum of microglia phenotypes that are determined by localization, aging and glioblastoma.

    • Roman Sankowski
    • , Chotima Böttcher
    • , Takahiro Masuda
    • , Laufey Geirsdottir
    • , Sagar
    • , Elena Sindram
    • , Tamara Seredenina
    • , Andreas Muhs
    • , Christian Scheiwe
    • , Mukesch Johannes Shah
    • , Dieter Henrik Heiland
    • , Oliver Schnell
    • , Dominic Grün
    • , Josef Priller
    •  & Marco Prinz
  • Resource |

    Munji et al. analyzed the transcriptomes of endothelial cells from multiple organs and in neural tissue of neurological disease models. They identified a blood–brain barrier dysfunction module in seizure, multiple sclerosis, stroke and brain trauma.

    • Roeben Nocon Munji
    • , Allison Luen Soung
    • , Geoffrey Aaron Weiner
    • , Fabien Sohet
    • , Bridgette Deanne Semple
    • , Alpa Trivedi
    • , Kayleen Gimlin
    • , Masakazu Kotoda
    • , Masaaki Korai
    • , Sidar Aydin
    • , Austin Batugal
    • , Anne Christelle Cabangcala
    • , Patrick Georg Schupp
    • , Michael Clark Oldham
    • , Tomoki Hashimoto
    • , Linda J. Noble-Haeusslein
    •  & Richard Daneman
  • Resource |

    This manuscript describes the systematic investigation of epigenomic signatures discriminating between regenerative success and failure in dorsal root ganglia sensory neurons following axonal injury. This epigenomic map offers a tool to design novel approaches for neuronal repair.

    • Ilaria Palmisano
    • , Matt C. Danzi
    • , Thomas H. Hutson
    • , Luming Zhou
    • , Eilidh McLachlan
    • , Elisabeth Serger
    • , Kirill Shkura
    • , Prashant K. Srivastava
    • , Arnau Hervera
    • , Nick O’ Neill
    • , Tong Liu
    • , Hassen Dhrif
    • , Zheng Wang
    • , Miroslav Kubat
    • , Stefan Wuchty
    • , Matthias Merkenschlager
    • , Liron Levi
    • , Evan Elliott
    • , John L. Bixby
    • , Vance P. Lemmon
    •  & Simone Di Giovanni
  • Resource |

    Dube et al. generated an atlas of human brain circular RNA (circRNA) expression in individuals with and without Alzheimer disease (AD). They demonstrated circRNA expression correlates with AD severity, even before substantial clinical symptom onset.

    • Umber Dube
    • , Jorge L Del-Aguila
    • , Zeran Li
    • , John P Budde
    • , Shan Jiang
    • , Simon Hsu
    • , Laura Ibanez
    • , Maria Victoria Fernandez
    • , Fabiana Farias
    • , Joanne Norton
    • , Jen Gentsch
    • , Fengxian Wang
    • , Ricardo Allegri
    • , Fatima Amtashar
    • , Tammie Benzinger
    • , Sarah Berman
    • , Courtney Bodge
    • , Susan Brandon
    • , William Brooks
    • , Jill Buck
    • , Virginia Buckles
    • , Sochenda Chea
    • , Patricio Chrem
    • , Helena Chui
    • , Jake Cinco
    • , Jack Clifford
    • , Mirelle D’Mello
    • , Tamara Donahue
    • , Jane Douglas
    • , Noelia Edigo
    • , Nilufer Erekin-Taner
    • , Anne Fagan
    • , Marty Farlow
    • , Angela Farrar
    • , Howard Feldman
    • , Gigi Flynn
    • , Nick Fox
    • , Erin Franklin
    • , Hisako Fujii
    • , Cortaiga Gant
    • , Samantha Gardener
    • , Bernardino Ghetti
    • , Alison Goate
    • , Jill Goldman
    • , Brian Gordon
    • , Julia Gray
    • , Jenny Gurney
    • , Jason Hassenstab
    • , Mie Hirohara
    • , David Holtzman
    • , Russ Hornbeck
    • , Siri Houeland DiBari
    • , Takeshi Ikeuchi
    • , Snezana Ikonomovic
    • , Gina Jerome
    • , Mathias Jucker
    • , Kensaku Kasuga
    • , Takeshi Kawarabayashi
    • , William Klunk
    • , Robert Koeppe
    • , Elke Kuder-Buletta
    • , Christoph Laske
    • , Johannes Levin
    • , Daniel Marcus
    • , Ralph Martins
    • , Neal Scott Mason
    • , Denise Maue-Dreyfus
    • , Eric McDade
    • , Lucy Montoya
    • , Hiroshi Mori
    • , Akem Nagamatsu
    • , Katie Neimeyer
    • , James Noble
    • , Joanne Norton
    • , Richard Perrin
    • , Marc Raichle
    • , John Ringman
    • , Jee Hoon Roh
    • , Peter Schofield
    • , Hiroyuki Shimada
    • , Tomoyo Shiroto
    • , Mikio Shoji
    • , Wendy Sigurdson
    • , Hamid Sohrabi
    • , Paige Sparks
    • , Kazushi Suzuki
    • , Laura Swisher
    • , Kevin Taddei
    • , Jen Wang
    • , Peter Wang
    • , Mike Weiner
    • , Mary Wolfsberger
    • , Chengjie Xiong
    • , Xiong Xu
    • , Stephen Salloway
    • , Colin L Masters
    • , Jae-Hong Lee
    • , Neill R Graff-Radford
    • , Jasmeer P Chhatwal
    • , Randall J Bateman
    • , John C Morris
    • , Celeste M Karch
    • , Oscar Harari
    •  & Carlos Cruchaga
  • Resource |

    A single-cell transcriptomic atlas of the aging mouse brain reveals coordinated and cell-type-specific aging signatures across multiple cell populations. Catalogs of aging-related genes, pathways and ligand–receptor interactions are reported.

    • Methodios Ximerakis
    • , Scott L. Lipnick
    • , Brendan T. Innes
    • , Sean K. Simmons
    • , Xian Adiconis
    • , Danielle Dionne
    • , Brittany A. Mayweather
    • , Lan Nguyen
    • , Zachary Niziolek
    • , Ceren Ozek
    • , Vincent L. Butty
    • , Ruth Isserlin
    • , Sean M. Buchanan
    • , Stuart S. Levine
    • , Aviv Regev
    • , Gary D. Bader
    • , Joshua Z. Levin
    •  & Lee L. Rubin
  • Resource |

    This work describes comprehensive transcriptomic sequencing from murine thalamic pathways. By integrating this molecular information with anatomical and functional features, this study reveals a repeated architecture across thalamocortical systems.

    • James W. Phillips
    • , Anton Schulmann
    • , Erina Hara
    • , Johan Winnubst
    • , Chenghao Liu
    • , Vera Valakh
    • , Lihua Wang
    • , Brenda C. Shields
    • , Wyatt Korff
    • , Jayaram Chandrashekar
    • , Andrew L. Lemire
    • , Brett Mensh
    • , Joshua T. Dudman
    • , Sacha B. Nelson
    •  & Adam W. Hantman
  • Resource |

    Multi-omic analyses of transcriptional, chromatin occupancy and chromatin interaction dynamics in hippocampal excitatory neurons of adult mice upon activation by status epilepticus or novel context exploration reveals short- and long-lasting changes.

    • Jordi Fernandez-Albert
    • , Michal Lipinski
    • , María T. Lopez-Cascales
    • , M. Jordan Rowley
    • , Ana M. Martin-Gonzalez
    • , Beatriz del Blanco
    • , Victor G. Corces
    •  & Angel Barco
  • Resource |

    Sun et al. built a comprehensive atlas of inputs to major types of GABAergic interneurons in the prefrontal cortex of mice. Through three-dimensional reconstruction of neural morphology, the authors classified input neurons and identified novel neural circuits.

    • Qingtao Sun
    • , Xiangning Li
    • , Miao Ren
    • , Mengting Zhao
    • , Qiuyuan Zhong
    • , Yuqi Ren
    • , Pan Luo
    • , Hong Ni
    • , Xiaoyu Zhang
    • , Chen Zhang
    • , Jing Yuan
    • , Anan Li
    • , Minmin Luo
    • , Hui Gong
    •  & Qingming Luo
  • Resource |

    Targeting genes to specific cell types is valuable for basic science and gene therapy. The authors describe a collection of AAVs containing synthetic promoters targeting a broad range of neuronal cell types in mice, non-human primates and humans.

    • Josephine Jüttner
    • , Arnold Szabo
    • , Brigitte Gross-Scherf
    • , Rei K. Morikawa
    • , Santiago B. Rompani
    • , Peter Hantz
    • , Tamas Szikra
    • , Federico Esposti
    • , Cameron S. Cowan
    • , Arjun Bharioke
    • , Claudia P. Patino-Alvarez
    • , Özkan Keles
    • , Akos Kusnyerik
    • , Thierry Azoulay
    • , Dominik Hartl
    • , Arnaud R. Krebs
    • , Dirk Schübeler
    • , Rozina I. Hajdu
    • , Akos Lukats
    • , Janos Nemeth
    • , Zoltan Z. Nagy
    • , Kun-Chao Wu
    • , Rong-Han Wu
    • , Lue Xiang
    • , Xiao-Long Fang
    • , Zi-Bing Jin
    • , David Goldblum
    • , Pascal W. Hasler
    • , Hendrik P. N. Scholl
    • , Jacek Krol
    •  & Botond Roska
  • Resource |

    Using a large task battery spanning motor, cognitive, social and affective domains, this functional MRI (fMRI) study provides a comprehensive functional map of the human cerebellum, along with a comparison to maps derived from anatomy and resting-state fMRI data.

    • Maedbh King
    • , Carlos R. Hernandez-Castillo
    • , Russell A. Poldrack
    • , Richard B. Ivry
    •  & Jörn Diedrichsen
  • Resource |

    Gouwens et al. established a morpho-electrical taxonomy of cell types for the mouse visual cortex via unsupervised clustering analysis of multiple quantitative features from 1,938 neurons available online at the Allen Cell Types Database.

    • Nathan W. Gouwens
    • , Staci A. Sorensen
    • , Jim Berg
    • , Changkyu Lee
    • , Tim Jarsky
    • , Jonathan Ting
    • , Susan M. Sunkin
    • , David Feng
    • , Costas A. Anastassiou
    • , Eliza Barkan
    • , Kris Bickley
    • , Nicole Blesie
    • , Thomas Braun
    • , Krissy Brouner
    • , Agata Budzillo
    • , Shiella Caldejon
    • , Tamara Casper
    • , Dan Castelli
    • , Peter Chong
    • , Kirsten Crichton
    • , Christine Cuhaciyan
    • , Tanya L. Daigle
    • , Rachel Dalley
    • , Nick Dee
    • , Tsega Desta
    • , Song-Lin Ding
    • , Samuel Dingman
    • , Alyse Doperalski
    • , Nadezhda Dotson
    • , Tom Egdorf
    • , Michael Fisher
    • , Rebecca A. de Frates
    • , Emma Garren
    • , Marissa Garwood
    • , Amanda Gary
    • , Nathalie Gaudreault
    • , Keith Godfrey
    • , Melissa Gorham
    • , Hong Gu
    • , Caroline Habel
    • , Kristen Hadley
    • , James Harrington
    • , Julie A. Harris
    • , Alex Henry
    • , DiJon Hill
    • , Sam Josephsen
    • , Sara Kebede
    • , Lisa Kim
    • , Matthew Kroll
    • , Brian Lee
    • , Tracy Lemon
    • , Katherine E. Link
    • , Xiaoxiao Liu
    • , Brian Long
    • , Rusty Mann
    • , Medea McGraw
    • , Stefan Mihalas
    • , Alice Mukora
    • , Gabe J. Murphy
    • , Lindsay Ng
    • , Kiet Ngo
    • , Thuc Nghi Nguyen
    • , Philip R. Nicovich
    • , Aaron Oldre
    • , Daniel Park
    • , Sheana Parry
    • , Jed Perkins
    • , Lydia Potekhina
    • , David Reid
    • , Miranda Robertson
    • , David Sandman
    • , Martin Schroedter
    • , Cliff Slaughterbeck
    • , Gilberto Soler-Llavina
    • , Josef Sulc
    • , Aaron Szafer
    • , Bosiljka Tasic
    • , Naz Taskin
    • , Corinne Teeter
    • , Nivretta Thatra
    • , Herman Tung
    • , Wayne Wakeman
    • , Grace Williams
    • , Rob Young
    • , Zhi Zhou
    • , Colin Farrell
    • , Hanchuan Peng
    • , Michael J. Hawrylycz
    • , Ed Lein
    • , Lydia Ng
    • , Anton Arkhipov
    • , Amy Bernard
    • , John W. Phillips
    • , Hongkui Zeng
    •  & Christof Koch
  • Resource |

    Van Hove et al. reveal the diversity of macrophages at the brain’s border regions via single-cell analysis and fate-mapping. This also identified a microglial subset at the surface of the choroid plexus, in direct contact with cerebrospinal fluid.

    • Hannah Van Hove
    • , Liesbet Martens
    • , Isabelle Scheyltjens
    • , Karen De Vlaminck
    • , Ana Rita Pombo Antunes
    • , Sofie De Prijck
    • , Niels Vandamme
    • , Sebastiaan De Schepper
    • , Gert Van Isterdael
    • , Charlotte L. Scott
    • , Jeroen Aerts
    • , Geert Berx
    • , Guy E. Boeckxstaens
    • , Roosmarijn E. Vandenbroucke
    • , Lars Vereecke
    • , Diederik Moechars
    • , Martin Guilliams
    • , Jo A. Van Ginderachter
    • , Yvan Saeys
    •  & Kiavash Movahedi
  • Resource |

    The connectivity of a cortical region is instrumental to its function. The authors generated brain-wide maps of the afferent input to four distinct cell types in the mPFC to reveal the structural architecture that underlies the mPFC’s functions.

    • Sofie Ährlund-Richter
    • , Yang Xuan
    • , Josina Anna van Lunteren
    • , Hoseok Kim
    • , Cantin Ortiz
    • , Iskra Pollak Dorocic
    • , Konstantinos Meletis
    •  & Marie Carlén
  • Resource |

    The lateral hypothalamic area (LHA) regulates fundamental aspects of innate behavior. However, the circuit-level underpinnings of LHA function are poorly understood given its cellular heterogeneity. Here, Mickelsen et al. employ a single-cell RNA-sequencing approach to classify molecularly distinct cell types in the mouse LHA.

    • Laura E. Mickelsen
    • , Mohan Bolisetty
    • , Brock R. Chimileski
    • , Akie Fujita
    • , Eric J. Beltrami
    • , James T. Costanzo
    • , Jacob R. Naparstek
    • , Paul Robson
    •  & Alexander C. Jackson
  • Resource |

    An extensive profile of DNA methylation in neuronal and non-neuronal cells across four brain regions is reported, showing that differential epigenetic marks are enriched for DNA variants associated with neuropsychiatric traits.

    • Lindsay F. Rizzardi
    • , Peter F. Hickey
    • , Varenka Rodriguez DiBlasi
    • , Rakel Tryggvadóttir
    • , Colin M. Callahan
    • , Adrian Idrizi
    • , Kasper D. Hansen
    •  & Andrew P. Feinberg
  • Resource |

    Highly dynamic miRNA networks mediate developmental transitions during human brain development. Single-cell networks were detected by combining single-cell miRNA and mRNA profiling with HITS-CLIP analyzed with bipartite and co-expression networks.

    • Tomasz J. Nowakowski
    • , Neha Rani
    • , Mahdi Golkaram
    • , Hongjun R. Zhou
    • , Beatriz Alvarado
    • , Kylie Huch
    • , Jay A. West
    • , Anne Leyrat
    • , Alex A. Pollen
    • , Arnold R. Kriegstein
    • , Linda R. Petzold
    •  & Kenneth S. Kosik
  • Resource |

    Bienkowski et al. have created a new subregional atlas of the mouse hippocampus that integrates gene expression with anatomical connectivity to reveal the multiscale organization of the hippocampus and its connections throughout the brain.

    • Michael S. Bienkowski
    • , Ian Bowman
    • , Monica Y. Song
    • , Lin Gou
    • , Tyler Ard
    • , Kaelan Cotter
    • , Muye Zhu
    • , Nora L. Benavidez
    • , Seita Yamashita
    • , Jaspar Abu-Jaber
    • , Sana Azam
    • , Darrick Lo
    • , Nicholas N. Foster
    • , Houri Hintiryan
    •  & Hong-Wei Dong
  • Resource |

    The BRAINcode consortium found that tens of thousands of transcribed noncoding elements (TNEs) from the ‘dark matter’ of our genome are active in dopamine neurons. They may be linked to schizophrenia, Parkinson’s disease, and addiction.

    • Xianjun Dong
    • , Zhixiang Liao
    • , David Gritsch
    • , Yavor Hadzhiev
    • , Yunfei Bai
    • , Joseph J. Locascio
    • , Boris Guennewig
    • , Ganqiang Liu
    • , Cornelis Blauwendraat
    • , Tao Wang
    • , Charles H. Adler
    • , John C. Hedreen
    • , Richard L. M. Faull
    • , Matthew P. Frosch
    • , Peter T. Nelson
    • , Patrizia Rizzu
    • , Antony A. Cooper
    • , Peter Heutink
    • , Thomas G. Beach
    • , John S. Mattick
    • , Ferenc Müller
    •  & Clemens R. Scherzer
  • Resource |

    Poulin et al. developed intersectional genetic approaches to target dopamine neuron subtypes defined by combinatorial gene expression. They demonstrate that dopamine neuron subtypes display distinctive projection patterns to forebrain regions.

    • Jean-Francois Poulin
    • , Giuliana Caronia
    • , Caitlyn Hofer
    • , Qiaoling Cui
    • , Brandon Helm
    • , Charu Ramakrishnan
    • , C. Savio Chan
    • , Daniel A. Dombeck
    • , Karl Deisseroth
    •  & Rajeshwar Awatramani
  • Resource |

    The authors surveyed gene expression across cortical development and in individuals with schizophrenia. Three-fold more risk variants influenced expression than known. Risk genes showed developmental regulation, while diagnosis changes implicated largely treatment effects.

    • Andrew E. Jaffe
    • , Richard E. Straub
    • , Joo Heon Shin
    • , Ran Tao
    • , Yuan Gao
    • , Leonardo Collado-Torres
    • , Tony Kam-Thong
    • , Hualin S. Xi
    • , Jie Quan
    • , Qiang Chen
    • , Carlo Colantuoni
    • , William S. Ulrich
    • , Brady J. Maher
    • , Amy Deep-Soboslay
    • , Alan J. Cross
    • , Nicholas J. Brandon
    • , Jeffrey T. Leek
    • , Thomas M. Hyde
    • , Joel E. Kleinman
    •  & Daniel R. Weinberger
  • Resource |

    This PsychENCODE resource presents 157 reference maps for open-chromatin-associated histone methylation and acetylation in prefrontal and anterior cingulate cortex, linking the neuronal epigenome to the genetic risk architecture of schizophrenia.

    • Kiran Girdhar
    • , Gabriel E. Hoffman
    • , Yan Jiang
    • , Leanne Brown
    • , Marija Kundakovic
    • , Mads E. Hauberg
    • , Nancy J. Francoeur
    • , Ying-chih Wang
    • , Hardik Shah
    • , David H. Kavanagh
    • , Elizabeth Zharovsky
    • , Rivka Jacobov
    • , Jennifer R. Wiseman
    • , Royce Park
    • , Jessica S. Johnson
    • , Bibi S. Kassim
    • , Laura Sloofman
    • , Eugenio Mattei
    • , Zhiping Weng
    • , Solveig K. Sieberts
    • , Mette A. Peters
    • , Brent T. Harris
    • , Barbara K. Lipska
    • , Pamela Sklar
    • , Panos Roussos
    •  & Schahram Akbarian
  • Resource |

    A localized set of mRNA at the synapse facilitates synapse formation and plasticity. The authors show an enrichment of N6-methyladenosine (m6A) modifications of these mRNA at the synapse and link m6A recognition by molecular readers to synaptic function.

    • Daria Merkurjev
    • , Wan-Ting Hong
    • , Kei Iida
    • , Ikumi Oomoto
    • , Belinda J. Goldie
    • , Hitoshi Yamaguti
    • , Takayuki Ohara
    • , Shin-ya Kawaguchi
    • , Tomoo Hirano
    • , Kelsey C. Martin
    • , Matteo Pellegrini
    •  & Dan Ohtan Wang
  • Resource |

    Using single-cell RNA-seq, the authors produced a comprehensive atlas of the somatosensory spinal cord. They found that neuron types build the dorsal horn by a discrete layering and to be differentially engaged by noxious heat and cold.

    • Martin Häring
    • , Amit Zeisel
    • , Hannah Hochgerner
    • , Puneet Rinwa
    • , Jon E. T. Jakobsson
    • , Peter Lönnerberg
    • , Gioele La Manno
    • , Nilesh Sharma
    • , Lotta Borgius
    • , Ole Kiehn
    • , Malin C. Lagerström
    • , Sten Linnarsson
    •  & Patrik Ernfors
  • Resource |

    The authors developed a CUBIC tissue clearing and expansion method to generate an editable, point-based single-cell-resolution brain atlas. This atlas, termed CUBIC-Atlas, can be used for unbiased systems-level cellular analysis in whole mouse brain.

    • Tatsuya C. Murakami
    • , Tomoyuki Mano
    • , Shu Saikawa
    • , Shuhei A. Horiguchi
    • , Daichi Shigeta
    • , Kousuke Baba
    • , Hiroshi Sekiya
    • , Yoshihiro Shimizu
    • , Kenji F. Tanaka
    • , Hiroshi Kiyonari
    • , Masamitsu Iino
    • , Hideki Mochizuki
    • , Kazuki Tainaka
    •  & Hiroki R. Ueda
  • Resource |

    Using single-cell RNA-sequencing, the authors record snapshots of the dynamic sensory-experience-dependent transcriptome across all cell types of the visual cortex in mice exposed to a light stimulus. The authors note diverse cell-type-specific programs in pyramidal neuron subtypes and robust non-neuronal responses that may regulate experience-dependent neurovascular coupling and myelination.

    • Sinisa Hrvatin
    • , Daniel R. Hochbaum
    • , M. Aurel Nagy
    • , Marcelo Cicconet
    • , Keiramarie Robertson
    • , Lucas Cheadle
    • , Rapolas Zilionis
    • , Alex Ratner
    • , Rebeca Borges-Monroy
    • , Allon M. Klein
    • , Bernardo L. Sabatini
    •  & Michael E. Greenberg
  • Resource |

    The protein composition of excitatory synapses differs in the areas of the human neocortex controlling language, emotion and other behaviors. This neocortical postsynaptic proteome data resource can be used to link genetics to brain imaging and behavior.

    • Marcia Roy
    • , Oksana Sorokina
    • , Nathan Skene
    • , Clémence Simonnet
    • , Francesca Mazzo
    • , Ruud Zwart
    • , Emanuele Sher
    • , Colin Smith
    • , J. Douglas Armstrong
    •  & Seth G. N. Grant
  • Resource |

    Quantitative mass spectrometry was used to produce a proteomic survey of postnatal human brain regions. Compared to matched RNA-seq, protein levels showed more regional variation, especially for membrane-associated proteins in the neocortex.

    • Becky C. Carlyle
    • , Robert R. Kitchen
    • , Jean E. Kanyo
    • , Edward Z. Voss
    • , Mihovil Pletikos
    • , André M. M. Sousa
    • , TuKiet T. Lam
    • , Mark B. Gerstein
    • , Nenad Sestan
    •  & Angus C. Nairn
  • Resource |

    This paper reports the availability of a new Resource with RNA-seq, DNA methylation and H3K9Ac QTL results from 411 brain samples. Many xQTL SNPs influence multiple molecular features, and the authors observe epigenetic mediation of eQTLs in some cases. Reanalyzing GWAS with an xQTL-weighted approach detected 20 new CNS disease susceptibility loci.

    • Bernard Ng
    • , Charles C White
    • , Hans-Ulrich Klein
    • , Solveig K Sieberts
    • , Cristin McCabe
    • , Ellis Patrick
    • , Jishu Xu
    • , Lei Yu
    • , Chris Gaiteri
    • , David A Bennett
    • , Sara Mostafavi
    •  & Philip L De Jager
  • Resource |

    Korin et al. use CyTOF mass cytometry to characterize immune cell populations in the naive mouse brain (parenchyma, choroid plexus and meninges). This single-cell analysis of cell-surface proteins reveals the presence and phenotype of distinctive immune populations in the mouse brain compartment.

    • Ben Korin
    • , Tamar L Ben-Shaanan
    • , Maya Schiller
    • , Tania Dubovik
    • , Hilla Azulay-Debby
    • , Nadia T Boshnak
    • , Tamar Koren
    •  & Asya Rolls
  • Resource |

    Microglia are the macrophages of the CNS, with innate neuroimmune function, and play important roles in tissue homeostasis, CNS development and neurodegeneration. Here human microglial gene expression profiles were generated. Human and mouse microglia were highly similar, except for aging-regulated genes, indicating that microglial aging differs between humans and mice.

    • Thais F Galatro
    • , Inge R Holtman
    • , Antonio M Lerario
    • , Ilia D Vainchtein
    • , Nieske Brouwer
    • , Paula R Sola
    • , Mariana M Veras
    • , Tulio F Pereira
    • , Renata E P Leite
    • , Thomas Möller
    • , Paul D Wes
    • , Mari C Sogayar
    • , Jon D Laman
    • , Wilfred den Dunnen
    • , Carlos A Pasqualucci
    • , Sueli M Oba-Shinjo
    • , Erik W G M Boddeke
    • , Suely K N Marie
    •  & Bart J L Eggen
  • Resource |

    Using large-scale analysis of protein interactions and bioinformatics, Li et al. describe the organization of the core-scaffold machinery of the postsynaptic density and its assembly in protein-interaction networks. The authors show how mutations associated with complex brain disorders are distributed along spatiotemporal protein complexes and modulate their protein interactions.

    • Jing Li
    • , Wangshu Zhang
    • , Hui Yang
    • , Daniel P Howrigan
    • , Brent Wilkinson
    • , Tade Souaiaia
    • , Oleg V Evgrafov
    • , Giulio Genovese
    • , Veronica A Clementel
    • , Jennifer C Tudor
    • , Ted Abel
    • , James A Knowles
    • , Benjamin M Neale
    • , Kai Wang
    • , Fengzhu Sun
    •  & Marcelo P Coba
  • Resource |

    By sectioning and sequencing the prefrontal cortex of humans, chimpanzees and macaques, He et al. compiled comprehensive transcriptome atlases of cortical layers. The study provides scores of previously uncharacterized layer-marker genes and more than a hundred human-specific genes, implying that the human neocortex has evolved more than was previously appreciated.

    • Zhisong He
    • , Dingding Han
    • , Olga Efimova
    • , Patricia Guijarro
    • , Qianhui Yu
    • , Anna Oleksiak
    • , Shasha Jiang
    • , Konstantin Anokhin
    • , Boris Velichkovsky
    • , Stefan Grünewald
    •  & Philipp Khaitovich
  • Resource |

    Yuen et al. developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate ASD-risk genes and approximately 100 risk genes and copy-number loci, which account for 11% of the cases. They also found that individuals bearing mutations in ASD-risk genes had lower adaptive ability.

    • Ryan K C Yuen
    • , Daniele Merico
    • , Matt Bookman
    • , Jennifer L Howe
    • , Bhooma Thiruvahindrapuram
    • , Rohan V Patel
    • , Joe Whitney
    • , Nicole Deflaux
    • , Jonathan Bingham
    • , Zhuozhi Wang
    • , Giovanna Pellecchia
    • , Janet A Buchanan
    • , Susan Walker
    • , Christian R Marshall
    • , Mohammed Uddin
    • , Mehdi Zarrei
    • , Eric Deneault
    • , Lia D'Abate
    • , Ada J S Chan
    • , Stephanie Koyanagi
    • , Tara Paton
    • , Sergio L Pereira
    • , Ny Hoang
    • , Worrawat Engchuan
    • , Edward J Higginbotham
    • , Karen Ho
    • , Sylvia Lamoureux
    • , Weili Li
    • , Jeffrey R MacDonald
    • , Thomas Nalpathamkalam
    • , Wilson W L Sung
    • , Fiona J Tsoi
    • , John Wei
    • , Lizhen Xu
    • , Anne-Marie Tasse
    • , Emily Kirby
    • , William Van Etten
    • , Simon Twigger
    • , Wendy Roberts
    • , Irene Drmic
    • , Sanne Jilderda
    • , Bonnie MacKinnon Modi
    • , Barbara Kellam
    • , Michael Szego
    • , Cheryl Cytrynbaum
    • , Rosanna Weksberg
    • , Lonnie Zwaigenbaum
    • , Marc Woodbury-Smith
    • , Jessica Brian
    • , Lili Senman
    • , Alana Iaboni
    • , Krissy Doyle-Thomas
    • , Ann Thompson
    • , Christina Chrysler
    • , Jonathan Leef
    • , Tal Savion-Lemieux
    • , Isabel M Smith
    • , Xudong Liu
    • , Rob Nicolson
    • , Vicki Seifer
    • , Angie Fedele
    • , Edwin H Cook
    • , Stephen Dager
    • , Annette Estes
    • , Louise Gallagher
    • , Beth A Malow
    • , Jeremy R Parr
    • , Sarah J Spence
    • , Jacob Vorstman
    • , Brendan J Frey
    • , James T Robinson
    • , Lisa J Strug
    • , Bridget A Fernandez
    • , Mayada Elsabbagh
    • , Melissa T Carter
    • , Joachim Hallmayer
    • , Bartha M Knoppers
    • , Evdokia Anagnostou
    • , Peter Szatmari
    • , Robert H Ring
    • , David Glazer
    • , Mathew T Pletcher
    •  & Stephen W Scherer
  • Resource |

    The hypothalamic arcuate–median eminence (Arc-ME) complex is rich with functionally distinct cell types, a fraction of which have been characterized. The authors profile 20,921 individual cells by single-cell RNA-seq, identifying 50 Arc-ME cell types and their markers, determining each's response to energy status and implicating two neuron populations in the genetic control of obesity.

    • John N Campbell
    • , Evan Z Macosko
    • , Henning Fenselau
    • , Tune H Pers
    • , Anna Lyubetskaya
    • , Danielle Tenen
    • , Melissa Goldman
    • , Anne M J Verstegen
    • , Jon M Resch
    • , Steven A McCarroll
    • , Evan D Rosen
    • , Bradford B Lowell
    •  & Linus T Tsai
  • Resource |

    Su et al. investigated the chromatin accessibility status of neurons in the adult mouse dentate gyrus at different timepoints after activation at the genome-wide level. Their study provides a potential mechanism by which neuronal activity may reshape the epigenetic landscape, thereby dynamically changing transcriptome and neuronal properties over time.

    • Yijing Su
    • , Jaehoon Shin
    • , Chun Zhong
    • , Sabrina Wang
    • , Prith Roychowdhury
    • , Jongseuk Lim
    • , David Kim
    • , Guo-li Ming
    •  & Hongjun Song
  • Resource |

    Top-down control is important for sensory processing. In this study, the authors used virus-assisted circuit mapping to identify the brain networks for top-down modulation of multiple sensory modalities and the subnetworks within the visual network, thus providing an anatomical foundation for understanding the brain mechanisms underlying top-down control of behavior.

    • Siyu Zhang
    • , Min Xu
    • , Wei-Cheng Chang
    • , Chenyan Ma
    • , Johnny Phong Hoang Do
    • , Daniel Jeong
    • , Tiffany Lei
    • , Jiang Lan Fan
    •  & Yang Dan
  • Resource |

    The UK Biobank combines detailed phenotyping and genotyping with tracking of long-term health outcomes in a large cohort. This study describes the recently launched brain-imaging component that will ultimately scan 100,000 individuals. Results from the first 5,000 subjects are reported, including thousands of associations, population modes and hypothesis-driven results.

    • Karla L Miller
    • , Fidel Alfaro-Almagro
    • , Neal K Bangerter
    • , David L Thomas
    • , Essa Yacoub
    • , Junqian Xu
    • , Andreas J Bartsch
    • , Saad Jbabdi
    • , Stamatios N Sotiropoulos
    • , Jesper L R Andersson
    • , Ludovica Griffanti
    • , Gwenaëlle Douaud
    • , Thomas W Okell
    • , Peter Weale
    • , Iulius Dragonu
    • , Steve Garratt
    • , Sarah Hudson
    • , Rory Collins
    • , Mark Jenkinson
    • , Paul M Matthews
    •  & Stephen M Smith