Transcriptomics

  • Article
    | Open Access

    Understanding tumour development at a granular level is a challenge in solid tumours. Here, the authors provide a cell atlas across tumour development in a genetic model of salivary gland squamous cell carcinoma using single-cell transcriptome and epitope profiling.

    • Samantha D. Praktiknjo
    • , Benedikt Obermayer
    • , Qionghua Zhu
    • , Liang Fang
    • , Haiyue Liu
    • , Hazel Quinn
    • , Marlon Stoeckius
    • , Christine Kocks
    • , Walter Birchmeier
    •  & Nikolaus Rajewsky
  • Article
    | Open Access

    Whether the immune system aging differs between men and women is barely known. Here the authors characterize gene expression, chromatin state and immune subset composition in the blood of healthy humans 22 to 93 years of age, uncovering shared as well as sex-unique alterations, and create a web resource to interactively explore the data.

    • Eladio J. Márquez
    • , Cheng-han Chung
    • , Radu Marches
    • , Robert J. Rossi
    • , Djamel Nehar-Belaid
    • , Alper Eroglu
    • , David J. Mellert
    • , George A. Kuchel
    • , Jacques Banchereau
    •  & Duygu Ucar
  • Article
    | Open Access

    Despite widespread transcription of LncRNA in mammalian systems, their contribution to metabolic homeostasis at the cellular and tissue level remains elusive. Here Pradas-Juni et al. describe a transcription factor–LncRNA pathway that couples hepatocyte nutrient sensing to regulation of glucose metabolism in mice.

    • Marta Pradas-Juni
    • , Nils R. Hansmeier
    • , Jenny C. Link
    • , Elena Schmidt
    • , Bjørk Ditlev Larsen
    • , Paul Klemm
    • , Nicola Meola
    • , Hande Topel
    • , Rute Loureiro
    • , Ines Dhaouadi
    • , Christoph A. Kiefer
    • , Robin Schwarzer
    • , Sajjad Khani
    • , Matteo Oliverio
    • , Motoharu Awazawa
    • , Peter Frommolt
    • , Joerg Heeren
    • , Ludger Scheja
    • , Markus Heine
    • , Christoph Dieterich
    • , Hildegard Büning
    • , Ling Yang
    • , Haiming Cao
    • , Dario F. De Jesus
    • , Rohit N. Kulkarni
    • , Branko Zevnik
    • , Simon E. Tröder
    • , Uwe Knippschild
    • , Peter A. Edwards
    • , Richard G. Lee
    • , Masayuki Yamamoto
    • , Igor Ulitsky
    • , Eduardo Fernandez-Rebollo
    • , Thomas Q. de Aguiar Vallim
    •  & Jan-Wilhelm Kornfeld
  • Article
    | Open Access

    The endothelial to haematopoietic transition (EHT) is the process where haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). Here the authors use single cell transcriptomics and antibody screening to identify CD44 as a marker of EHT that is required for EHT and HSPC development.

    • Morgan Oatley
    • , Özge Vargel Bölükbası
    • , Valentine Svensson
    • , Maya Shvartsman
    • , Kerstin Ganter
    • , Katharina Zirngibl
    • , Polina V. Pavlovich
    • , Vladislava Milchevskaya
    • , Vladimira Foteva
    • , Kedar N. Natarajan
    • , Bianka Baying
    • , Vladimir Benes
    • , Kiran R. Patil
    • , Sarah A. Teichmann
    •  & Christophe Lancrin
  • Article
    | Open Access

    The kidney is vascularized with highly specialized and zonated endothelial cells that are essential for its filtration function. Here, Barry et al. provide a single-cell RNA sequencing analysis of the kidney vasculature that highlights its transcriptional heterogeneity and uncovers pathways important for its development and function.

    • David M. Barry
    • , Elizabeth A. McMillan
    • , Balvir Kunar
    • , Raphael Lis
    • , Tuo Zhang
    • , Tyler Lu
    • , Edward Daniel
    • , Masataka Yokoyama
    • , Jesus M. Gomez-Salinero
    • , Angara Sureshbabu
    • , Ondine Cleaver
    • , Annarita Di Lorenzo
    • , Mary E. Choi
    • , Jenny Xiang
    • , David Redmond
    • , Sina Y. Rabbany
    • , Thangamani Muthukumar
    •  & Shahin Rafii
  • Article
    | Open Access

    Thymic epithelial cells (TEC) are essential for the maturation of functional T cells, while thymus size is proportional to the overall output efficiency. Here the authors show, using transcriptome analyses, that mouse fetal TEC maintain a Myc-dependent genetic program to ensure a rapid increase in thymus size, and thereby expedited T cell generation.

    • Jennifer E. Cowan
    • , Justin Malin
    • , Yongge Zhao
    • , Mina O. Seedhom
    • , Christelle Harly
    • , Izumi Ohigashi
    • , Michael Kelly
    • , Yousuke Takahama
    • , Jonathan W. Yewdell
    • , Maggie Cam
    •  & Avinash Bhandoola
  • Article
    | Open Access

    The neural tissues of coleoids have a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of A-to-I RNA editing, a pattern thought to indicate widespread adaptive editing. Here the authors propose and provide evidence for an alternative, nonadaptive explanation.

    • Daohan Jiang
    •  & Jianzhi Zhang
  • Article
    | Open Access

    The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.

    • Deborah J. Weinstein
    • , Sarah E. Allen
    • , Maggie C. Y. Lau
    • , Mariana Erasmus
    • , Kathryn C. Asalone
    • , Kathryn Walters-Conte
    • , Gintaras Deikus
    • , Robert Sebra
    • , Gaetan Borgonie
    • , Esta van Heerden
    • , Tullis C. Onstott
    •  & John R. Bracht
  • Article
    | Open Access

    Parkinson’s disease (PD) is characterized by neurodegeneration associated with loss of dopaminergic (DA) neurons and deposition of Lewy bodies. Here, Wang et al. use co-expression network analysis to pinpoint disease pathways and propose reduced expression of STMN2 as a cause of presynaptic function loss in PD.

    • Qian Wang
    • , Yuanxi Zhang
    • , Minghui Wang
    • , Won-Min Song
    • , Qi Shen
    • , Andrew McKenzie
    • , Insup Choi
    • , Xianxiao Zhou
    • , Ping-Yue Pan
    • , Zhenyu Yue
    •  & Bin Zhang
  • Article
    | Open Access

    It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.

    • Xi Wang
    • , Xintian You
    • , Julian D. Langer
    • , Jingyi Hou
    • , Fiona Rupprecht
    • , Irena Vlatkovic
    • , Claudia Quedenau
    • , Georgi Tushev
    • , Irina Epstein
    • , Bernhard Schaefke
    • , Wei Sun
    • , Liang Fang
    • , Guipeng Li
    • , Yuhui Hu
    • , Erin M. Schuman
    •  & Wei Chen
  • Article
    | Open Access

    Here, the authors report transcriptomes and proteomes of oocyst sporozoite and salivary gland sporozoite stages in rodent-infectious Plasmodium yoelii parasites and human infectious Plasmodium falciparum parasites and define two waves of translational repression during sporozoite maturation.

    • Scott E. Lindner
    • , Kristian E. Swearingen
    • , Melanie J. Shears
    • , Michael P. Walker
    • , Erin N. Vrana
    • , Kevin J. Hart
    • , Allen M. Minns
    • , Photini Sinnis
    • , Robert L. Moritz
    •  & Stefan H. I. Kappe
  • Article
    | Open Access

    Herpes simplex virus 1 (HSV-1) induces major reprogramming of the host cell environment. Here, the authors profile the transcriptomes of individual HSV-1-infected human fibroblasts and provide evidence of an antiviral program mediated by the activation of the host transcription factor NRF2.

    • Emanuel Wyler
    • , Vedran Franke
    • , Jennifer Menegatti
    • , Christine Kocks
    • , Anastasiya Boltengagen
    • , Samantha Praktiknjo
    • , Barbara Walch-Rückheim
    • , Jens Bosse
    • , Nikolaus Rajewsky
    • , Friedrich Grässer
    • , Altuna Akalin
    •  & Markus Landthaler
  • Article
    | Open Access

    In-depth functional characterization of genomes relies on comprehensive transcriptome data. Here, the authors employ four complementary RNA sequencing technologies to explore the transcription landscape across 16 tissues or different organ types in diploid A genome cotton using a newly developed computational pipeline.

    • Kun Wang
    • , Dehe Wang
    • , Xiaomin Zheng
    • , Ai Qin
    • , Jie Zhou
    • , Boyu Guo
    • , Yanjun Chen
    • , Xingpeng Wen
    • , Wen Ye
    • , Yu Zhou
    •  & Yuxian Zhu
  • Article
    | Open Access

    An understanding of the ancestral state of the neural crest (NC) gene regulatory network (GRN) gives insight into vertebrate evolution. Here, the authors use transcriptomic and chromatin accessibility analyses of the lamprey NC, as well as cross-species enhancer assays, to identify GRN elements conserved throughout vertebrates.

    • Dorit Hockman
    • , Vanessa Chong-Morrison
    • , Stephen A. Green
    • , Daria Gavriouchkina
    • , Ivan Candido-Ferreira
    • , Irving T. C. Ling
    • , Ruth M. Williams
    • , Chris T. Amemiya
    • , Jeramiah J. Smith
    • , Marianne E. Bronner
    •  & Tatjana Sauka-Spengler
  • Article
    | Open Access

    There has been a rapid rise in single cell RNA-seq methods and associated pipelines. Here the authors use simulated data to systematically evaluate the performance of 3000 possible pipelines to derive recommendations for data processing and analysis of different types of scRNA-seq experiments.

    • Beate Vieth
    • , Swati Parekh
    • , Christoph Ziegenhain
    • , Wolfgang Enard
    •  & Ines Hellmann
  • Article
    | Open Access

    Evolution of optimal gene expression in females is expected to be constrained by sexually-antagonistic selection on males. Here, Parker and colleagues show that gene expression has in fact become masculinized in female stick insects across five independent transitions to asexual reproduction.

    • Darren J. Parker
    • , Jens Bast
    • , Kirsten Jalvingh
    • , Zoé Dumas
    • , Marc Robinson-Rechavi
    •  & Tanja Schwander
  • Article
    | Open Access

    Interactions between metabolites and transcription factors are known to control gene expression but analyzing these events at genome-scale is challenging. Here, the authors integrate dynamic metabolome and transcriptome data from E.coli to predict regulatory metabolite-transcription factor interactions.

    • Martin Lempp
    • , Niklas Farke
    • , Michelle Kuntz
    • , Sven Andreas Freibert
    • , Roland Lill
    •  & Hannes Link
  • Article
    | Open Access

    Myoepithelial cells prevent tumour growth and invasion in DCIS. Here, the authors show that p63 and TCF7 cooperate to regulate a transcription factor network for the maintenance of normal myoepithelial function and altered expression of these genes perturb myoepithelial function in DCIS to promote invasive progression.

    • Lina Ding
    • , Ying Su
    • , Anne Fassl
    • , Kunihiko Hinohara
    • , Xintao Qiu
    • , Nicholas W. Harper
    • , Sung Jin Huh
    • , Noga Bloushtain-Qimron
    • , Bojana Jovanović
    • , Muhammad Ekram
    • , Xiaoyuan Zi
    • , William C. Hines
    • , Maša Alečković
    • , Carlos Gil del Alcazar
    • , Ryan J. Caulfield
    • , Dennis M. Bonal
    • , Quang-De Nguyen
    • , Vanessa F. Merino
    • , Sibgat Choudhury
    • , Gabrielle Ethington
    • , Laura Panos
    • , Michael Grant
    • , William Herlihy
    • , Alfred Au
    • , Gedge D. Rosson
    • , Pedram Argani
    • , Andrea L. Richardson
    • , Deborah Dillon
    • , D. Craig Allred
    • , Kirsten Babski
    • , Elizabeth Min Hui Kim
    • , Charles H. McDonnell III
    • , Jon Wagner
    • , Ron Rowberry
    • , Kristie Bobolis
    • , Celina G. Kleer
    • , E. Shelley Hwang
    • , Joanne L. Blum
    • , Simona Cristea
    • , Piotr Sicinski
    • , Rong Fan
    • , Henry W. Long
    • , Saraswati Sukumar
    • , So Yeon Park
    • , Judy E. Garber
    • , Mina Bissell
    • , Jun Yao
    •  & Kornelia Polyak
  • Article
    | Open Access

    UPF1 mediates the decay of target mRNA in a 3′ untranslated region (UTR)-length-dependent manner. Here the authors reveal that the 3′UTR-length-dependent regulation of UPF1-dependent mRNA decay occurs through EJC-independent but miRNA-dependent regulation.

    • Jungyun Park
    • , Jwa-Won Seo
    • , Narae Ahn
    • , Seokju Park
    • , Jungwook Hwang
    •  & Jin-Wu Nam
  • Article
    | Open Access

    Using a combination of single-cell RNA sequencing and TCR clonotype analysis on longitudinal samples from dengue vaccinated individuals, Waickman et al. here define a transcriptional signature in acutely-activated T cells that is associated with durable CD8+ T cell memory.

    • Adam T. Waickman
    • , Kaitlin Victor
    • , Tao Li
    • , Kristin Hatch
    • , Wiriya Rutvisuttinunt
    • , Carey Medin
    • , Benjamin Gabriel
    • , Richard G. Jarman
    • , Heather Friberg
    •  & Jeffrey R. Currier
  • Article
    | Open Access

    The Oxford Nanopore system is capable of direct RNA sequencing but complex transcriptome analysis still remains to be thoroughly investigated. Here the authors perform sequencing of native RNA as well as cDNA to characterise the strengths and weaknesses of the system.

    • Charlotte Soneson
    • , Yao Yao
    • , Anna Bratus-Neuenschwander
    • , Andrea Patrignani
    • , Mark D. Robinson
    •  & Shobbir Hussain
  • Article
    | Open Access

    Interactions between protein and RNA occur on a large scale, and are often studied from a proteincentric point of view. Here the authors show that the number and strength of RNA-protein interactions correlate with the amount of RNA structure, which impacts the biological activity of the transcript.

    • Natalia Sanchez de Groot
    • , Alexandros Armaos
    • , Ricardo Graña-Montes
    • , Marion Alriquet
    • , Giulia Calloni
    • , R. Martin Vabulas
    •  & Gian Gaetano Tartaglia
  • Article
    | Open Access

    Bulk RNA-seq data harbors valuable information about gene expression levels from different cell types in tissue samples. Here, the authors develop DWLS, a computational method for estimating cell-type composition of bulk data by leveraging single-cell RNA-seq-derived cell-type signatures.

    • Daphne Tsoucas
    • , Rui Dong
    • , Haide Chen
    • , Qian Zhu
    • , Guoji Guo
    •  & Guo-Cheng Yuan
  • Article
    | Open Access

    A rapid cellular response to interferons (IFNs) is critical for establishing antimicrobial immunity, but how cells switch from from homeostasis to IFN signaling is not fully understood. Here, the authors provide evidence that IFNs induce gene expression by alternating subunits of transcription factor ISGF3.

    • Ekaterini Platanitis
    • , Duygu Demiroz
    • , Anja Schneller
    • , Katrin Fischer
    • , Christophe Capelle
    • , Markus Hartl
    • , Thomas Gossenreiter
    • , Mathias Müller
    • , Maria Novatchkova
    •  & Thomas Decker
  • Article
    | Open Access

    Acinetobacter baumannii is generally considered an opportunistic pathogen. Here, Di Venanzio et al. develop a mouse model of catheter-associated urinary tract infection and show that a plasmid confers niche specificity to an A. baumannii urinary isolate by regulating the expression of chromosomal genes.

    • Gisela Di Venanzio
    • , Ana L. Flores-Mireles
    • , Juan J. Calix
    • , M. Florencia Haurat
    • , Nichollas E. Scott
    • , Lauren D. Palmer
    • , Robert F. Potter
    • , Michael E. Hibbing
    • , Laura Friedman
    • , Bin Wang
    • , Gautam Dantas
    • , Eric P. Skaar
    • , Scott J. Hultgren
    •  & Mario F. Feldman
  • Article
    | Open Access

    Our understanding of the functional link between differential DNA methylation and type 2 diabetes and obesity remains limited. Here the authors present a blood-based EWAS of fasting glucose and insulin among 4808 non-diabetic Europeans and identify nine CpGs not previously implicated in glucose, insulin homeostasis and diabetes.

    • Jun Liu
    • , Elena Carnero-Montoro
    • , Jenny van Dongen
    • , Samantha Lent
    • , Ivana Nedeljkovic
    • , Symen Ligthart
    • , Pei-Chien Tsai
    • , Tiphaine C. Martin
    • , Pooja R. Mandaviya
    • , Rick Jansen
    • , Marjolein J. Peters
    • , Liesbeth Duijts
    • , Vincent W. V. Jaddoe
    • , Henning Tiemeier
    • , Janine F. Felix
    • , Gonneke Willemsen
    • , Eco J. C. de Geus
    • , Audrey Y. Chu
    • , Daniel Levy
    • , Shih-Jen Hwang
    • , Jan Bressler
    • , Rahul Gondalia
    • , Elias L. Salfati
    • , Christian Herder
    • , Bertha A. Hidalgo
    • , Toshiko Tanaka
    • , Ann Zenobia Moore
    • , Rozenn N. Lemaitre
    • , Min A Jhun
    • , Jennifer A. Smith
    • , Nona Sotoodehnia
    • , Stefania Bandinelli
    • , Luigi Ferrucci
    • , Donna K. Arnett
    • , Harald Grallert
    • , Themistocles L. Assimes
    • , Lifang Hou
    • , Andrea Baccarelli
    • , Eric A. Whitsel
    • , Ko Willems van Dijk
    • , Najaf Amin
    • , André G. Uitterlinden
    • , Eric J. G. Sijbrands
    • , Oscar H. Franco
    • , Abbas Dehghan
    • , Tim D. Spector
    • , Josée Dupuis
    • , Marie-France Hivert
    • , Jerome I. Rotter
    • , James B. Meigs
    • , James S. Pankow
    • , Joyce B. J. van Meurs
    • , Aaron Isaacs
    • , Dorret I. Boomsma
    • , Jordana T. Bell
    • , Ayşe Demirkan
    •  & Cornelia M. van Duijn
  • Article
    | Open Access

    Protein degradation in clinical samples is largely unexplored. Here, the authors analyze the transcriptome and proteome of clinical tissue samples and develop an algorithm to assess protein degradation, showing that protein degradation is negligible in most tissue samples and does not correlate with transcript degradation.

    • Wenguang Shao
    • , Tiannan Guo
    • , Nora C. Toussaint
    • , Peng Xue
    • , Ulrich Wagner
    • , Li Li
    • , Konstantina Charmpi
    • , Yi Zhu
    • , Jianmin Wu
    • , Marija Buljan
    • , Rui Sun
    • , Dorothea Rutishauser
    • , Thomas Hermanns
    • , Christian Daniel Fankhauser
    • , Cedric Poyet
    • , Jelena Ljubicic
    • , Niels Rupp
    • , Jan H. Rüschoff
    • , Qing Zhong
    • , Andreas Beyer
    • , Jiafu Ji
    • , Ben C. Collins
    • , Yansheng Liu
    • , Gunnar Rätsch
    • , Peter J. Wild
    •  & Ruedi Aebersold
  • Article
    | Open Access

    It is unclear if early pathological changes in normal-appearing multiple sclerosis (MS) tissue are reflected by molecular changes in microglia, which might contribute to lesion initiation. Here, authors demonstrate significant intrinsic differences in the human microglial transcriptome between grey and white matter regions, isolated from MS and non-neurological control donors, and show early microglial changes related to MS pathology.

    • Marlijn van der Poel
    • , Thomas Ulas
    • , Mark R. Mizee
    • , Cheng-Chih Hsiao
    • , Suzanne S. M. Miedema
    • , Adelia
    • , Karianne G. Schuurman
    • , Boy Helder
    • , Sander W. Tas
    • , Joachim L. Schultze
    • , Jörg Hamann
    •  & Inge Huitinga
  • Article
    | Open Access

    Aging impacts lung functionality and makes it more susceptible to chronic diseases. Combining proteomics and single cell transcriptomics, the authors chart molecular and cellular changes in the aging mouse lung, discover aging hallmarks, and predict the cellular sources of regulated proteins.

    • Ilias Angelidis
    • , Lukas M. Simon
    • , Isis E. Fernandez
    • , Maximilian Strunz
    • , Christoph H. Mayr
    • , Flavia R. Greiffo
    • , George Tsitsiridis
    • , Meshal Ansari
    • , Elisabeth Graf
    • , Tim-Matthias Strom
    • , Monica Nagendran
    • , Tushar Desai
    • , Oliver Eickelberg
    • , Matthias Mann
    • , Fabian J. Theis
    •  & Herbert B. Schiller
  • Article
    | Open Access

    Here, Depledge et al. use nanopore arrays for direct RNA sequencing to profile the HSV-1 transcriptome in productively infected cells. Sequencing of individual RNAs reveals a highly complex viral transcriptome including mRNAs encoding new viral fusion proteins derived by read-through transcription.

    • Daniel P. Depledge
    • , Kalanghad Puthankalam Srinivas
    • , Tomohiko Sadaoka
    • , Devin Bready
    • , Yasuko Mori
    • , Dimitris G. Placantonakis
    • , Ian Mohr
    •  & Angus C. Wilson
  • Article
    | Open Access

    ER stress and UPR are implicated in various cancers. Here, the authors show that one of the canonical UPR pathways, IRE1α-XBP1 regulates c-MYC signaling to promote prostate tumorigenesis, and pharmacological inhibition of IRE1α with MKC8866 inhibits prostate cancer growth and synergizes with clinically used prostate cancer drugs.

    • Xia Sheng
    • , Hatice Zeynep Nenseth
    • , Su Qu
    • , Omer F. Kuzu
    • , Turid Frahnow
    • , Lukas Simon
    • , Stephanie Greene
    • , Qingping Zeng
    • , Ladan Fazli
    • , Paul S. Rennie
    • , Ian G. Mills
    • , Håvard Danielsen
    • , Fabian Theis
    • , John B. Patterson
    • , Yang Jin
    •  & Fahri Saatcioglu
  • Article
    | Open Access

    Plasmodium vivax biology is not well understood, due to a lack of in vitro culture systems and difficulties associated with studying clinical blood samples. Here, Kim et al. use gene expression profiles from P. vivax infected patient blood and show stage-specific chloroquine response and differential regulation of male and female gametocytes.

    • Adam Kim
    • , Jean Popovici
    • , Didier Menard
    •  & David Serre
  • Article
    | Open Access

    Bulk tissue RNA-seq data reveals transcriptomic profiles but masks the contributions of different cell types. Here, the authors develop a new method for estimating cell type proportions from bulk tissue RNA-seq data guided by multi-subject single-cell expression reference.

    • Xuran Wang
    • , Jihwan Park
    • , Katalin Susztak
    • , Nancy R. Zhang
    •  & Mingyao Li
  • Article
    | Open Access

    Early human embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here the authors present LiCAT-seq, a method enabling simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells and map chromatin accessibility and transcriptome landscapes for human pre-implantation embryos.

    • Longqi Liu
    • , Lizhi Leng
    • , Chuanyu Liu
    • , Changfu Lu
    • , Yue Yuan
    • , Liang Wu
    • , Fei Gong
    • , Shuoping Zhang
    • , Xiaoyu Wei
    • , Mingyue Wang
    • , Lei Zhao
    • , Liang Hu
    • , Jian Wang
    • , Huanming Yang
    • , Shida Zhu
    • , Fang Chen
    • , Guangxiu Lu
    • , Zhouchun Shang
    •  & Ge Lin
  • Article
    | Open Access

    The authors perform single-cell RNA-seq of the mouse neocortex at an embryonic time point and at birth, and identify new and known cell types, and cell relatedness within and across age. These data serve as a resource to understand brain development and the cellular origins of brain diseases.

    • Lipin Loo
    • , Jeremy M. Simon
    • , Lei Xing
    • , Eric S. McCoy
    • , Jesse K. Niehaus
    • , Jiami Guo
    • , E. S. Anton
    •  & Mark J. Zylka
  • Article
    | Open Access

    Single-cell RNA sequencing allows characterizing cell-to-cell heterogeneity at transcriptome scale. Here, the authors present an approach that enables microRNA and mRNA sequencing in the same single cell, providing insights into the origins of non-genetic cellular variability and mechanisms of miRNA regulation.

    • Nayi Wang
    • , Ji Zheng
    • , Zhuo Chen
    • , Yang Liu
    • , Burak Dura
    • , Minsuk Kwak
    • , Juliana Xavier-Ferrucio
    • , Yi-Chien Lu
    • , Miaomiao Zhang
    • , Christine Roden
    • , Jijun Cheng
    • , Diane S. Krause
    • , Ye Ding
    • , Rong Fan
    •  & Jun Lu
  • Article
    | Open Access

    The respiratory system is transformed in terms of functional change at birth to adapt to breathing air. Here, the authors examine the molecular changes behind the first breath in the mouse by Drop-seq based RNA sequencing, identifying activation of the unfolded protein response as a perinatal adaptation of the lung.

    • Minzhe Guo
    • , Yina Du
    • , Jason J. Gokey
    • , Samriddha Ray
    • , Sheila M. Bell
    • , Mike Adam
    • , Parvathi Sudha
    • , Anne Karina Perl
    • , Hitesh Deshmukh
    • , S. Steven Potter
    • , Jeffrey A. Whitsett
    •  & Yan Xu
  • Article
    | Open Access

    Copy number variants in the human genome (CNVs) are associated with neurodevelopmental and psychiatric disorders such as schizophrenia and autism. Here the authors investigate how  the large deletion CNV on chromosome 22q11.2 alters chromatin organization.

    • Xianglong Zhang
    • , Ying Zhang
    • , Xiaowei Zhu
    • , Carolin Purmann
    • , Michael S. Haney
    • , Thomas Ward
    • , Arineh Khechaduri
    • , Jie Yao
    • , Sherman M. Weissman
    •  & Alexander E. Urban
  • Article
    | Open Access

    Increasing insecticide resistance of mosquitoes represents a public health threat, and underlying mechanisms are poorly understood. Here, Ingham et al. identify putative insecticide resistance genes in Anopheles gambiae populations across Africa and develop a web-based application that maps their expression.

    • V. A. Ingham
    • , S. Wagstaff
    •  & H. Ranson
  • Article
    | Open Access

    miRNAs have emerged as regulators of diverse biological processes including cancer. Here the authors present an extended pan-cancer analysis of the miRNAs in 15 epithelial cancers; integrating methylation, transcriptomic and mutation data they reveal alternative mechanisms of tumour suppressors’ regulation in absence of mutation, methylation or copy number alterations.

    • Andrew Dhawan
    • , Jacob G. Scott
    • , Adrian L. Harris
    •  & Francesca M. Buffa
  • Article
    | Open Access

    Proteome and transcriptome often show poor correlation, hindering the system-wide analysis of post-transcriptional regulation. Here, the authors study proteome and transcriptome dynamics during Drosophila embryogenesis and present basic mathematical models describing the temporal regulation of most protein-RNA pairs.

    • Kolja Becker
    • , Alina Bluhm
    • , Nuria Casas-Vila
    • , Nadja Dinges
    • , Mario Dejung
    • , Sergi Sayols
    • , Clemens Kreutz
    • , Jean-Yves Roignant
    • , Falk Butter
    •  & Stefan Legewie
  • Article
    | Open Access

    The mammalian stomach is a complex organ with diverse roles in health and disease. Here, the authors integrate proteomics and transcriptomics to analyze the mouse stomach at 15 time points during development, providing molecular level insights into system-wide developmental changes.

    • Xianju Li
    • , Chunchao Zhang
    • , Tongqing Gong
    • , Xiaotian Ni
    • , Jin’e Li
    • , Dongdong Zhan
    • , Mingwei Liu
    • , Lei Song
    • , Chen Ding
    • , Jianming Xu
    • , Bei Zhen
    • , Yi Wang
    •  & Jun Qin
  • Article
    | Open Access

    The Androgen Receptor (AR) is the main driver of prostate cancer and functions in conjunction with chromatin modifications. Here, the authors comprehensively profile 100 primary prostate carcinomas by sequencing RNA transcripts in combination with ChIP-sequencing for AR and the active histone marks H3K27ac, H3K4me3 and repressive mark H3K27me3.

    • Suzan Stelloo
    • , Ekaterina Nevedomskaya
    • , Yongsoo Kim
    • , Karianne Schuurman
    • , Eider Valle-Encinas
    • , João Lobo
    • , Oscar Krijgsman
    • , Daniel Simon Peeper
    • , Seiwon Laura Chang
    • , Felix Yi-Chung Feng
    • , Lodewyk Frederik Ary Wessels
    • , Rui Henrique
    • , Carmen Jerónimo
    • , Andries Marinus Bergman
    •  & Wilbert Zwart
  • Article
    | Open Access

    Transcripts from highly-similar multigene families are challenging to decipher. Here, the authors develop IsoCon, a tool for detecting and reconstructing isoforms from multigene families by analyzing long PacBio Iso-Seq reads.

    • Kristoffer Sahlin
    • , Marta Tomaszkiewicz
    • , Kateryna D. Makova
    •  & Paul Medvedev
  • Article
    | Open Access

    Vascular smooth muscle cell (VSMC) accumulation is associated with cardiovascular disease. Here, the authors combine single-cell RNA sequencing with lineage labelling to profile VSMC heterogeneity in healthy mice. They show that upregulation of Sca1 in a rare VSMC subpopulation marks a cell phenotype that is prevalent in disease.

    • Lina Dobnikar
    • , Annabel L. Taylor
    • , Joel Chappell
    • , Phoebe Oldach
    • , Jennifer L. Harman
    • , Erin Oerton
    • , Elaine Dzierzak
    • , Martin R. Bennett
    • , Mikhail Spivakov
    •  & Helle F. Jørgensen
  • Article
    | Open Access

    RNA-seq is a powerful tool to investigate how drugs affect the transcriptome but library construction can be costly. Here the authors introduce DRUG-seq, an automated platform for high-throughput transcriptome profiling.

    • Chaoyang Ye
    • , Daniel J. Ho
    • , Marilisa Neri
    • , Chian Yang
    • , Tripti Kulkarni
    • , Ranjit Randhawa
    • , Martin Henault
    • , Nadezda Mostacci
    • , Pierre Farmer
    • , Steffen Renner
    • , Robert Ihry
    • , Leandra Mansur
    • , Caroline Gubser Keller
    • , Gregory McAllister
    • , Marc Hild
    • , Jeremy Jenkins
    •  & Ajamete Kaykas
  • Article
    | Open Access

    Primordial Germ Cell-Like Cells (PGCLCs) are an in vitro model for primordial germ cell development. Here, the authors couple a novel compound reporter with CRISPR screening to identify key genes for exit from pluripotency and acquisition of PGCLC fate; specifically identifying Nr5a2 and Zfp296.

    • Jamie A. Hackett
    • , Yun Huang
    • , Ufuk Günesdogan
    • , Kristjan A. Gretarsson
    • , Toshihiro Kobayashi
    •  & M. Azim Surani
  • Article
    | Open Access

    Fibro-adipogenic progenitors (FAPs) resident in skeletal muscle are involved in both regeneration and maladaptive processes. Here, the authors identify subpopulations of FAPs with biological activities implicated in physiological muscle repair that are altered in pathological conditions such as muscular dystrophies.

    • Barbora Malecova
    • , Sole Gatto
    • , Usue Etxaniz
    • , Magda Passafaro
    • , Amy Cortez
    • , Chiara Nicoletti
    • , Lorenzo Giordani
    • , Alessio Torcinaro
    • , Marco De Bardi
    • , Silvio Bicciato
    • , Francesca De Santa
    • , Luca Madaro
    •  & Pier Lorenzo Puri
  • Article
    | Open Access

    Human development provides a roadmap for advancing pluripotent stem cell-based regenerative therapies. Here the authors mapped human skeletogenesis using RNA sequencing on 5 cell types from a single foetal stage as well as chondrocytes at 4 stages in vivo and 2 stages during in vitro differentiation.

    • Gabriel B. Ferguson
    • , Ben Van Handel
    • , Maxwell Bay
    • , Petko Fiziev
    • , Tonis Org
    • , Siyoung Lee
    • , Ruzanna Shkhyan
    • , Nicholas W. Banks
    • , Mila Scheinberg
    • , Ling Wu
    • , Biagio Saitta
    • , Joseph Elphingstone
    • , A. Noelle Larson
    • , Scott M. Riester
    • , April D. Pyle
    • , Nicholas M. Bernthal
    • , Hanna KA Mikkola
    • , Jason Ernst
    • , Andre J. van Wijnen
    • , Michael Bonaguidi
    •  & Denis Evseenko