Single-cell transcriptomics enters the age of mass production.

Abstract:

:Two publications in the current issue of Cell introduce novel methods for high-throughput single-cell transcriptomics by using droplet microfluidics and sophisticated barcoding schemes for transcriptional profiling of thousands of individual cells.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Junker JP,van Oudenaarden A

doi

10.1016/j.molcel.2015.05.019

subject

Has Abstract

pub_date

2015-05-21 00:00:00

pages

563-4

issue

4

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(15)00355-X

journal_volume

58

pub_type

评论,杂志文章
  • Functional proteomics defines the molecular switch underlying FGF receptor trafficking and cellular outputs.

    abstract::The stimulation of fibroblast growth factor receptors (FGFRs) with distinct FGF ligands generates specific cellular responses. However, the mechanisms underlying this paradigm have remained elusive. Here, we show that FGF-7 stimulation leads to FGFR2b degradation and, ultimately, cell proliferation, whereas FGF-10 pro...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2013.08.002

    authors: Francavilla C,Rigbolt KT,Emdal KB,Carraro G,Vernet E,Bekker-Jensen DB,Streicher W,Wikström M,Sundström M,Bellusci S,Cavallaro U,Blagoev B,Olsen JV

    更新日期:2013-09-26 00:00:00

  • ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth.

    abstract::Histone H2B monoubiquitination (H2Bub1) is centrally involved in gene regulation. The deubiquitination module (DUBm) of the SAGA complex is a major regulator of global H2Bub1 levels, and components of this DUBm are linked to both neurodegenerative diseases and cancer. Unexpectedly, we find that ablation of USP22, the ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2016.03.030

    authors: Atanassov BS,Mohan RD,Lan X,Kuang X,Lu Y,Lin K,McIvor E,Li W,Zhang Y,Florens L,Byrum SD,Mackintosh SG,Calhoun-Davis T,Koutelou E,Wang L,Tang DG,Tackett AJ,Washburn MP,Workman JL,Dent SY

    更新日期:2016-05-19 00:00:00

  • Oncogenic Ras and Akt signaling contribute to glioblastoma formation by differential recruitment of existing mRNAs to polysomes.

    abstract::In order to determine the global effects of oncogenic Ras and Akt signaling pathways on translational efficiencies, we compared the gene expression profiles of total cellular mRNA and mRNA associated with polysomes. We found that the immediate effect of Ras and Akt signaling blockade on transcription was relatively mo...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00395-2

    authors: Rajasekhar VK,Viale A,Socci ND,Wiedmann M,Hu X,Holland EC

    更新日期:2003-10-01 00:00:00

  • Unraveling a connection between DNA demethylation repair and cancer.

    abstract::In this issue of Molecular Cell, Dango and Mosammaparast discover that the human oxidative demethylase ALKBH3 functions in complex with a DNA helicase to eliminate N3-methylcytosine lesions from ssDNA and that specific cancer cell lines are dependent on this activity for proliferation (Dango et al., 2011). ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2011.10.009

    authors: Camps M,Eichman BF

    更新日期:2011-11-04 00:00:00

  • Telomerase and ATM/Tel1p protect telomeres from nonhomologous end joining.

    abstract::Telomeres protect chromosome ends from fusing to double-stranded breaks (DSBs). Using a quantitative real-time PCR assay, we show that nonhomologous end joining between a telomere and an inducible DSB was undetectable in wild-type cells, but occurred within a few hours of DSB induction in approximately 1/2000 genomes ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00174-6

    authors: Chan SW,Blackburn EH

    更新日期:2003-05-01 00:00:00

  • VE-cadherin signaling induces EB3 phosphorylation to suppress microtubule growth and assemble adherens junctions.

    abstract::Vascular endothelial (VE)-cadherin homophilic adhesion controls endothelial barrier permeability through assembly of adherens junctions (AJs). We observed that loss of VE-cadherin-mediated adhesion induced the activation of Src and phospholipase C (PLC)γ2, which mediated Ca(2+) release from endoplasmic reticulum (ER) ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.10.011

    authors: Komarova YA,Huang F,Geyer M,Daneshjou N,Garcia A,Idalino L,Kreutz B,Mehta D,Malik AB

    更新日期:2012-12-28 00:00:00

  • A dynamic role of HAUSP in the p53-Mdm2 pathway.

    abstract::Our previous study showed that ubiquitination of p53 is reversible and that the ubiquitin hydrolase HAUSP can stabilize p53 by deubiquitination. Here, we found that partial reduction of endogenous HAUSP levels by RNAi indeed destabilizes endogenous p53; surprisingly, however, nearly complete ablation of HAUSP stabiliz...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(04)00157-1

    authors: Li M,Brooks CL,Kon N,Gu W

    更新日期:2004-03-26 00:00:00

  • Protein Aggregation Triggered by Rewired Protein Homeostasis during Neuronal Differentiation.

    abstract::In this issue of Molecular Cell, Vonk et al. (2020) and Thiruvalluvan et al. (2020) identify key chaperones that confer resistance to protein aggregation in neural stem cells and become reduced upon differentiation. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2020.03.028

    authors: Molzahn CM,Mayor T

    更新日期:2020-04-16 00:00:00

  • Identification of the TRiC/CCT substrate binding sites uncovers the function of subunit diversity in eukaryotic chaperonins.

    abstract::The ring-shaped hetero-oligomeric chaperonin TRiC/CCT uses ATP to fold a diverse subset of eukaryotic proteins. To define the basis of TRiC/CCT substrate recognition, we mapped the chaperonin interactions with the VHL tumor suppressor. VHL has two well-defined TRiC binding determinants. Each determinant contacts a spe...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.09.003

    authors: Spiess C,Miller EJ,McClellan AJ,Frydman J

    更新日期:2006-10-06 00:00:00

  • An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.

    abstract::Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to pre...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2017.07.023

    authors: Worden EJ,Dong KC,Martin A

    更新日期:2017-09-07 00:00:00

  • Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs.

    abstract::Upon glucose restriction, eukaryotic cells upregulate oxidative metabolism to maintain homeostasis. Using genetic screens, we find that the mitochondrial serine hydroxymethyltransferase (SHMT2) is required for robust mitochondrial oxygen consumption and low glucose proliferation. SHMT2 catalyzes the first step in mito...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.01.024

    authors: Minton DR,Nam M,McLaughlin DJ,Shin J,Bayraktar EC,Alvarez SW,Sviderskiy VO,Papagiannakopoulos T,Sabatini DM,Birsoy K,Possemato R

    更新日期:2018-02-15 00:00:00

  • Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility.

    abstract::Genes are transcribed in a discontinuous pattern referred to as RNA bursting, but the mechanisms regulating this process are unclear. Although many physiological signals, including glucocorticoid hormones, are pulsatile, the effects of transient stimulation on bursting are unknown. Here we characterize RNA synthesis f...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.06.042

    authors: Stavreva DA,Garcia DA,Fettweis G,Gudla PR,Zaki GF,Soni V,McGowan A,Williams G,Huynh A,Palangat M,Schiltz RL,Johnson TA,Presman DM,Ferguson ML,Pegoraro G,Upadhyaya A,Hager GL

    更新日期:2019-09-19 00:00:00

  • Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism.

    abstract::Circadian rhythms in mammals are generated by a transcriptional negative feedback loop that is driven primarily by oscillations of PER and CRY, which inhibit their own transcriptional activators, CLOCK and BMAL1. Current models posit that CRY is the dominant repressor, while PER may play an accessory role. In this stu...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.10.012

    authors: Chen R,Schirmer A,Lee Y,Lee H,Kumar V,Yoo SH,Takahashi JS,Lee C

    更新日期:2009-11-13 00:00:00

  • EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency.

    abstract::Trimethylation on H3K27 (H3K27me3) mediated by Polycomb repressive complex 2 (PRC2) has been linked to embryonic stem cell (ESC) identity and pluripotency. EZH2, the catalytic subunit of PRC2, has been reported as the sole histone methyltransferase that methylates H3K27 and mediates transcriptional silencing. Analysis...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2008.10.016

    authors: Shen X,Liu Y,Hsu YJ,Fujiwara Y,Kim J,Mao X,Yuan GC,Orkin SH

    更新日期:2008-11-21 00:00:00

  • Stopping the Clock with MYC.

    abstract::In a recent paper in Cell Metabolism, Altman et al. (2015) report that MYC disrupts the molecular clock in cancer cells and describe a link between oncogenesis, circadian rhythms, and metabolism. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2015.11.008

    authors: Lau AN,Vander Heiden MG

    更新日期:2015-11-19 00:00:00

  • VSV disrupts the Rae1/mrnp41 mRNA nuclear export pathway.

    abstract::Interference with nucleocytoplasmic transport is a strategy employed by certain viruses to compromise host cellular function. While it has been shown that the matrix (M) protein of the vesicular stomatitis virus (VSV) inhibits nuclear export of host cell mRNAs, the underlying mechanism has not been fully established. ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2004.11.023

    authors: Faria PA,Chakraborty P,Levay A,Barber GN,Ezelle HJ,Enninga J,Arana C,van Deursen J,Fontoura BM

    更新日期:2005-01-07 00:00:00

  • RPA-like mammalian Ctc1-Stn1-Ten1 complex binds to single-stranded DNA and protects telomeres independently of the Pot1 pathway.

    abstract::Budding yeast Cdc13, Stn1, and Ten1 form the CST complex to protect telomeres from lethal DNA degradation. It remains unknown whether similar complexes are conserved in higher eukaryotes or not. Here we isolated mammalian STN1 and TEN1 homologs and CTC1 (conserved telomere maintenance component 1). The three proteins ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.08.009

    authors: Miyake Y,Nakamura M,Nabetani A,Shimamura S,Tamura M,Yonehara S,Saito M,Ishikawa F

    更新日期:2009-10-23 00:00:00

  • An acid test for g proteins.

    abstract::In this issue, Isom et al. (2013) report their exciting discovery that G proteins can sense pH changes to fine-tune signaling in response to metabolic changes. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2013.08.012

    authors: Sprang SR

    更新日期:2013-08-22 00:00:00

  • A Therapeutic Double Whammy: Transcriptional or Post-transcriptional Suppression of Microsatellite Repeat Toxicity by Cas9.

    abstract::Microsatellite expansion diseases are caused by unstable tandem repeats of 3-10 nucleotides that become pathogenic beyond a threshold number of copies. Two groups present different approaches to reduce pathogenesis by targeting deactivated Cas9 to either the DNA (Pinto et al., 2017) or the RNA (Batra et al., 2017) rep...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2017.10.023

    authors: Rao AN,Cooper TA

    更新日期:2017-11-02 00:00:00

  • Spoon-Feeding Ribosomes to Autophagy.

    abstract::The ribosome, a ribonucleoprotein machine for protein synthesis, can also serve as an abundant nutrient source under starvation conditions. In a recent issue of Science, Wyant et al. (2018) discovered a specialized "spoon" to "scoop up" more ribosomes for degradation by autophagy. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2018.07.003

    authors: Nakatogawa H

    更新日期:2018-07-19 00:00:00

  • FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates.

    abstract::The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326-380 of p62 directly interact with the C-termina...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.01.035

    authors: Turco E,Witt M,Abert C,Bock-Bierbaum T,Su MY,Trapannone R,Sztacho M,Danieli A,Shi X,Zaffagnini G,Gamper A,Schuschnig M,Fracchiolla D,Bernklau D,Romanov J,Hartl M,Hurley JH,Daumke O,Martens S

    更新日期:2019-04-18 00:00:00

  • Detection of high-affinity and sliding clamp modes for MSH2-MSH6 by single-molecule unzipping force analysis.

    abstract::Mismatch repair (MMR) is initiated by MutS family proteins (MSH) that recognize DNA mismatches and recruit downstream repair factors. We used a single-molecule DNA-unzipping assay to probe interactions between S. cerevisiae MSH2-MSH6 and a variety of DNA mismatch substrates. This work revealed a high-specificity bindi...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.10.014

    authors: Jiang J,Bai L,Surtees JA,Gemici Z,Wang MD,Alani E

    更新日期:2005-12-09 00:00:00

  • Stalled fork rescue via dormant replication origins in unchallenged S phase promotes proper chromosome segregation and tumor suppression.

    abstract::Eukaryotic cells license far more origins than are actually used for DNA replication, thereby generating a large number of dormant origins. Accumulating evidence suggests that such origins play a role in chromosome stability and tumor suppression, though the underlying mechanism is largely unknown. Here, we show that ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.02.006

    authors: Kawabata T,Luebben SW,Yamaguchi S,Ilves I,Matise I,Buske T,Botchan MR,Shima N

    更新日期:2011-03-04 00:00:00

  • A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis.

    abstract::DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. 24-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a disti...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.11.015

    authors: Ye R,Chen Z,Lian B,Rowley MJ,Xia N,Chai J,Li Y,He XJ,Wierzbicki AT,Qi Y

    更新日期:2016-01-21 00:00:00

  • ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals.

    abstract::Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In t...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.04.009

    authors: Ishidate T,Ozturk AR,Durning DJ,Sharma R,Shen EZ,Chen H,Seth M,Shirayama M,Mello CC

    更新日期:2018-05-17 00:00:00

  • p58(IPK)-mediated attenuation of the proapoptotic PERK-CHOP pathway allows malignant progression upon low glucose.

    abstract::As solid tumors expand, oxygen and nutrients become limiting owing to inadequate vascularization and diffusion. How malignant cells cope with this potentially lethal metabolic stress remains poorly understood. We found that glucose shortage associated with malignant progression triggers apoptosis through the endoplasm...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2013.01.009

    authors: Huber AL,Lebeau J,Guillaumot P,Pétrilli V,Malek M,Chilloux J,Fauvet F,Payen L,Kfoury A,Renno T,Chevet E,Manié SN

    更新日期:2013-03-28 00:00:00

  • The dissociation of cohesin from chromosomes in prophase is regulated by Polo-like kinase.

    abstract::The separation of sister chromatids in anaphase depends on the dissociation of cohesin from chromosomes. In vertebrates, some cohesin is removed from chromosomes at the onset of anaphase by proteolytic cleavage. In contrast, the bulk of cohesin is removed from chromosomes already in prophase and prometaphase by an unk...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(02)00473-2

    authors: Sumara I,Vorlaufer E,Stukenberg PT,Kelm O,Redemann N,Nigg EA,Peters JM

    更新日期:2002-03-01 00:00:00

  • Hsp90-dependent activation of protein kinases is regulated by chaperone-targeted dephosphorylation of Cdc37.

    abstract::Activation of protein kinase clients by the Hsp90 system is mediated by the cochaperone protein Cdc37. Cdc37 requires phosphorylation at Ser13, but little is known about the regulation of this essential posttranslational modification. We show that Ser13 of uncomplexed Cdc37 is phosphorylated in vivo, as well as in bin...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2008.07.021

    authors: Vaughan CK,Mollapour M,Smith JR,Truman A,Hu B,Good VM,Panaretou B,Neckers L,Clarke PA,Workman P,Piper PW,Prodromou C,Pearl LH

    更新日期:2008-09-26 00:00:00

  • Structure and Function in Drosophila Chromosomes: Visualizing Topological Domains.

    abstract::Cardozo Gizzi et al. (2019) develop a new sequential imaging methodology (Hi-M) for observing chromosome structure in the Drosophila blastoderm and find that topological domains in single nuclei change in response to transcriptional activation. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2019.03.017

    authors: Larson DR

    更新日期:2019-04-04 00:00:00

  • PRC1 Catalytic Activity Is Central to Polycomb System Function.

    abstract::The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how the Polycomb system selects its target genes is poorly understood, and whether its histone-modifying activities are required for transcriptional repression remains controversial. Here, we...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.12.001

    authors: Blackledge NP,Fursova NA,Kelley JR,Huseyin MK,Feldmann A,Klose RJ

    更新日期:2020-02-20 00:00:00