Gene-Specific Control of tRNA Expression by RNA Polymerase II.

Abstract:

:Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Gerber A,Ito K,Chu CS,Roeder RG

doi

10.1016/j.molcel.2020.03.023

subject

Has Abstract

pub_date

2020-05-21 00:00:00

pages

765-778.e7

issue

4

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(20)30191-X

journal_volume

78

pub_type

杂志文章
  • Assembly of a double hexameric helicase.

    abstract::Viral initiators perform multiple functions in initiation of DNA replication including ori binding, melting, and unwinding, culminating in the formation of a double hexameric (DH) helicase. We have recapitulated the assembly of the papillomavirus E1 initiator DH helicase, providing the first description of how such a ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.09.020

    authors: Schuck S,Stenlund A

    更新日期:2005-11-11 00:00:00

  • Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.

    abstract::Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational framework consisti...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2017.06.003

    authors: Song Y,Botvinnik OB,Lovci MT,Kakaradov B,Liu P,Xu JL,Yeo GW

    更新日期:2017-07-06 00:00:00

  • Regulation of DNA-end resection by hnRNPU-like proteins promotes DNA double-strand break signaling and repair.

    abstract::DNA double-strand break (DSB) signaling and repair are critical for cell viability, and rely on highly coordinated pathways whose molecular organization is still incompletely understood. Here, we show that heterogeneous nuclear ribonucleoprotein U-like (hnRNPUL) proteins 1 and 2 play key roles in cellular responses to...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.12.035

    authors: Polo SE,Blackford AN,Chapman JR,Baskcomb L,Gravel S,Rusch A,Thomas A,Blundred R,Smith P,Kzhyshkowska J,Dobner T,Taylor AM,Turnell AS,Stewart GS,Grand RJ,Jackson SP

    更新日期:2012-02-24 00:00:00

  • Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase.

    abstract::Nucleosomes are surprisingly dynamic structures in vivo, showing transcription-independent exchange of histones H2A-H2B genome-wide and exchange of H3-H4 mainly within the promoters of transcribed genes. In addition, nucleosomes are disrupted in front of and reassembled behind the elongating RNA polymerase. Here we sh...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.07.001

    authors: Jamai A,Puglisi A,Strubin M

    更新日期:2009-08-14 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

  • MitoCPR: Meticulous Monitoring of Mitochondrial Proteostasis.

    abstract::Mitochondrial protein import stress compromises functioning of the organelles, due to inadequate supply of inner mitochondrial proteins. Weidberg and Amon (2018) describe a new monitoring pathway in budding yeast, which restores mitochondrial function following the clearing of accumulated unfolded pre-transported mito...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2018.06.027

    authors: Desai R,Campanella M

    更新日期:2018-07-05 00:00:00

  • A yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing.

    abstract::Three introns whose splicing is activated during meiosis in S. cerevisiae contain a Mer1p-dependent splicing enhancer. The enhancer can impose Mer1p-activated splicing upon the constitutively spliced actin intron provided the basal splicing efficiency of actin is first reduced. Of several nonessential splicing factors...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00033-2

    authors: Spingola M,Ares M Jr

    更新日期:2000-08-01 00:00:00

  • Structure of small virus-like particles assembled from the L1 protein of human papillomavirus 16.

    abstract::The papillomavirus major late protein, L1, forms the pentameric assembly unit of the viral shell. Recombinant HPV16 L1 pentamers assemble in vitro into capsid-like structures, and truncation of ten N-terminal residues leads to a homogeneous preparation of 12-pentamer, icosahedral particles. X-ray crystallographic anal...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80449-9

    authors: Chen XS,Garcea RL,Goldberg I,Casini G,Harrison SC

    更新日期:2000-03-01 00:00:00

  • Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay.

    abstract::Nonsense-mediated decay (NMD) is a surveillance system that degrades mRNAs containing a premature termination codon (PTC) and plays important roles in protein homeostasis and disease. The efficiency of NMD is variable, impacting the clinical outcome of genetic mutations. However, limited resolution of bulk analyses ha...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.05.008

    authors: Hoek TA,Khuperkar D,Lindeboom RGH,Sonneveld S,Verhagen BMP,Boersma S,Vermeulen M,Tanenbaum ME

    更新日期:2019-07-25 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

  • Angiogenin-induced tRNA fragments inhibit translation initiation.

    abstract::Angiogenin is a stress-activated ribonuclease that cleaves tRNA within anticodon loops to produce tRNA-derived stress-induced fragments (tiRNAs). Transfection of natural or synthetic tiRNAs inhibits protein synthesis and triggers the phospho-eIF2α-independent assembly of stress granules (SGs), essential components of ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.06.022

    authors: Ivanov P,Emara MM,Villen J,Gygi SP,Anderson P

    更新日期:2011-08-19 00:00:00

  • Phosphorylation-dependent regulation of PSF by GSK3 controls CD45 alternative splicing.

    abstract::Signal-induced alternative splicing of the CD45 gene in human T cells is essential for proper immune function. Skipping of the CD45 variable exons is controlled, in large part, by the recruitment of PSF to the pre-mRNA substrate upon T cell activation; however, the signaling cascade leading to exon exclusion has remai...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2010.09.013

    authors: Heyd F,Lynch KW

    更新日期:2010-10-08 00:00:00

  • A steroid-triggered transcriptional hierarchy controls salivary gland cell death during Drosophila metamorphosis.

    abstract::The steroid hormone ecdysone signals the stage-specific programmed cell death of the larval salivary glands during Drosophila metamorphosis. This response is preceded by an ecdysone-triggered switch in gene expression in which the diap2 death inhibitor is repressed and the reaper (rpr) and head involution defective (h...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80439-6

    authors: Jiang C,Lamblin AF,Steller H,Thummel CS

    更新日期:2000-03-01 00:00:00

  • Homologous recombination is promoted by translesion polymerase poleta.

    abstract::Two new studies provide in vivo ( [this issue of Molecular Cell]) and in vitro ( [this issue of Molecular Cell]) evidence that poleta functions to extend 3' strands exchanged during homologous recombination and raise the issue of how TLS polymerases are selected onto different substrates. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章,评审

    doi:10.1016/j.molcel.2005.11.018

    authors: Rattray AJ,Strathern JN

    更新日期:2005-12-09 00:00:00

  • The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.

    abstract::Comparisons of bacteriophage PRD1 and adenovirus protein structures and virion architectures have been instrumental in unraveling an evolutionary relationship and have led to a proposal of a phylogeny-based virus classification. The structure of the PRD1 spike protein P5 provides further insight into the evolution of ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.03.019

    authors: Merckel MC,Huiskonen JT,Bamford DH,Goldman A,Tuma R

    更新日期:2005-04-15 00:00:00

  • The survivin-like C. elegans BIR-1 protein acts with the Aurora-like kinase AIR-2 to affect chromosomes and the spindle midzone.

    abstract::Baculoviral IAP repeat proteins (BIRPs) may affect cell death, cell division, and tumorigenesis. The C. elegans BIRP BIR-1 was localized to chromosomes and to the spindle midzone. Embryos and fertilized oocytes lacking BIR-1 had defects in chromosome behavior, spindle midzone formation, and cytokinesis. We observed in...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00023-x

    authors: Speliotes EK,Uren A,Vaux D,Horvitz HR

    更新日期:2000-08-01 00:00:00

  • Adjacent residues in the E1 initiator beta-hairpin define different roles of the beta-hairpin in Ori melting, helicase loading, and helicase activity.

    abstract::We have analyzed two residues in the helicase domain of the E1 initiator protein. These residues are part of a highly conserved structural motif, the beta-hairpin, which is present in the helicase domain of all papovavirus initiator proteins. These proteins are unique in their ability to transition from local template...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.02.009

    authors: Liu X,Schuck S,Stenlund A

    更新日期:2007-03-23 00:00:00

  • BRCA1 Haploinsufficiency Is Masked by RNF168-Mediated Chromatin Ubiquitylation.

    abstract::BRCA1 functions at two distinct steps during homologous recombination (HR). Initially, it promotes DNA end resection, and subsequently it recruits the PALB2 and BRCA2 mediator complex, which stabilizes RAD51-DNA nucleoprotein filaments. Loss of 53BP1 rescues the HR defect in BRCA1-deficient cells by increasing resecti...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.12.010

    authors: Zong D,Adam S,Wang Y,Sasanuma H,Callén E,Murga M,Day A,Kruhlak MJ,Wong N,Munro M,Ray Chaudhuri A,Karim B,Xia B,Takeda S,Johnson N,Durocher D,Nussenzweig A

    更新日期:2019-03-21 00:00:00

  • A critical role for noncoding 5S rRNA in regulating Mdmx stability.

    abstract::Both p53 and Mdmx are ubiquitinated and degraded by the same E3 ligase Mdm2; interestingly, however, while p53 is rapidly degraded by Mdm2, Mdmx is a stable protein in most cancer cells. Thus, the mechanism by which Mdmx is degraded by Mdm2 needs further elucidation. Here, we identified the noncoding 5S rRNA as a majo...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.08.020

    authors: Li M,Gu W

    更新日期:2011-09-16 00:00:00

  • HuR and translation--the missing linc(RNA).

    abstract::In this issue, Yoon et al. (2012) reveal that HuR influences decay of a long noncoding RNA (lincRNA-p21) that in turn hybridizes to mRNA targets and represses their translation-an indirect, but elegant explanation for the impact of HuR on translation efficiency. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2012.08.005

    authors: Wilusz CJ,Wilusz J

    更新日期:2012-08-24 00:00:00

  • Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells.

    abstract::Eukaryotic cells compartmentalize biochemical processes in different organelles, often relying on metabolic cycles to shuttle reducing equivalents across intracellular membranes. NADPH serves as the electron carrier for the maintenance of redox homeostasis and reductive biosynthesis, with separate cytosolic and mitoch...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2014.05.008

    authors: Lewis CA,Parker SJ,Fiske BP,McCloskey D,Gui DY,Green CR,Vokes NI,Feist AM,Vander Heiden MG,Metallo CM

    更新日期:2014-07-17 00:00:00

  • SR proteins function in coupling RNAP II transcription to pre-mRNA splicing.

    abstract::Transcription and splicing are functionally coupled, resulting in highly efficient splicing of RNA polymerase II (RNAP II) transcripts. The mechanism involved in this coupling is not known. To identify potential coupling factors, we carried out a comprehensive proteomic analysis of immunopurified human RNAP II, identi...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.05.036

    authors: Das R,Yu J,Zhang Z,Gygi MP,Krainer AR,Gygi SP,Reed R

    更新日期:2007-06-22 00:00:00

  • Reversible SUMOylation of TBL1-TBLR1 regulates β-catenin-mediated Wnt signaling.

    abstract::Dysregulation of Wnt signaling has been implicated in tumorigenesis. The role of Transducin β-like proteins TBL1-TBLR1 in the promotion of Wnt/β-catenin-mediated oncogenesis has recently been emphasized; however, the molecular basis of activation of Wnt signaling by the corepressor TBL1-TBLR1 is incompletely understoo...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.05.027

    authors: Choi HK,Choi KC,Yoo JY,Song M,Ko SJ,Kim CH,Ahn JH,Chun KH,Yook JI,Yoon HG

    更新日期:2011-07-22 00:00:00

  • The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome.

    abstract::Metazoan spliceosomes exhibit an elaborate protein composition required for canonical and alternative splicing. Thus, the minimal set of proteins essential for activation and catalysis remains elusive. We therefore purified in vitro assembled, precatalytic spliceosomal complex B, activated B(act), and step 1 complex C...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.09.040

    authors: Fabrizio P,Dannenberg J,Dube P,Kastner B,Stark H,Urlaub H,Lührmann R

    更新日期:2009-11-25 00:00:00

  • Global Mapping of Human RNA-RNA Interactions.

    abstract::The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2016.04.030

    authors: Sharma E,Sterne-Weiler T,O'Hanlon D,Blencowe BJ

    更新日期:2016-05-19 00:00:00

  • Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29.

    abstract::The DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein. The crystal structure of phi29 DNA polymerase determined at 2.2 A resolution provides expl...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2004.10.019

    authors: Kamtekar S,Berman AJ,Wang J,Lázaro JM,de Vega M,Blanco L,Salas M,Steitz TA

    更新日期:2004-11-19 00:00:00

  • Unweaving the meanings of messenger RNA sequences.

    abstract::In addition to protein-coding information, mRNAs harbor regulatory sequences necessary for appropriate processing of their precursors. Goren et al. (2006) and Wang et al. (2006) explore the diversity of these signals and the rules by which they function. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章,评审

    doi:10.1016/j.molcel.2006.07.003

    authors: Guigó R,Valcárcel J

    更新日期:2006-07-21 00:00:00

  • Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.

    abstract::Yeast histone H2A is phosphorylated on Ser129 upon DNA damage, an event required for efficient repair. We show that phosphorylation occurs rapidly over a large region around DNA double-strand breaks (DSBs). Histone H4 acetylation is also important for DSB repair, and we found that the NuA4 HAT complex associates speci...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2004.12.003

    authors: Downs JA,Allard S,Jobin-Robitaille O,Javaheri A,Auger A,Bouchard N,Kron SJ,Jackson SP,Côté J

    更新日期:2004-12-22 00:00:00

  • An Epigenetic Clock Measures Accelerated Aging in Treated HIV Infection.

    abstract::In this issue of Molecular Cell, Gross et al. (2016) find a CpG DNA methylation signature in blood cells of patients with chronic well-controlled HIV infection that correlates with accelerated aging. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2016.04.008

    authors: Boulias K,Lieberman J,Greer EL

    更新日期:2016-04-21 00:00:00

  • The APC/C subunit Mnd2/Apc15 promotes Cdc20 autoubiquitination and spindle assembly checkpoint inactivation.

    abstract::The fidelity of chromosome segregation depends on the spindle assembly checkpoint (SAC). In the presence of unattached kinetochores, anaphase is delayed when three SAC components (Mad2, Mad3/BubR1, and Bub3) inhibit Cdc20, the activating subunit of the anaphase-promoting complex (APC/C). We analyzed the role of Cdc20 ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.07.031

    authors: Foster SA,Morgan DO

    更新日期:2012-09-28 00:00:00