Exo- and Endoribonucleolytic Activities of Yeast Cytoplasmic and Nuclear RNA Exosomes Are Dependent on the Noncatalytic Core and Central Channel

HOLE: A program for the analysis of the pore dimensions of ion channel structural models

Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A., & Sansom, M. S. P. (1996) · Journal of Molecular Graphics · doi:10.1016/s0263-7855(97)00009-x · Cited by 1,803 · see citing works

Bidirectional promoters generate pervasive transcription in yeast

Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder‐Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. K., & Steinmetz, L. M. (2009) · Nature · doi:10.1038/nature07728 · Cited by 926 · see citing works

Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase

Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.-C., Dufour, M., Boulay, J., Regnault, B., Devaux, F., Namane, A., Séraphin, B., et al. (2005) · Cell · doi:10.1016/j.cell.2005.04.030 · Cited by 843 · see citing works

Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation

Doma, M. K., & Parker, R. (2006) · Nature · doi:10.1038/nature04530 · Cited by 764 · see citing works

The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex

Anderson, J. S. J., & Parker, R. (1998) · The EMBO Journal · doi:10.1093/emboj/17.5.1497 · Cited by 652 · see citing works

RNA-quality control by the exosome

Houseley, J. M., LaCava, J., & Tollervey, D. W. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1964 · Cited by 645 · see citing works

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

Neil, H., Malabat, C., D'Aubenton-Carafa, Y., Xu, Z.-Y., Steinmetz, L., & Jacquier, A. (2009) · Nature · doi:10.1038/nature07747 · Cited by 626 · see citing works

Functions of the exosome in rRNA, snoRNA and snRNA synthesis

Allmang, C., Kufel, J., Chanfreau, G., Mitchell, P., Petfalski, E., & Tollervey, D. W. (1999) · The EMBO Journal · doi:10.1093/emboj/18.19.5399 · Cited by 618 · see citing works

Exosome-Mediated Recognition and Degradation of mRNAs Lacking a Termination Codon

van Hoof, A., Frischmeyer, P. A., Dietz, H. C., & Parker, R. (2002) · Science · doi:10.1126/science.1067272 · Cited by 592 · see citing works

Reconstitution, Activities, and Structure of the Eukaryotic RNA Exosome

Liu, Q., Greimann, J. C., & Lima, C. D. (2006) · Cell · doi:10.1016/j.cell.2006.10.037 · Cited by 544 · see citing works

A single subunit, Dis3, is essentially responsible for yeast exosome core activity

Dziembowski, A., Lorentzen, E., Conti, E., & Séraphin, B. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1184 · Cited by 421 · see citing works

Yeast Exosome Mutants Accumulate 3′-Extended Polyadenylated Forms of U4 Small Nuclear RNA and Small Nucleolar RNAs

van Hoof, A., Lennertz, P., & Parker, R. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.2.441-452.2000 · Cited by 366 · see citing works

Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome

Orbán, T. I., & Izaurralde, E. (2005) · RNA · doi:10.1261/rna.7231505 · Cited by 356 · see citing works

Endonucleolytic RNA cleavage by a eukaryotic exosome

Lebreton, A., Tomecki, R., Dziembowski, A., & Séraphin, B. (2008) · Nature · doi:10.1038/nature07480 · Cited by 335 · see citing works

The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates

Basu, U., Meng, F., Keim, C., Grinstein, V., Pefanis, E., Eccleston, J., Zhang, T., Myers, D. R., Wasserman, C. R., Wesemann, D. R., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.001 · Cited by 315 · see citing works

The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities

Schaeffer, D., Tsanova, B., Barbas, A., Reis, F. P., Dastidar, E. G., Sanchez-Rotunno, M., Arraiano, C. M., & van Hoof, A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1528 · Cited by 305 · see citing works

A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.

Symmons, M., Jones, G., & Luisi, B. (2000) · Structure · doi:10.1016/s0969-2126(00)00521-9 · Cited by 279 · see citing works

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

Tomecki, R., Kristiansen, M. S., Lykke‐Andersen, S., Chlebowski, A., Larsen, K. M., Szczęsny, R. J., Drążkowska, K., Pastuła, A., Andersen, J., Stępień, P. P., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.121 · Cited by 272 · see citing works

Degradation of ribosomal RNA precursors by the exosome

Allmang, C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.8.1684 · Cited by 254 · see citing works

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation

Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E., & Conti, E. (2009) · Cell · doi:10.1016/j.cell.2009.08.042 · Cited by 245 · see citing works

RNAi-Dependent and -Independent RNA Turnover Mechanisms Contribute to Heterochromatic Gene Silencing

Bühler, M., Haas, W., Gygi, S. P., & Moazed, D. (2007) · Cell · doi:10.1016/j.cell.2007.03.038 · Cited by 233 · see citing works

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae

Davis, C., & Ares, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507783103 · Cited by 232 · see citing works

The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome

Schneider, C., Leung, E., Brown, J. D., & Tollervey, D. W. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn1020 · Cited by 231 · see citing works

MicroRNA Biogenesis via Splicing and Exosome-Mediated Trimming in Drosophila

Flynt, A. S., Greimann, J. C., Chung, W., Lima, C. D., & Lai, E. C. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.06.014 · Cited by 183 · see citing works

Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the RNase II Nuclease Family

Lorentzen, E., Basquin, J., Tomecki, R., Dziembowski, A., & Conti, E. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.018 · Cited by 180 · see citing works

Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U‐snRNPs.

Tollervey, D. W., & Mattaj, I. W. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb04777.x · Cited by 173 · see citing works

Disruption of the gene XRN1, coding for a 5′→3′ exoribonuclease, restricts yeast cell growth

Larimer, F. W., & Stevens, A. (1990) · Gene · doi:10.1016/0378-1119(90)90417-p · Cited by 159 · see citing works

Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking

Seol, Y., Skinner, G. M., Visscher, K. M., Buhot, A., & Halperin, A. (2007) · Physical Review Letters · doi:10.1103/physrevlett.98.158103 · Cited by 153 · see citing works

Elastic Properties of a Single-Stranded Charged Homopolymeric Ribonucleotide

Seol, Y., Skinner, G. M., & Visscher, K. M. (2004) · Physical Review Letters · doi:10.1103/physrevlett.93.118102 · Cited by 148 · see citing works

Activities of human RRP6 and structure of the human RRP6 catalytic domain

Januszyk, K., Liu, Q., & Lima, C. D. (2011) · RNA · doi:10.1261/rna.2763111 · Cited by 120 · see citing works

TRAMP Complex Enhances RNA Degradation by the Nuclear Exosome Component Rrp6

Callahan, K. P., & Butler, J. S. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.058396 · Cited by 111 · see citing works

Architecture of the yeast Rrp44–exosome complex suggests routes of RNA recruitment for 3′ end processing

Wang, H., Wang, J., Ding, F., Callahan, K. P., Bratkowski, M. A., Butler, J. S., Nogales, E., & Ke, A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705526104 · Cited by 99 · see citing works

Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p

Callahan, K. P., & Butler, J. S. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn743 · Cited by 98 · see citing works

Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain

Midtgaard, S. F., Assenholt, J., Jonstrup, A. T., van Eck, L., Jensen, T. H., & Brodersen, D. E. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604731103 · Cited by 88 · see citing works

The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein

Stead, J. A., Costello, J. L., Livingstone, M. J., & Mitchell, P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm614 · Cited by 82 · see citing works

The Exosome and the Proteasome: Nano-Compartments for Degradation

Lorentzen, E., & Conti, E. (2006) · Cell · doi:10.1016/j.cell.2006.05.002 · Cited by 76 · see citing works

Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs

Schaeffer, D., & van Hoof, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013180108 · Cited by 72 · see citing works

RNA channelling by the eukaryotic exosome

Malet, H., Topf, M., Clare, D. K., Ebert, J., Bonneau, F., Basquin, J., Drążkowska, K., Tomecki, R., Dziembowski, A., Conti, E., et al. (2010) · EMBO Reports · doi:10.1038/embor.2010.164 · Cited by 68 · see citing works

Rrp6, Rrp47 and Cofactors of the Nuclear Exosome

Butler, J. S., & Mitchell, P. (2010) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-7841-7_8 · Cited by 62 · see citing works

Exonucleolysis is required for nuclear mRNA quality control in yeast THO mutants

Assenholt, J., Mouaikel, J., Andersen, K. R., Brodersen, D. E., Libri, D., & Jensen, T. H. (2008) · RNA · doi:10.1261/rna.1108008 · Cited by 58 · see citing works

The exosome: a macromolecular cage for controlled RNA degradation

Büttner, K., Wenig, K., & Hopfner, K. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05331.x · Cited by 48 · see citing works

Structural components and architectures of RNA exosomes.

Januszyk, K., & Lima, C. D. (2010) · PubMed · doi:10.1007/978-1-4419-7841-7_2 · Cited by 34 · see citing works

Chapter 10 Reconstitution of RNA Exosomes from Human and Saccharomyces cerevisiae

Greimann, J. C., & Lima, C. D. (2008) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(08)02610-4 · Cited by 26 · see citing works

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

Pefanis, E., Wang, J., Rothschild, G., Lim, J., Kazadi, D., Sun, J., Federation, A., Chao, J., Elliott, O., Liu, Z.-P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.034 · Cited by 464 · see citing works

The regulation and functions of the nuclear RNA exosome complex

Kilchert, C., Wittmann, S., & Vasiljeva, L. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.15 · Cited by 444 · see citing works

Regulation of gene expression in trypanosomatids: living with polycistronic transcription

CLAYTON, C. E. (2019) · Open Biology · doi:10.1098/rsob.190072 · Cited by 283 · see citing works

RNA decay machines: The exosome

Chlebowski, A., Lubas, M., Jensen, T. H., & Dziembowski, A. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2013.01.006 · Cited by 246 · see citing works

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex

Makino, D. L., Baumgärtner, M., & Conti, E. (2013) · Nature · doi:10.1038/nature11870 · Cited by 240 · see citing works

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactorsPreprint

Zinder, J. C., & Lima, C. D. (2017) · Genes & Development · doi:10.1101/gad.294769.116 · Cited by 234 · see citing works

The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex

Halbach, F., Reichelt, P., Rode, M., & Conti, E. (2013) · Cell · doi:10.1016/j.cell.2013.07.017 · Cited by 210 · see citing works

The eukaryotic RNA exosome

Januszyk, K., & Lima, C. D. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.01.011 · Cited by 199 · see citing works

Exonuclease hDIS3L2 specifies an exosome‐independent 3′‐5′ degradation pathway of human cytoplasmic mRNA

Lubas, M., Damgaard, C. K., Tomecki, R., Cysewski, D., Jensen, T. H., & Dziembowski, A. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.135 · Cited by 152 · see citing works

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex

Weick, E.-M., Puno, M. R., Januszyk, K., Zinder, J. C., DiMattia, M. A., & Lima, C. D. (2018) · Cell · doi:10.1016/j.cell.2018.05.041 · Cited by 153 · see citing works

Structure of an Rrp6–RNA exosome complex bound to poly(A) RNA

Wasmuth, E. V., Januszyk, K., & Lima, C. D. (2014) · Nature · doi:10.1038/nature13406 · Cited by 151 · see citing works

Threading the barrel of the RNA exosome

Schneider, C., & Tollervey, D. W. (2013) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.06.013 · Cited by 144 · see citing works

RNA degradation paths in a 12-subunit nuclear exosome complex

Makino, D. L., Schuch, B., Stegmann, E., Baumgärtner, M., Minard‐Basquin, C., & Conti, E. (2015) · Nature · doi:10.1038/nature14865 · Cited by 142 · see citing works

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

Tomecki, R., Sikorski, P. J., & Zakrzewska‐Placzek, M. (2017) · FEBS Letters · doi:10.1002/1873-3468.12682 · Cited by 131 · see citing works

The Human Nuclear Poly(A)-Binding Protein Promotes RNA Hyperadenylation and Decay

Bresson, S. M., & Conrad, N. K. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003893 · Cited by 128 · see citing works

Structure of the nuclear exosome captured on a maturing preribosome

Schuller, J. M., Falk, S., Fromm, L., Hurt, E., & Conti, E. (2018) · Science · doi:10.1126/science.aar5428 · Cited by 124 · see citing works

The exosome‐binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase

Schuch, B., Feigenbutz, M., Makino, D. L., Falk, S., Minard‐Basquin, C., Mitchell, P., & Conti, E. (2014) · The EMBO Journal · doi:10.15252/embj.201488757 · Cited by 110 · see citing works

Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex

Kowalinski, E., Kögel, A., Ebert, J., Reichelt, P., Stegmann, E., Habermann, B. H., & Conti, E. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.028 · Cited by 96 · see citing works

The RNA exosome promotes transcription termination of backtracked RNA polymerase II

Lemay, J., Larochelle, M., Marguerat, S., Atkinson, S. R., Bähler, J., & Bachand, F. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2893 · Cited by 91 · see citing works

A MicroRNA Precursor Surveillance System in Quality Control of MicroRNA Synthesis

Liu, X., Zheng, Q., Vrettos, N., Maragkakis, M., Alexiou, P., Gregory, B. D., & Mourelatos, Z. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.017 · Cited by 90 · see citing works

Nuclear RNA Exosome at 3.1 Å Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3

Zinder, J. C., Wasmuth, E. V., & Lima, C. D. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.09.038 · Cited by 87 · see citing works

The RNA exosome and proteasome: common principles of degradation control

Makino, D. L., Halbach, F., & Conti, E. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3657 · Cited by 82 · see citing works

Reconstitution of the complete pathway of ITS2 processing at the pre-ribosome

Fromm, L., Falk, S., Flemming, D., Schuller, J. M., Thoms, M., Conti, E., & Hurt, E. (2017) · Nature Communications · doi:10.1038/s41467-017-01786-9 · Cited by 77 · see citing works

Multiple myeloma-associated hDIS3 mutations cause perturbations in cellular RNA metabolism and suggest hDIS3 PIN domain as a potential drug target

Tomecki, R., Drążkowska, K., Kuciński, I., Stoduś, K., Szczęsny, R. J., Gruchota, J., Owczarek, E. P., Kalisiak, K., & Dziembowski, A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt930 · Cited by 79 · see citing works

Surveillance-ready transcription: nuclear RNA decay as a default fate

Bresson, S. M., & Tollervey, D. W. (2018) · Open Biology · doi:10.1098/rsob.170270 · Cited by 74 · see citing works

The 3' to 5' Exoribonuclease DIS3: From Structure and Mechanisms to Biological Functions and Role in Human Disease

Robinson, S., Oliver, A., Chevassut, T., & Newbury, S. (2015) · Biomolecules · doi:10.3390/biom5031515 · Cited by 71 · see citing works

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

Lange, H., Ndecky, S. Y. A., Diaz, C. G., Pflieger, D., Butel, N., Zumsteg, J., Kühn, L., Piermaria, C., Chicher, J., Christie, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11807-4 · Cited by 70 · see citing works

Intracellular ribonucleases involved in transcript processing and decay: Precision tools for RNA

Arraiano, C. M., Mauxion, F., Viegas, S. C., Matos, R. G., & Séraphin, B. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2013.03.009 · Cited by 66 · see citing works

Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM

Liu, J., Bratkowski, M. A., Liu, X., Niu, C.-Y., Ke, A., & Wang, H. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2736 · Cited by 62 · see citing works

The RNA exosome complex central channel controls both exonuclease and endonuclease Dis3 activities in vivo and in vitro

Drążkowska, K., Tomecki, R., Stoduś, K., Kowalska, K., Czarnocki-Cieciura, M., & Dziembowski, A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt060 · Cited by 60 · see citing works

Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase

Wasmuth, E. V., Zinder, J. C., Zattas, D., Das, M., & Lima, C. D. (2017) · eLife · doi:10.7554/elife.29062 · Cited by 60 · see citing works

Extraction of mRNA from Stalled Ribosomes by the Ski Complex

Zinoviev, A., Ayupov, R. K., Abaeva, I. S., Hellen, C. U. T., & Pestova, T. V. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.011 · Cited by 60 · see citing works

Distinct and evolutionary conserved structural features of the human nuclear exosome complex

Gerlach, P., Schuller, J. M., Bonneau, F., Basquin, J., Reichelt, P., Falk, S., & Conti, E. (2018) · eLife · doi:10.7554/elife.38686 · Cited by 59 · see citing works

Whole-exome analysis in osteosarcoma to identify a personalized therapy

Chiappetta, C., Mancini, M., Lessi, F., Aretini, P., Gregorio, V. D., Puggioni, C., Carletti, R., Petrozza, V., Civita, P., Franceschi, S., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.19010 · Cited by 54 · see citing works

The multitasking polyA tail: nuclear RNA maturation, degradation and export

Tudek, A., Lloret-Llinares, M., & Jensen, T. H. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0169 · Cited by 56 · see citing works

Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome

Gerlach, P., Garland, W., Lingaraju, M., Salerno-Kochan, A., Bonneau, F., Basquin, J., Jensen, T. H., & Conti, E. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.04.011 · Cited by 55 · see citing works

The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome

Wasmuth, E. V., & Lima, C. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1152 · Cited by 55 · see citing works

A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans

Kalisiak, K., Kuliński, T. M., Tomecki, R., Cysewski, D., Pietras, Z., Chlebowski, A., Kowalska, K. J., & Dziembowski, A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw862 · Cited by 48 · see citing works

Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome

Lau, B. H. S., Cheng, J., Flemming, D., Venuta, G. L., Berninghausen, O., Beckmann, R., & Hurt, E. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.009 · Cited by 48 · see citing works

Rarely at rest

Hardwick, S., & Luisi, B. (2013) · RNA Biology · doi:10.4161/rna.22270 · Cited by 28 · see citing works

The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions

Han, J., & van Hoof, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.08.059 · Cited by 37 · see citing works

The Exosome Cofactor Rrp47 Is Critical for the Stability and Normal Expression of Its Associated Exoribonuclease Rrp6 in Saccharomyces cerevisiae

Feigenbutz, M., Garland, W., Turner, M., & Mitchell, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080752 · Cited by 36 · see citing works

RNA Exosome Regulates AID DNA Mutator Activity in the B Cell Genome

Pefanis, E., & Basu, U. (2015) · Advances in immunology · doi:10.1016/bs.ai.2015.04.002 · Cited by 35 · see citing works

An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi

Li, J., Liu, X., Yin, Z., Hú, Z., & Zhang, K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.638617 · Cited by 34 · see citing works

Exosome substrate targeting: the long and short of it

Mitchell, P. (2014) · Biochemical Society Transactions · doi:10.1042/bst20140088 · Cited by 33 · see citing works

Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes

Lange, H., & Gagliardi, D. (2021) · The Plant Cell · doi:10.1093/plcell/koab310 · Cited by 32 · see citing works

Noncoding RNA Surveillance: The Ends Justify the Means

Belair, C., Sim, S., & Wolin, S. L. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00462 · Cited by 29 · see citing works

The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes

Saramago, M., da Costa, P. J., Viegas, S. C., & Arraiano, C. M. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-19966-1_4 · Cited by 29 · see citing works

Rrp6 Regulates Heterochromatic Gene Silencing via ncRNA RUF6 Decay in Malaria Parasites

Fan, Y., Shen, S., Wei, G., Tang, J., Zhao, Y., Wang, F., He, X., Guo, G., Shang, X., Yu, X., et al. (2020) · mBio · doi:10.1128/mbio.01110-20 · Cited by 29 · see citing works

Assembly of the Yeast Exoribonuclease Rrp6 with Its Associated Cofactor Rrp47 Occurs in the Nucleus and Is Critical for the Controlled Expression of Rrp47

Feigenbutz, M., Jones, R. M., Besong, T. M. D., Harding, S. E., & Mitchell, P. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.445759 · Cited by 27 · see citing works

Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus

Paul, B., & Montpetit, B. (2016) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-04-0244 · Cited by 26 · see citing works

Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction

Lorentzen, E., & Conti, E. (2012) · Archaea · doi:10.1155/2012/721869 · Cited by 25 · see citing works

The RNA exosome complex degrades expanded hexanucleotide repeat RNA in C9orf72 FTLD/ALS

Kawabe, Y., Mori, K., Yamashita, T., Gotoh, S., & Ikeda, M. (2020) · The EMBO Journal · doi:10.15252/embj.2019102700 · Cited by 24 · see citing works

Pervasive transcription: a controlled risk

Villa, T., & Porrúa, O. (2022) · FEBS Journal · doi:10.1111/febs.16530 · Cited by 20 · see citing works

Structure and Activities of the Eukaryotic RNA Exosome

Wasmuth, E. V., & Lima, C. D. (2012) · The Enzymes · doi:10.1016/b978-0-12-404740-2.00003-3 · Cited by 21 · see citing works

Elimination of 01/A′–A0 pre-rRNA processing by-product in human cells involves cooperative action of two nuclear exosome-associated nucleases: RRP6 and DIS3

Kobyłecki, K., Drążkowska, K., Kuliński, T. M., Dziembowski, A., & Tomecki, R. (2018) · RNA · doi:10.1261/rna.066589.118 · Cited by 21 · see citing works

HELZ2: a new, interferon-regulated, human 3′-5′ exoribonuclease of the RNB family is expressed from a non-canonical initiation codon

Huntzinger, E., Sinteff, J., Morlet, B., & Séraphin, B. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad673 · Cited by 19 · see citing works

Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome

Telekawa, C., Boisvert, F., & Bachand, F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky915 · Cited by 19 · see citing works

DIS3 isoforms vary in their endoribonuclease activity and are differentially expressed within haematological cancers

Robinson, S. R., Viegas, S. C., Matos, R. G., Domingues, S., Bedir, M., Helen, S., Chevassut, T. J. T., Oliver, A. W., Arraiano, C. M., & Newbury, S. F. (2018) · Biochemical Journal · doi:10.1042/bcj20170962 · Cited by 19 · see citing works

DIS3: The Enigmatic Gene in Multiple Myeloma

Ohguchi, Y., & Ohguchi, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24044079 · Cited by 18 · see citing works

Cyclin B3 is dispensable for mouse spermatogenesis

Karasu, M. E., & Keeney, S. (2019) · Chromosoma · doi:10.1007/s00412-019-00725-5 · Cited by 18 · see citing works

RNA Degradation in Eukaryotic Cells

Tatosyan, K. A., Ustyantsev, I. G., & Kramerov, D. A. (2020) · Molecular Biology · doi:10.1134/s0026893320040159 · Cited by 18 · see citing works

Purification and analysis of endogenous human RNA exosome complexes

Domanski, M., Upla, P., Rice, W. J., Molloy, K. R., Ketaren, N. E., Stokes, D. L., Jensen, T. H., Rout, M. P., & LaCava, J. (2016) · RNA · doi:10.1261/rna.057760.116 · Cited by 16 · see citing works

Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6

Garland, W., Feigenbutz, M., Turner, M., & Mitchell, P. (2013) · RNA · doi:10.1261/rna.039388.113 · Cited by 16 · see citing works

Exosome-Bound WD Repeat Protein Monad Inhibits Breast Cancer Cell Invasion by Degrading Amphiregulin mRNA

Saeki, M., Egusa, H., Kamano, Y., Kakihara, Y., Houry, W. A., Yatani, H., Noguchi, S., & Kamisaki, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067326 · Cited by 14 · see citing works

RNA Exosomes and Their Cofactors

Kilchert, C. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9822-7_11 · Cited by 14 · see citing works

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Das, M., Zattas, D., Zinder, J. C., Wasmuth, E. V., Henri, J., & Lima, C. D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024846118 · Cited by 14 · see citing works

Yeast RNA exosome activity is necessary for maintaining cell wall stability through proper protein glycosylation

Novačić, A., Beauvais, V., Oskomić, M., Štrbac, L., Dantec, A. L., Rahmouni, A. R., & Stuparević, I. (2021) · Molecular Biology of the Cell · doi:10.1091/mbc.e20-08-0544-t · Cited by 14 · see citing works

Looking into the barrel of the RNA exosome

Schneider, C., & Tollervey, D. W. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2750 · Cited by 13 · see citing works

Molecular Mechanism of Processive 3′ to 5′ RNA Translocation in the Active Subunit of the RNA Exosome Complex

Vuković, L., Chipot, C. J., Makino, D. L., Conti, E., & Schulten, K. J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.5b12065 · Cited by 14 · see citing works

Relative contributions of the structural and catalytic roles of Rrp6 in exosomal degradation of individual mRNAs

Mukherjee, K., Gardin, J., Futcher, B., & Leatherwood, J. (2016) · RNA · doi:10.1261/rna.051490.115 · Cited by 13 · see citing works

Regulation of cytoplasmic RNA stability: Lessons from Drosophila

Towler, B. P., & Newbury, S. F. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1499 · Cited by 12 · see citing works

DIS3 depletion in multiple myeloma causes extensive perturbation in cell cycle progression and centrosome amplification

Favasuli, V. K., Ronchetti, D., Silvestris, I., Puccio, N., Fabbiano, G., Traini, V., Todoerti, K., Erratico, S., Ciarrocchi, A., Fragliasso, V., et al. (2023) · Haematologica · doi:10.3324/haematol.2023.283274 · Cited by 11 · see citing works

RRP6 from Trypanosoma brucei: Crystal Structure of the Catalytic Domain, Association with EAP3 and Activity towards Structured and Non-Structured RNA Substrates

Barbosa, R. L., Legrand, P., Wien, F., Pineau, B., Thompson, A., & Guimarães, B. G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089138 · Cited by 10 · see citing works

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus

Fujiwara, N., Shigemoto, M., Hirayama, M., Fujita, K., Seno, S., Matsuda, H., Nagahama, M., & Masuda, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac559 · Cited by 10 · see citing works

Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates

Cesaro, G., da Soler, H. T., Guerra-Slompo, E. P., Haouz, A., Legrand, P., Zanchin, N. I. T., & Guimarães, B. G. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1199 · Cited by 10 · see citing works

Trypanosoma brucei RRP44 is involved in an early stage of large ribosomal subunit RNA maturation

Cesaro, G., Carneiro, F. R. G., Ávila, A. R., Zanchin, N. I. T., & Guimarães, B. G. (2018) · RNA Biology · doi:10.1080/15476286.2018.1564463 · Cited by 10 · see citing works

Substrate selectivity by the exonuclease Rrp6p

Axhemi, A. A., Wasmuth, E. V., Lima, C. D., & Jankowsky, E. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913236117 · Cited by 10 · see citing works

Proteomic Analysis of Yeast Mutant RNA Exosome Complexes

Lourenço, R. F., Leme, A. F. P., & Oliveira, C. C. (2013) · Journal of Proteome Research · doi:10.1021/pr400972x · Cited by 9 · see citing works

Genome-Wide Characterization of the RNA Exosome Complex in Relation to Growth, Development, and Pathogenicity of Fusarium graminearum

Yuan, Y., Mao, X., Abubakar, Y. S., Zheng, W., Wang, Z., Zhou, J., & Zheng, H. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05058-22 · Cited by 8 · see citing works

Деградация РНК в эукариотических клетках

Tatosyan, K. A., Ustyantsev, I. G., & Kramerov, D. A. (2020) · Molecular Biology · doi:10.31857/s0026898420040163 · Cited by 8 · see citing works

4D structural biology–quantitative dynamics in the eukaryotic RNA exosome complex

Liebau, J., Lazzaretti, D., Fürtges, T., Bichler, A., Pilsl, M., Rudack, T., & Sprangers, R. (2025) · Nature Communications · doi:10.1038/s41467-025-62982-6 · Cited by 7 · see citing works

Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast

Greenlaw, A. C., Alavattam, K. G., & Tsukiyama, T. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1147 · Cited by 7 · see citing works

Purification of Eukaryotic Exoribonucleases Following Heterologous Expression in Bacteria and Analysis of Their Biochemical Properties by In Vitro Enzymatic Assays

Tomecki, R., Drążkowska, K., Krawczyk, A. O., Kowalska, K. J., & Dziembowski, A. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-2214-7_25 · Cited by 7 · see citing works

Experimental analysis of co-evolution within protein complexes: The yeast exosome as a model

Sandler, I., Medalia, O., & Aharoni, A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24360 · Cited by 7 · see citing works

RNA substrate length as an indicator of exosome interactions in vivo

Delan‐Forino, C., Schneider, C., & Tollervey, D. W. (2017) · Wellcome Open Research · doi:10.12688/wellcomeopenres.10724.2 · Cited by 6 · see citing works

Characterization of the Catalytic Subunits of the RNA Exosome‐like Complex in Plasmodium falciparum

Jiang, N., Yu, S., Yang, N., Feng, Y., Sang, X., Wang, Y., Wahlgren, M., & Chen, Q. (2018) · Journal of Eukaryotic Microbiology · doi:10.1111/jeu.12625 · Cited by 5 · see citing works

Assembly of multicomponent machines in RNA metabolism: A common theme in mRNA decay pathways

de Amorim, A. M., & Chakrabarti, S. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1684 · Cited by 5 · see citing works

Regulation of Toxic RNA Foci and Mutant DMPK Transcripts: Role of MBNL Proteins and RNA Decay PathwaysPreprint

Xing, X., Márkus, R., Ghosh, T., Buxton, S., Nieves, D. J., Wojciechowska, M., & Brook, J. D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.28.559487 · Cited by 5 · see citing works

A Comparative Overview of the Role of Human Ribonucleases in Nonsense-Mediated mRNA Decay

da Costa, P. J., Menezes, J., Guedes, R., Reis, F. P., Teixeira, A., Saramago, M., Viegas, S. C., Arraiano, C. M., & Romão, L. (2024) · Genes · doi:10.3390/genes15101308 · Cited by 4 · see citing works

Reconstitution of the Human Nuclear RNA Exosome

Januszyk, K., Weick, E., & Lima, C. D. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9822-7_23 · Cited by 4 · see citing works

mRNA Decay Pathways Use Translation Fidelity and Competing Decapping Complexes for Substrate Selection

Celik, A. (2017) · eScholarship@UMassChan · doi:10.13028/m2h38v · Cited by 4 · see citing works

mRNA Degradation and Decay

Fromont‐Racine, M., & Saveanu, C. (2014) · Springer eBooks · doi:10.1007/978-3-319-05687-6_7 · Cited by 4 · see citing works

New insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

Neto, V. G., Cepeda, L. P. P., Queiroz, B. R. S., Cantaloube, S., Léger‐Silvestre, I., Mangeat, T., Albert, B., Gadal, O., & Oliveira, C. C. (2025) · Molecular Biology of the Cell · doi:10.1091/mbc.e25-02-0078 · Cited by 3 · see citing works

Current insight into the role of mRNA decay pathways in fungal pathogenesis

Firdous, Z., Kalra, S., Chattopadhyay, R., & Bari, V. K. (2024) · Microbiological Research · doi:10.1016/j.micres.2024.127671 · Cited by 2 · see citing works

Polyadenylated versions of small non-coding RNAs in Saccharomyces cerevisiae are degraded by Rrp6p/Rrp47p independent of the core nuclear exosome

Chaudhuri, A., Paul, S., Banerjea, M., & Das, B. (2024) · Microbial Cell · doi:10.15698/mic2024.05.823 · Cited by 2 · see citing works

EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery

Wijeratne, H. R. S., Runnebohm, A. M., Barron, M. P., Hampton, A. J., Li, R., Peck Justice, S. A., Lenceski, S. H., Rooney, J. D., Smith-Kinnaman, W. R., Chang, G. S., et al. (2026) · doi:10.64898/2026.01.26.701775 · Cited by 1 · see citing works

Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts

Weick, E., Zinder, J. C., & Lima, C. D. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9822-7_20 · Cited by 1 · see citing works

AtSIEK, an EXD1-like protein with KH domain, involves in salt stress response by interacting with FRY2/CPL1

Zhang, X., Xie, Q., Xiang, L., Lei, Z., Huang, Q., Zhang, J., Cai, M., & Chen, T. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.123369 · Cited by 2 · see citing works

Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins

Zinder, J. C., & Lima, C. D. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9822-7_21 · Cited by 1 · see citing works

The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139

Bonneau, F., Ebert, J., Lorentzen, E., & Conti, E. (2009)

The eukaryotic RNA exosome

Januszyk, K., & Lima, C. D. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.01.011 · Cited by 199 · see citing works

The RNA exosome complex central channel controls both exonuclease and endonuclease Dis3 activities in vivo and in vitro

Drążkowska, K., Tomecki, R., Stoduś, K., Kowalska, K., Czarnocki-Cieciura, M., & Dziembowski, A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt060 · Cited by 60 · see citing works

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation

Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E., & Conti, E. (2009) · Cell · doi:10.1016/j.cell.2009.08.042 · Cited by 245 · see citing works

The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome

Wasmuth, E. V., & Lima, C. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1152 · Cited by 55 · see citing works