PMC Links for GEO Profiles (Select 122760349) - PMC

Select item 93807451.

A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation

Nele Hug, Stuart Aitken, Dasa Longman, Michaela Raab, Hannah Armes, Abigail R. Mann, Ana Rio-Machin, Jude Fitzgibbon, Kevin Rouault-Pierre, Javier F. Cáceres

RNA. 2022 Sep; 28(9): 1224–1238. doi: 10.1261/rna.079277.122

PMCID:: PMC9380745

Abstract Article PDF–6.0M

Select item 92626142.

A dual-activity topoisomerase complex regulates mRNA translation and turnover

Shuaikun Su, Yutong Xue, Alexei Sharov, Yongqing Zhang, Seung Kyu Lee, Jennifer L Martindale, Wen Li, Wai Lim Ku, Keji Zhao, Supriyo De, Weiping Shen, Payel Sen, Myriam Gorospe, Dongyi Xu, Weidong Wang

Nucleic Acids Res. 2022 Jul 8; 50(12): 7013–7033. Published online 2022 Jun 24. doi: 10.1093/nar/gkac538

PMCID:: PMC9262614

Abstract Article PDF–3.6M

Select item 82827643.

N6-methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation

Yuanming Cheng, Wei Xie, Brian F Pickering, Karen L Chu, Angela M Savino, Xuejing Yang, Hanzhi Luo, Diu TT Nguyen, Shanlan Mo, Ersilia Barin, Anthony Velleca, Thomas Rohwetter, Dinshaw J Patel, Samie R Jaffrey, Michael G Kharas

Cancer Cell. Author manuscript; available in PMC 2022 Jul 12.

Published in final edited form as: Cancer Cell. 2021 Jul 12; 39(7): 958–972.e8. Published online 2021 May 27. doi: 10.1016/j.ccell.2021.04.017

PMCID:: PMC8282764

Abstract Article PDF–3.4M

Select item 81650304.

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Edward L. Huttlin, Raphael J. Bruckner, Jose Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab, Melanie P. Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam, John Szpyt, Brandon M. Gassaway, Alexandra Panov, Hannah Parzen, Sipei Fu, Arvene Golbazi, Eila Maenpaa, Keegan Stricker, Sanjukta Guha Thakurta, Tian Zhang, Ramin Rad, Joshua Pan, David P. Nusinow, Joao A. Paulo, Devin K. Schweppe, Laura Pontano Vaites, J. Wade Harper, Steven P. Gygi

Cell. Author manuscript; available in PMC 2022 May 27.

Published in final edited form as: Cell. 2021 May 27; 184(11): 3022–3040.e28. Published online 2021 May 6. doi: 10.1016/j.cell.2021.04.011

PMCID:: PMC8165030

Abstract Article PDF–2.2M

Select item 80177205.

SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors

Ukhyun Jo, Yasuhisa Murai, Sirisha Chakka, Lu Chen, Ken Cheng, Junko Murai, Liton Kumar Saha, Lisa M. Miller Jenkins, Yves Pommier

Proc Natl Acad Sci U S A. 2021 Feb 9; 118(6): e2015654118. Published online 2021 Feb 3. doi: 10.1073/pnas.2015654118

PMCID:: PMC8017720

Abstract Article PDF–1.9M

Select item 77078356.

Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM

Andres López-Perrote, Nele Hug, Ana González-Corpas, Carlos F Rodríguez, Marina Serna, Carmen García-Martín, Jasminka Boskovic, Rafael Fernandez-Leiro, Javier F Caceres, Oscar Llorca

eLife. 2020; 9: e63042. Published online 2020 Nov 18. doi: 10.7554/eLife.63042

PMCID:: PMC7707835

Abstract Article PDF–2.9M

Select item 69420447.

Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity

Jae Jin Kim, Seo Yun Lee, Fade Gong, Anna M. Battenhouse, Daniel R. Boutz, Aarti Bashyal, Samantha T. Refvik, Cheng-Ming Chiang, Blerta Xhemalce, Tanya T. Paull, Jennifer S. Brodbelt, Edward M. Marcotte, Kyle M. Miller

Genes Dev. 2019 Dec 1; 33(23-24): 1751–1774. doi: 10.1101/gad.331231.119

PMCID:: PMC6942044

Abstract Article PDF–10M

Select item 66988038.

Paralog Studies Augment Gene Discovery: DDX and DHX Genes

Ingrid Paine, Jennifer E. Posey, Christopher M. Grochowski, Shalini N. Jhangiani, Sarah Rosenheck, Robert Kleyner, Taylor Marmorale, Margaret Yoon, Kai Wang, Reid Robison, Gerarda Cappuccio, Michele Pinelli, Adriano Magli, Zeynep Coban Akdemir, Joannie Hui, Wai Lan Yeung, Bibiana K.Y. Wong, Lucia Ortega, Mir Reza Bekheirnia, Tatjana Bierhals, Maja Hempel, Jessika Johannsen, René Santer, Dilek Aktas, Mehmet Alikasifoglu, Sevcan Bozdogan, Hatip Aydin, Ender Karaca, Yavuz Bayram, Hadas Ityel, Michael Dorschner, Janson J. White, Ekkehard Wilichowski, Saskia B. Wortmann, Erasmo B. Casella, Joao Paulo Kitajima, Fernando Kok, Fabiola Monteiro, Donna M. Muzny, Michael Bamshad, Richard A. Gibbs, V. Reid Sutton, University of Washington Center for Mendelian Genomics, Baylor-Hopkins Center for Mendelian Genomics, Telethon Undiagnosed Diseases Program, Hilde Van Esch, Nicola Brunetti-Pierri, Friedhelm Hildebrandt, Ariel Brautbar, Ignatia B. Van den Veyver, Ian Glass, Davor Lessel, Gholson J. Lyon, James R. Lupski

Am J Hum Genet. 2019 Aug 1; 105(2): 302–316. Published online 2019 Jun 27. doi: 10.1016/j.ajhg.2019.06.001

PMCID:: PMC6698803

Abstract Article PDF–2.3M

Select item 65945519.

PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling

Adnan Shami Shah, Alex G. Batrouni, Dongsung Kim, Amith Punyala, Wendy Cao, Chun Han, Michael L. Goldberg, Marcus B. Smolka, Jeremy M. Baskin

Cell Rep. Author manuscript; available in PMC 2019 Jun 26.

Published in final edited form as: Cell Rep. 2019 May 14; 27(7): 2157–2170.e8. doi: 10.1016/j.celrep.2019.04.060

PMCID:: PMC6594551

Abstract Article PDF–1.4M

Select item 589141710.

Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc function

Jan B Heidelberger, Andrea Voigt, Marina E Borisova, Giuseppe Petrosino, Stefanie Ruf, Sebastian A Wagner, Petra Beli

EMBO Rep. 2018 Apr; 19(4): e44754. Published online 2018 Feb 21. doi: 10.15252/embr.201744754

PMCID:: PMC5891417

Abstract Article PDF–1.0M

Select item 567858111.

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello, Gracjan Michlewski

BMC Biol. 2017; 15: 105. Published online 2017 Nov 8. doi: 10.1186/s12915-017-0444-9

PMCID:: PMC5678581

Abstract Article PDF–3.2M

Select item 480585512.

Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways

Javier Rodriguez, Ruth Pilkington, Amaya Garcia Munoz, Lan K. Nguyen, Nora Rauch, Susan Kennedy, Naser Monsefi, Ana Herrero, Cormac T. Taylor, Alex von Kriegsheim

Cell Rep. 2016 Mar 22; 14(11): 2745–2760. Published online 2016 Mar 10. doi: 10.1016/j.celrep.2016.02.043

PMCID:: PMC4805855

Abstract Article PDF–4.6M

Select item 474301013.

The RNA helicase DHX34 functions as a scaffold for SMG1-mediated UPF1 phosphorylation

Roberto Melero, Nele Hug, Andrés López-Perrote, Akio Yamashita, Javier F. Cáceres, Oscar Llorca

Nat Commun. 2016; 7: 10585. Published online 2016 Feb 4. doi: 10.1038/ncomms10585

PMCID:: PMC4743010

Abstract Article PDF–3.3M

Select item 453457514.

The RNA Helicase DHX34 Activates NMD by Promoting a Transition from the Surveillance to the Decay-Inducing Complex

Nele Hug, Javier F. Cáceres

Cell Rep. 2014 Sep 25; 8(6): 1845–1856. Published online 2014 Sep 15. doi: 10.1016/j.celrep.2014.08.020

PMCID:: PMC4534575

Abstract Article PDF–2.5M

Select item 378316815.

DHX34 and NBAS form part of an autoregulatory NMD circuit that regulates endogenous RNA targets in human cells, zebrafish and Caenorhabditis elegans

Dasa Longman, Nele Hug, Marianne Keith, Corina Anastasaki, E. Elizabeth Patton, Graeme Grimes, Javier F. Cáceres

Nucleic Acids Res. 2013 Sep; 41(17): 8319–8331. Published online 2013 Jul 4. doi: 10.1093/nar/gkt585

PMCID:: PMC3783168

Abstract Article PDF–3.0M

Select item 347780416.

A Census of Human Soluble Protein Complexes

Pierre C. Havugimana, G. Traver Hart, Tamás Nepusz, Haixuan Yang, Andrei L. Turinsky, Zhihua Li, Peggy I. Wang, Daniel R. Boutz, Vincent Fong, Sadhna Phanse, Mohan Babu, Stephanie A. Craig, Pingzhao Hu, Cuihong Wan, James Vlasblom, Vaqaarun-Nisa Dar, Alexander Bezginov, Gregory W. Clark, Gabriel C. Wu, Shoshana J. Wodak, Elisabeth R.M. Tillier, Alberto Paccanaro, Edward M. Marcotte, Andrew Emili

Cell. Author manuscript; available in PMC 2013 Aug 31.

Published in final edited form as: Cell. 2012 Aug 31; 150(5): 1068–1081. doi: 10.1016/j.cell.2012.08.011

PMCID:: PMC3477804

Abstract Article PDF–7.7M

Select item 317805917.

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

Pascale Gaudet, Michael S. Livstone, Suzanna E. Lewis, Paul D. Thomas

Brief Bioinform. 2011 Sep; 12(5): 449–462. Published online 2011 Aug 27. doi: 10.1093/bib/bbr042

PMCID:: PMC3178059

Abstract Article PDF–1.0M

Select item 135612918.

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

Kouichi Kimura, Ai Wakamatsu, Yutaka Suzuki, Toshio Ota, Tetsuo Nishikawa, Riu Yamashita, Jun-ichi Yamamoto, Mitsuo Sekine, Katsuki Tsuritani, Hiroyuki Wakaguri, Shizuko Ishii, Tomoyasu Sugiyama, Kaoru Saito, Yuko Isono, Ryotaro Irie, Norihiro Kushida, Takahiro Yoneyama, Rie Otsuka, Katsuhiro Kanda, Takahide Yokoi, Hiroshi Kondo, Masako Wagatsuma, Katsuji Murakawa, Shinichi Ishida, Tadashi Ishibashi, Asako Takahashi-Fujii, Tomoo Tanase, Keiichi Nagai, Hisashi Kikuchi, Kenta Nakai, Takao Isogai, Sumio Sugano

Genome Res. 2006 Jan; 16(1): 55–65. doi: 10.1101/gr.4039406

PMCID:: PMC1356129

Abstract Article PDF–438K

Select item 13924119.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

Mammalian Gene Collection (MGC) Program Team

Proc Natl Acad Sci U S A. 2002 Dec 24; 99(26): 16899–16903. Published online 2002 Dec 11. doi: 10.1073/pnas.242603899

PMCID:: PMC139241

Abstract Article PDF–118K

Select item 1626720.

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags

Emmanuel Dias Neto, Ricardo Garcia Correa, Sergio Verjovski-Almeida, Marcelo R. S. Briones, Maria Aparecida Nagai, Wilson da Silva, Jr., Marco Antonio Zago, Silvana Bordin, Fernando Ferreira Costa, Gustavo Henrique Goldman, Alex F. Carvalho, Adriana Matsukuma, Gilson S. Baia, David H. Simpson, Adriana Brunstein, Paulo S. L. de Oliveira, Philipp Bucher, C. Victor Jongeneel, Michael J. O'Hare, Fernando Soares, Ricardo R. Brentani, Luis F. L. Reis, Sandro J. de Souza, Andrew J. G. Simpson

Proc Natl Acad Sci U S A. 2000 Mar 28; 97(7): 3491–3496. doi: 10.1073/pnas.97.7.3491

PMCID:: PMC16267

Abstract Article PDF–111K

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