2021 Breakthrough Articles

Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs

Yuri V Svitkin, Anne-Claude Gingras, and Nahum Sonenberg

Nucleic Acids Research, gkab1241, https://doi.org/10.1093/nar/gkab1241

Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor

Prajwal Karki, Travis D Carney, Cristina Maracci, Andriy S Yatsenko, Halyna R Shcherbata, and Marina V Rodnina

Nucleic Acids Research, gkab1189, https://doi.org/10.1093/nar/gkab1189

Using a quadruplet codon to expand the genetic code of an animal

Zhiyan Xi, Lloyd Davis, Kieran Baxter, Ailish Tynan, Angeliki Goutou, Sebastian Greiss

Nucleic Acids Research, gkab1168, https://doi.org/10.1093/nar/gkab1168

Sensory neuron transcriptomes reveal complex neuron-specific function and regulation of mec-2/Stomatin splicing

Xiaoyu Liang, Canyon Calovich-Benne, Adam Norris

Nucleic Acids Research, gkab1134, https://doi.org/10.1093/nar/gkab1134

RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis

Florian Richter, Johanna E Plehn, Larissa Bessler, Jasmin Hertler, Marko Jörg, Cansu Cirzi, Francesca Tuorto, Kristina Friedland, and Mark Helm

Nucleic Acids Research, gkab1150, https://doi.org/10.1093/nar/gkab1150

Formation and persistence of polyglutamine aggregates in mistranslating cells

Jeremy T Lant, Rashmi Kiri, Martin L Duennwald, and Patrick O’Donoghue

Nucleic Acids Research, Volume 49, Issue 20, 18 November 2021, Pages 11883–11899, https://doi.org/10.1093/nar/gkab898

RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids

Hyunjee Lee, HyeokJin Cho, Jooyoung Kim, Sua Lee, Jungmin Yoo, Daeho Park, and Gwangrog Lee

Nucleic Acids Research, gkab1064, https://doi.org/10.1093/nar/gkab1064

Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA

Alexander M Price, Robert T Steinbock, Chao Di, Katharina E Hayer, Yize Li, Christin Herrmann, Nicholas A Parenti, Jillian N Whelan, Susan R Weiss, and Matthew D Weitzman

Nucleic Acids Research, gkab896, https://doi.org/10.1093/nar/gkab896

Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome

Keisuke Oki, Mariko Nagata, Takeshi Yamagami, Tomoyuki Numata, Sonoko Ishino, Takuji Oyama, and Yoshizumi Ishino

Nucleic Acids Research, gkab799, https://doi.org/10.1093/nar/gkab799

Pathways of thymidine hypermodification

Yan-Jiun Lee, Nan Dai, Stephanie I Müller, Chudi Guan, Mackenzie J Parker, Morgan E Fraser, Shannon E Walsh, Janani Sridar, Andrew Mulholland, Krutika Nayak, Zhiyi Sun, Yu-Cheng Lin, Donald G Comb, Katherine Marks, Reyaz Gonzalez, Daniel P Dowling, Vahe Bandarian, Lana Saleh, Ivan R Corrêa, Jr, and Peter R Weigele

Nucleic Acids Research, gkab1064, https://doi.org/10.1093/nar/gkab1064

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit

Masahiko Okuda, Tetsufumi Suwa, Hidefumi Suzuki, Yuki Yamaguchi, and Yoshifumi Nishimura

Nucleic Acids Research, Volume 50, Issue 1, 11 January 2022, Pages 1–16, https://doi.org/10.1093/nar/gkab612

Mapping yeast mitotic 5′ resection at base resolution reveals the sequence and positional dependence of nucleases in vivo

Dominic Bazzano, Stephanie Lomonaco, and Thomas E Wilson

Nucleic Acids Research, Volume 49, Issue 22, 16 December 2021, Pages 12607–12621, https://doi.org/10.1093/nar/gkab597

Engineering large-scale chromosomal deletions by CRISPR-Cas9

Thomas F Eleveld, Chaimaa Bakali, Paul P Eijk, Phylicia Stathi, Lianne E Vriend, Pino J Poddighe, and Bauke Ylstra

Nucleic Acids Research, Volume 49, Issue 21, 2 December 2021, Pages 12007–12016, https://doi.org/10.1093/nar/gkab557

Directed evolution of orthogonal RNA–RBP pairs through library-vs-library in vitro selection

Keisuke Fukunaga, and Yohei Yokobayashi

Nucleic Acids Research, Volume 50, Issue 2, 25 January 2022, Pages 601–616, https://doi.org/10.1093/nar/gkab527

High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification

Ken-ichiro Matsunaga, Michiko Kimoto, Vanessa Weixun Lim, Hui Pen Tan, Yu Qian Wong, William Sun, Shawn Vasoo, Yee Sin Leo, and Ichiro Hirao

Nucleic Acids Research, Volume 49, Issue 20, 18 November 2021, Pages 11407–11424, https://doi.org/10.1093/nar/gkab515

The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast

Timothy Hoggard, Allison J Hollatz, Rachel E Cherney, Melissa R Seman, and Catherine A Fox

Nucleic Acids Research, Volume 49, Issue 18, 11 October 2021, Pages 10207–10220, https://doi.org/10.1093/nar/gkab450

RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

Charu Mehta, Isabela Fraga de Andrade, Daniel R Matson, Colin N Dewey, and Emery H Bresnick

Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9007–9025, https://doi.org/10.1093/nar/gkab367

Uniform affinity-tuning of N-methyl-aminoacyl-tRNAs to EF-Tu enhances their multiple incorporation

Yoshihiko Iwane, Hiroyuki Kimura, Takayuki Katoh, and Hiroaki Suga

Nucleic Acids Research, Volume 49, Issue 19, 8 November 2021, Pages 10807–10817, https://doi.org/10.1093/nar/gkab288

Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes

Tatsuya Yoneji, Hironobu Fujita, Takahito Mukai, and Masayuki Su’etsugu

Nucleic Acids Research, Volume 49, Issue 15, 7 September 2021, Pages 8407–8418, https://doi.org/10.1093/nar/gkab298

NMR solution structures of Runella slithyformis RNA 2′-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity

Sébastien Alphonse, Ankan Banerjee, Swathi Dantuluri, Stewart Shuman, and Ranajeet Ghose

Nucleic Acids Research, Volume 49, Issue 17, 27 September 2021, Pages 9607–9624, https://doi.org/10.1093/nar/gkab241

Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids

Romain Durand, Kévin T Huguet, Nicolas Rivard, Nicolas Carraro, Sébastien Rodrigue, and Vincent Burrus

Nucleic Acids Research, Volume 49, Issue 14, 20 August 2021, Pages 7807–7824, https://doi.org/10.1093/nar/gkab204

microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development

Vinay K Mayya, Mathieu N Flamand, Alice M Lambert, Seyed Mehdi Jafarnejad, James A Wohlschlegel, Nahum Sonenberg, and Thomas F Duchaine

Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4803–4815, https://doi.org/10.1093/nar/gkab162

Identification and structural analysis of the Schizosaccharomyces pombe SMN complex

Jyotishman Veepaschit, Aravindan Viswanathan, Rémy Bordonné, Clemens Grimm, and Utz Fischer

Nucleic Acids Research, Volume 49, Issue 13, 21 July 2021, Pages 7207–7223, https://doi.org/10.1093/nar/gkab158

SIRT3 consolidates heterochromatin and counteracts senescence

Zhiqing Diao, Qianzhao Ji, Zeming Wu, Weiqi Zhang, Yusheng Cai, Zehua Wang, Jianli Hu, Zunpeng Liu, Qiaoran Wang, Shijia Bi, Daoyuan Huang, Zhejun Ji, Guang-Hui Liu, Si Wang, Moshi Song, and Jing Qu

Nucleic Acids Research, Volume 49, Issue 8, 7 May 2021, Pages 4203–4219, https://doi.org/10.1093/nar/gkab161

The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover

Julian Grützner, Fabian Billenkamp, Daniel-Timon Spanka, Tim Rick, Vivian Monzon, Konrad U Förstner, and Gabriele Klug

Nucleic Acids Research, Volume 49, Issue 6, 6 April 2021, Pages 3003–3019, https://doi.org/10.1093/nar/gkab146

Tandem RNA binding sites induce self-association of the stress granule marker protein TIA-1

Fionna E Loughlin, Danella L West, Menachem J Gunzburg, Saboora Waris, Simon A Crawford, Matthew C J Wilce, and Jacqueline A Wilce

Nucleic Acids Research, Volume 49, Issue 5, 18 March 2021, Pages 2403–2417, https://doi.org/10.1093/nar/gkab080

Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

David A Garcia, Gregory Fettweis, Diego M Presman, Ville Paakinaho, Christopher Jarzynski, Arpita Upadhyaya, and Gordon L Hager

Nucleic Acids Research, Volume 49, Issue 12, 9 July 2021, Pages 6605–6620, https://doi.org/10.1093/nar/gkab072

Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences

Agnes Karasik, Grant D Jones, Andrew V DePass, and Nicholas R Guydosh

Nucleic Acids Research, Volume 49, Issue 11, 21 June 2021, Pages 6007–6026, https://doi.org/10.1093/nar/gkab036