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Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana Jonathan Cahn , James P.B. Lloyd , Ino D. Karemaker , Pascal W.T.C. Jansen , Jahnvi Pflueger...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
....trono@epfl.chAbstractKrüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...ISWI1 complex proteins facilitate developmental editing in Paramecium Aditi Singh1,5, Lilia Häußermann1,5, Christiane Emmerich1, Emily Nischwitz2, Brandon K.B. Seah1, Falk Butter2,3, Mariusz Nowacki4 and Estienne C. Swart1 1Max Planck Institute for Biology, 72076 Tübingen, Germany; 2Institute...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and evolution Kai Otsuka1,2, Akihiko Sakashita3,4, So Maezawa2, Richard M. Schultz1,5 and Satoshi H. Namekawa1,3 1Department of Microbiology and Molecular Genetics, University of California, Davis...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...-SBP–tagged fusion proteins (top left) were purified and incubated with barcoded RNA selection ligands. RNA ligands bound by the proteins were recovered by RT-PCR, followed by in vitro transcription to generate the RNA for the next cycle of SELEX (middle left). The procedure was repeated at least three...
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Resource: Human proteins that interact with RNA/DNA hybrids
- Isabel X. Wang,
- Christopher Grunseich,
- Jennifer Fox,
- Joshua Burdick,
- Zhengwei Zhu,
- Niema Ravazian,
- Markus Hafner,
- and Vivian G. Cheung
Genome Res. September 2018 28: 1405-1414; Published in Advance August 14, 2018, doi:10.1101/gr.237362.118
..., is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions...
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...) slows down translation elongation rate; and (3) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon activation. We identified trans-factors by profiling RNA–protein interactions and found that poly(U)-binding proteins are preferentially associated with 3′ UTR sequences and stabilizing motifs. We show...
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Research: Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins
- Eric T. Wang,
- Amanda J. Ward,
- Jennifer M. Cherone,
- Jimena Giudice,
- Thomas T. Wang,
- Daniel J. Treacy,
- Nicole J. Lambert,
- Peter Freese,
- Tanvi Saxena,
- Thomas A. Cooper,
- and Christopher B. Burge
Genome Res. June 2015 25: 858-871; Published in Advance April 16, 2015, doi:10.1101/gr.184390.114
...Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins Eric T. Wang 1 , 2 , Amanda J. Ward 2 , 3 , Jennifer M. Cherone 1 , Jimena Giudice 3 , Thomas T. Wang 1 , 6 , Daniel J. Treacy 1 , Nicole J...
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