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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...to this work. Corresponding author: john.rinn@colorado.eduAbstractMany essential cellular processes require RNA to interact with protein(s) to form ribonucleic protein complexes (RNPs). For example, all cellular proteins are produced by the ribosome, a large and stable RNP. Gene splicing requires...
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Research: Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method
- Koji Makanae,
- Reiko Kintaka,
- Takashi Makino,
- Hiroaki Kitano,
- and Hisao Moriya
Genome Res. February 2013 23: 300-311; Published in Advance December 28, 2012, doi:10.1101/gr.146662.112
...Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method Koji Makanae 1 , Reiko Kintaka 2 , Takashi Makino 3 , Hiroaki Kitano 4 , 5 , 6 and Hisao Moriya 1 , 7 1 Research...
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Research: Genome-wide uniformity of human ‘open’ pre-initiation complexes
- William K.M. Lai and
- B. Franklin Pugh
Genome Res. January 2017 27: 15-26; Published in Advance November 10, 2016, doi:10.1101/gr.210955.116
...location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...of Oxford, Oxford, OX1 3QU, United Kingdom; 3Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom Corresponding authors: cornelia.kilchert@chemie.bio.uni-giessen.de, lidia.vasilieva@bioch.ox.ac.ukAbstractLarge RNA-binding complexes play a central role...
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Research: Genome-wide activities of Polycomb complexes control pervasive transcription
- Hun-Goo Lee,
- Tatyana G. Kahn,
- Amanda Simcox,
- Yuri B. Schwartz,
- and Vincenzo Pirrotta
Genome Res. August 2015 25: 1170-1181; Published in Advance May 18, 2015, doi:10.1101/gr.188920.114
..., Ohio, USA Corresponding author: pirrotta@dls.rutgers.edu AbstractPolycomb group (PcG) complexes PRC1 and PRC2 are well known for silencing specific developmental genes. PRC2 is a methyltransferase targeting histone H3K27 and producing H3K27me3, essential for stable silencing. Less well known...
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Method: High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
- Marie-Odile Baudement,
- Axel Cournac,
- Franck Court,
- Marie Seveno,
- Hugues Parrinello,
- Christelle Reynes,
- Robert Sabatier,
- Tristan Bouschet,
- Zhou Yi,
- Sephora Sallis,
- Mathilde Tancelin,
- Cosette Rebouissou,
- Guy Cathala,
- Annick Lesne,
- Julien Mozziconacci,
- Laurent Journot,
- and Thierry Forné
Genome Res. November 2018 28: 1733-1746; Published in Advance October 4, 2018, doi:10.1101/gr.237073.118
...of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward -wide approach whereby we...
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Research: Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
- Daniel W. Hagey,
- Cécile Zaouter,
- Gaëlle Combeau,
- Monika Andersson Lendahl,
- Olov Andersson,
- Mikael Huss,
- and Jonas Muhr
Genome Res. July 2016 26: 908-917; Published in Advance May 2, 2016, doi:10.1101/gr.203513.115
..., which provide a steric hindrance to transcription factor binding (Iwafuchi-Doi and Zaret 2014). However, chromatin accessibility can also be increased in several ways, such as through shifting nucleosome positioning via ATP-dependent remodeling complexes (Boeger et al. 2003; Reinke and Hörz 2003...
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Method: Inferring chromatin-bound protein complexes from genome-wide binding assays
- Eugenia G. Giannopoulou and
- Olivier Elemento
Genome Res. August 2013 23: 1295-1306; Published in Advance April 3, 2013, doi:10.1101/gr.149419.112
...Inferring chromatin-bound protein complexes from genome-wide binding assays Eugenia G. Giannopoulou 1 , 2 and Olivier Elemento 1 , 2 , 3 1 HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell...
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METHODS: Interdigitated Deletion Complexes on Mouse Chromosome 5 Induced by Irradiation of Embryonic Stem Cells
- John C. Schimenti,
- Brian J. Libby,
- Rebecca A. Bergstrom,
- Lawriston A. Wilson,
- Dieter Naf,
- Lisa M. Tarantino,
- Alireza Alavizadeh,
- Andreas Lengeling,
- and Maja Bucan
Genome Res. July 1, 2000 10: 1043-1050; doi:10.1101/gr.10.7.1043
...Interdigitated Deletion Complexes on Mouse Chromosome 5 Induced by Irradiation of Embryonic Stem Cells John C. Schimenti 1 , 5 , Brian J. Libby 1 , Rebecca A. Bergstrom 1 , Lawriston A. Wilson 1 , Dieter Naf 1 , Lisa M. Tarantino 2...
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Letter: Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets
- Jean Hausser,
- Markus Landthaler,
- Lukasz Jaskiewicz,
- Dimos Gaidatzis,
- and Mihaela Zavolan
Genome Res. November 2009 19: 2009-2020; Published in Advance September 18, 2009, doi:10.1101/gr.091181.109
...Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets Jean Hausser 1 , 3 , Markus Landthaler 2 , 3 , 4 , Lukasz Jaskiewicz 1 , Dimos Gaidatzis 1 , 5...
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