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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...(Supplemental Fig. S15). Fractionation purity was verified by western blotting (Fig. 7E) and qRT-PCR (Fig. 7F), and stringent DNase-treatment ensured that plasmid DNA made negligible contributions to our results (Supplemental Fig. S16).With this setup, we compared the nuclear/cytoplasmic localization of lnc...
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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
...but not to the corresponding dsDNA. These include several members of the nuclear exosomes such as DIS3L, EXOSC3, and EXOSC6. In addition, there are 350 proteins that favor the hybrid forms of BAMBI and DPP9 compared to the corresponding dsDNA. We validated the affinity of some of these proteins to RNA/DNA hybrids versus dsDNA...
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LETTER: Evolution of base-substitution gradients in primate mitochondrial genomes
- Sameer Z. Raina,
- Jeremiah J. Faith,
- Todd R. Disotell,
- Hervé Seligmann,
- Caro-Beth Stewart,
- and David D. Pollock
Genome Res. May 2005 15: 665-673; doi:10.1101/gr.3128605
.... Evol. 17 : 1776 –1788. Raaum, R.L., Sterner, K.N., Noviello, C.M., Stewart, C.-B., and Disotell, T.R. 2005 . Catarrhine primate divergence dates estimated from complete mitochondrial s: Concordance with fossil and nuclear DNA evidence. J. Hum. Evol. (in press). ↵ Ray, D.A., Xing, J., Hedges, D.J., Hall...
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Letter: Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus
- Adam Monier,
- António Pagarete,
- Colomban de Vargas,
- Michael J. Allen,
- Betsy Read,
- Jean-Michel Claverie,
- and Hiroyuki Ogata
Genome Res. August 2009 19: 1441-1449; Published in Advance May 18, 2009, doi:10.1101/gr.091686.109
.... Methods Mol Biol 132: 365–386. Schroeder DC, Oke J, Malin G, Wilson WH. 2002. Coccolithovirus (Phycodnaviridae): Characterisation of a new large dsDNA algal virus that infects Emiliana huxleyi. Arch Virol 147: 1685–1698. Siskind LJ. 2005. Mitochondrial ceramide and the induction of apoptosis. J Bioenerg...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...of electrophoretic mobility shift assays (EMSA) (Hellman and Fried 2007). In an EMSA, labeled probes corresponding to the DNA of interest are synthesized or isolated and are consequently incubated with a purified protein of interest or with a mixture of proteins (e.g., a nuclear extract). To determine if direct...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...) by technical advances that move beyond the comparative analyses of linear DNA sequences alone. These include chromosome conformation capture (3C) techniques and derivatives (including Hi-C), which enhance our understanding of the three-dimensional (3D) organization of s (Lieberman-Aiden et al. 2009; Rao et al...
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Research: A-to-I RNA editing promotes developmental stage–specific gene and lncRNA expression
- Boaz Goldstein,
- Lily Agranat-Tamir,
- Dean Light,
- Orna Ben-Naim Zgayer,
- Alla Fishman,
- and Ayelet T. Lamm
Genome Res. March 2017 27: 462-470; Published in Advance December 28, 2016, doi:10.1101/gr.211169.116
...are expected to be RNA editing sites (Fig. 2A,B). The sequences were aligned to the and not to the cDNA to maximize information and eliminate biases; therefore, editing in transcripts that are transcribed in antisense to the reference were represented as T-to-C changes. Overall, we found 15,139 RNA editing...
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Research: nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
- Valentina Gandin,
- Laia Masvidal,
- Laura Hulea,
- Simon-Pierre Gravel,
- Marie Cargnello,
- Shannon McLaughlan,
- Yutian Cai,
- Preetika Balanathan,
- Masahiro Morita,
- Arjuna Rajakumar,
- Luc Furic,
- Michael Pollak,
- John A. Porco, Jr.,
- Julie St-Pierre,
- Jerry Pelletier,
- Ola Larsson,
- and Ivan Topisirovic
Genome Res. May 2016 26: 636-648; Published in Advance March 16, 2016, doi:10.1101/gr.197566.115
...by changes in mitochondrial functions mTORC1/EIF4EBP1/EIF4E axis bolsters mitochondrial biogenesis and ATP production by stimulating translation of nuclear-encoded mRNAs with mitochondrial functions, including respiratory chain components, e.g., ATP5O (Morita et al. 2013). Here, nanoCAGE identified a subset...
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LETTER: Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage
- Belen Hurle,
- Willie Swanson,
- NISC Comparative Sequencing Program,
- and Eric D. Green
Genome Res. March 2007 17: 276-286; Published in Advance January 31, 2007, doi:10.1101/gr.6004607
...of variation, which is suggestive of a selective sweep ( Schwartz et al. 2003b ; Hinds et al. 2005 ) Some of these regions are particularly large, encompassing as much as a megabase of DNA and containing up to 16 genes ( Carlson et al. 2005 ). While these regions are likely to contain at least one gene...
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Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
- Owen Thompson,
- Mark Edgley,
- Pnina Strasbourger,
- Stephane Flibotte,
- Brent Ewing,
- Ryan Adair,
- Vinci Au,
- Iasha Chaudhry,
- Lisa Fernando,
- Harald Hutter,
- Armelle Kieffer,
- Joanne Lau,
- Norris Lee,
- Angela Miller,
- Greta Raymant,
- Bin Shen,
- Jay Shendure,
- Jon Taylor,
- Emily H. Turner,
- LaDeana W. Hillier,
- Donald G. Moerman,
- and Robert H. Waterston
Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
...correlation in rDNA and 5S repeat number, but no correlation for either of these repeats to the telomere repeat number. We also failed to find any mutant genes overrepresented in the extreme strains. Alterations in the mitochondria encoded The mitochondrial in C. elegans is 13,794 nucleotides (nt) in length...
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