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Enhancing Nuclear Receptor-Induced Transcription Requires Nuclear Motor and LSD1-Dependent Gene Networking in Interchromatin Granules

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Enhancing Nuclear Receptor-Induced Transcription Requires Nuclear Motor and LSD1-Dependent Gene Networking in Interchromatin Granules Corrections BIOCHEMISTRY Correction for “Enhancing nuclear receptor-induced transcrip- Sci USA (105:19199–19204; first published December 3, 2008; tion requires nuclear motor and LSD1-dependent gene net- 10.1073/pnas.0810634105). working in interchromatin granules,” by Qidong Hu, Young-Soo The authors wish to note, “The legend of Fig. 2B should Kwon, Esperanza Nunez, Maria Dafne Cardamone, Kasey R. state that the experiment was performed in HMEC cells, rather Hutt, Kenneth A. Ohgi, Ivan Garcia-Bassets, David W. Rose, than in MCF7 cells, similar to the confirmatory experiment Christopher K. Glass, Michael G. Rosenfeld, and Xiang-Dong Fu, presented in Fig. 2C.” The figure and its corrected legend which appeared in issue 49, December 9, 2008, of Proc Natl Acad appear below. Fig. 2. Rapid induction of interchromosomal interactions by nuclear hormone signaling. (A) 3D-FISH confirmation of E2-induced (60 min) TFF1:GREB1 in- terchromosomal interactions in HMECs with the distribution of loci distances measured (box plot with scatter plot) and quantification of colocalization (bar graph) before and after E2 treatment. Cells exhibiting mono- or biallelic interactions were combined for comparison with cells showing no colocalization; statistical sig- nificance in the bar graph was determined by χ2 test (**, P < 0.001). (B) 2D FISH confirmation of the interchromosomal interactions in HMEC cells by combining chromosome paint (aqua) and specific DNA probes (green and red). (Upper) Illustrates two examples of mock-treated cells. (Lower) Shows the biallelic interactions/ nuclear reorganization after E2 treatment for 60 min, exhibiting kissing events between chromosome 21 and chromosome 2. (C) Similar analysis on HMECs, but in this case using 3D FISH to paint chromosome 2 (red) and chromosome 21 (green), showing E2-induced chromosome 2–chromosome 21 interaction. Both assays revealed neither chromosome 21–chromosome 21 nor chromosome 2–chromosome 2 interactions in response to E2. (D) Temporal kinetics of GREB1:TFF1 interactions 2 by 3D FISH in HMECs (**, P < 0.001 by χ ). (E–G) Nuclear microinjection of siRNA against ERα, CBP/p300,orSRC1/pCIP prevented E2-induced interchromosomal interactions, counting both mono- and biallelic interactions (**, P < 0.001 by χ2). The injection of siER and siDLC1 were done in the same experiment, sharing the same control group. (H) Nuclear microinjection of siRNA against LSD1, which was shown to be required for estrogen-induced gene expression (22), did not block E2-induced interchromosomal interactions. The injection of siLSD1 and SRC1/pCIP were done in a single experiment, sharing the same control group. www.pnas.org/cgi/doi/10.1073/pnas.1400054111 2046–2047 | PNAS | February 4, 2014 | vol. 111 | no. 5 www.pnas.org Downloaded by guest on September 28, 2021 BIOCHEMISTRY IMMUNOLOGY Update to Correction for “Confinement of caspase-12 proteolytic Correction for “MicroRNA-directed program of cytotoxic CD8+ activity to autoprocessing,” by Sophie Roy, Jeffrey R. Sharom, T-cell differentiation,” by Sara Trifari, Matthew E. Pipkin, Caroline Houde, Thomas P. Loisel, John P. Vaillancourt, Wei Hozefa S. Bandukwala, Tarmo Äijö, Jed Bassein, Runqiang Shao, Maya Saleh, and Donald W. Nicholson, which appeared in Chen, Gustavo J. Martinez, and Anjana Rao, which appeared issue 11, March 18, 2008, of Proc Natl Acad Sci USA (105:4133– in issue 46, November 12, 2013, of Proc Natl Acad Sci USA 4138; first published March 10, 2008; 10.1073/pnas.0706658105). (110:18608–18613; first published October 25, 2013; 10.1073/ The authors wish to note: “We recently published corrections pnas.1317191110). to two articles that describe the functional role (1) and enzy- The authors note that the accession number for the GEO mology (2) of caspase-12. The figures in these two articles have database is GSE51393. been thoroughly investigated by a committee at McGill Univer- sity. With regard to Fig. 6 in the article in PNAS, two findings www.pnas.org/cgi/doi/10.1073/pnas.1400120111 were determined: First, that republication of the data was a consequence of miscommunication among co-authors working in different locations, and second, that the molecular weight markers were unintentionally mislabeled. The latter issue has recently been corrected (3). The former issue has recently been MEDICAL SCIENCES, ENGINEERING rectified because figure 4 of the Nature article was replaced with Correction for “Generation of functionally competent and du- a de novo independent experiment (4). Interpretation of the rable engineered blood vessels from human induced pluripotent experiment and the conclusions of both the PNAS article and the stem cells,” by Rekha Samuel, Laurence Daheron, Shan Liao, Nature article are unaffected by these changes. The authors Trupti Vardam, Walid S. Kamoun, Ana Batista, Christa Buecker, apologize for any confusion.” Richard Schäfer, Xiaoxing Han, Patrick Au, David T. Scadden, Dan G. Duda, Dai Fukumura, and Rakesh K. Jain, which appeared in issue 31, July 30, 2013, of Proc Natl Acad Sci USA (110:12774– 1. Saleh M, et al. (2006) Enhanced bacterial clearance and sepsis resistance in caspase-12- deficient mice. Nature 440(7087):1064–1068. 12779; first published July 16, 2013; 10.1073/pnas.1310675110). 2. Roy S, et al. (2008) Confinement of caspase-12 proteolytic activity to autoprocessing. The authors note that the following statement should be Proc Natl Acad Sci USA 105(11):4133–4138. added to the Acknowledgments: “This work is in part supported 3. Roy S, et al. (2013) Correction: Confinement of caspase-12 proteolytic activity to au- by Department of Defense (DoD) Breast Cancer Research In- toprocessing. Proc Natl Acad Sci USA 110(12):4852. ” 4. Saleh M, et al. (2013) Corrigendum: Enhanced bacterial clearance and sepsis resistance novator Award W81XWH-10-1-0016 (to R.K.J.). in caspase-12-deficient mice. Nature, 10.1038/nature12181. www.pnas.org/cgi/doi/10.1073/pnas.1400494111 www.pnas.org/cgi/doi/10.1073/pnas.1323789111 CORRECTIONS PNAS | February 4, 2014 | vol. 111 | no. 5 | 2047 Downloaded by guest on September 28, 2021 Editorial Expression of Concern and Correction BIOCHEMISTRY NEUROSCIENCE PNAS is publishing an Editorial Expression of Concern regarding Correction for “When recognition memory is independent of the following article: “Enhancing nuclear receptor-induced tran- hippocampal function,” by Christine N. Smith, Annette Jeneson, scription requires nuclear motor and LSD1-dependent gene Jennifer C. Frascino, C. Brock Kirwan, Ramona O. Hopkins, and networking in interchromatin granules,” by Qidong Hu, Young-Soo Larry R. Squire, which appeared in issue 27, July 8, 2014, of Proc Kwon, Esperanza Nunez, Maria Dafne Cardamone, Kasey R. Natl Acad Sci USA (111:9935–9940; first published June 23, Hutt, Kenneth A. Ohgi, Ivan Garcia-Bassets, David W. Rose, 2014; 10.1073/pnas.1409878111). Christopher K. Glass, Michael G. Rosenfeld, and Xiang-Dong Fu, The authors note that the following statement should be added which appeared in issue 49, December 9, 2008, of Proc Natl as a new Acknowledgments section: “We thank Erin Light, Ashley Acad Sci USA (105:19199–19204; first published December 3, Knutson, Kristin Mauldin, John Wixted, and Flora Suh for assis- 2008; 10.1073/pnas.0810634105). tance. This work was supported by the Medical Research Service The editors note that in January 2014, upon the authors’ re- of the Department of Veteran Affairs, the National Institute of quest, PNAS published a correction to three figures in this ar- Mental Health Grant MH24600, and National Science Founda- ticle. Subsequent to the publication of the correction, the editors tion (NSF) Grant SMA-1041755 to the Temporal Dynamics of received concerns regarding images appearing in two of the Learning Center, an NSF Science of Learning Center. We also corrected figures (Fig. 2B and Fig. S2) when compared with the acknowledge the University of Bern face images database and face data in the retracted Cell paper (1). In this regard, the authors images from the Massachusetts Institute of Technology and the B ” note that the images in both the corrected Fig. 2 and Fig. S2 cor- Center for Biological and Computational Learning. CORRECTION respond to specific cells saved from large, multi-nuclei–containing photographic images. The authors note that this image-to-cell www.pnas.org/cgi/doi/10.1073/pnas.1415194111 correspondence indicates that the incorrect cells shown in the retracted Cell paper resulted from errors in image processing. However, the original microscopy data is no longer available to further verify the accuracy of the images in question. Inder M. Verma Editor-in-Chief 1. Nunez E, et al. (2008) Nuclear receptor-enhanced transcription requires motor- and LSD1-dependent gene networking in interchromatin granules. Cell 132(6):996–1010, and retraction (2008) 134(1):189. www.pnas.org/cgi/doi/10.1073/pnas.1415649111 www.pnas.org PNAS | September 9, 2014 | vol. 111 | no. 36 | 13241 Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules Qidong Hua,1, Young-Soo Kwonb,1, Esperanza Nuneza,c,1, Maria Dafne Cardamonea,d, Kasey R. Hutta,e, Kenneth A. Ohgia, Ivan Garcia-Bassetsa, David W. Rosef, Christopher K. Glassb, Michael G. Rosenfelda,2, and Xiang-Dong Fub,2 aDepartment of Medicine, Howard Hughes Medical Institute, bDepartment of Cellular and Molecular Medicine, cBiomedical Sciences Graduate Program, eBioinformatics Graduate Program, fDepartment of Medicine, Division of Endocrinology and Metabolism,
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