Nakagawa Group
Original Research Papers
Komatsu, T., Yokoi, S., Mito, M., Fujii, K., Kimura, Y., Iwasaki, S. & Nakagawa, S. (2018) UPA-Seq: Prediction of Functional LncRNAs Using Differential Sensitivity to UV Crosslinking. RNA. in press
Mito, M., Kadota, M., Tanaka, K., Furuta, Y., Abe, K., Iwasaki, S. & Nakagawa, S. (2018) Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing. Sci Rep 8, 1143.
Sakaguchi T, Hasegawa, Y, Brockdorff, N, Tsutsui K, Tsutsui KM, Sado, T, and Nakagawa, S (2016) Control of chromosomal localization of Xist by hnRNP U family molecules. Dev Cell. i39:11-12
West, JA, Mito, M, Kurosaka, S, Takumi, T, Tanegashima, C, Chujo, T, Yanaka, K, Kingston, RE, Hirose, T, Bond, C, Fox, A, and Nakagawa, S (2016) Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol. 214: 817-830
Ip JY, Sone M, Nashiki C, Pan Q, Kitaichi K, Yanaka K, Abe T, Takao K, Miyakawa T, Blencowe BJ, Nakagawa S (2016) Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine. Sci Rep 6: 27204
Ishida K, Miyauchi K, Kimura Y, Mito M, Okada S, Suzuki T, Nakagawa S (2015) Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNA. Genes Cells 20: 887-901
Nakagawa S, Shimada M, Yanaka K, Mito M, Arai T, Takahashi E, Fujita Y, Fujimori T, Standaert L, Marine JC, Hirose T (2014) The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice. Development 141: 4618-27
Ishizuka A, Hasegawa Y, Ishida K, Yanaka K, Nakagawa S (2014) Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Genes Cells 19: 704-21
Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X, Hirose T, Prasanth KV. (2012) Malat1 is not an essential component of nuclear speckles in mice. RNA 18:1487-99
Nakagawa S, Naganuma T, Shioi G, Hirose T. (2011) Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol 193: 31-39
Tsuiji H, Yoshimoto R, Hasegawa Y, Furuno M, Yoshida M, Nakagawa S (2011) Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells 16: 479-90
Kubo F, Nakagawa S (2010) Cath6, a bHLH atonal family proneural gene, negatively regulates neuronal differentiation in the retina. Dev Dyn 239: 2492-500
Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S (2010) The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev Cell 19: 469-76
Suga A, Taira M, Nakagawa S (2009) LIM family transcription factors regulate the subtype-specific morphogenesis of retinal horizontal cells at post-migratory stages. Developmental biology 330: 318-28
Kubo F, Nakagawa S (2009) Hairy1 acts as a node downstream of Wnt signaling to maintain retinal stem cell-like progenitor cells in the chick ciliary marginal zone. Development 136: 1823-33
Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120: 2498-506
Tanabe K, Takahashi Y, Sato Y, Kawakami K, Takeichi M, Nakagawa S (2006) Cadherin is required for dendritic morphogenesis and synaptic terminal organization of retinal horizontal cells. Development 133: 4085-96
Kubo F, Takeichi M, Nakagawa S (2005) Wnt2b inhibits differentiation of retinal progenitor cells in the absence of Notch activity by downregulating the expression of proneural genes. Development 132: 2759-70
Tanabe K, Takeichi M, Nakagawa S (2004) Identification of a nonchordate-type classic cadherin in vertebrates: chicken Hz-cadherin is expressed in horizontal cells of the neural retina and contains a nonchordate-specific domain complex. Dev Dyn 229: 899-906
Nakagawa S, Takada S, Takada R, Takeichi M (2003) Identification of the laminar-inducing factor: Wnt-signal from the anterior rim induces correct laminar formation of the neural retina in vitro. Developmental biology 260: 414-25
Kubo F, Takeichi M, Nakagawa S (2003) Wnt2b controls retinal cell differentiation at the ciliary marginal zone. Development 130: 587-98
Nakagawa S, Brennan C, Johnson KG, Shewan D, Harris WA, Holt CE (2000) Ephrin-B regulates the Ipsilateral routing of retinal axons at the optic chiasm. Neuron 25: 599-610
Nakagawa S, Takeichi M (1998) Neural crest emigration from the neural tube depends on regulated cadherin expression. Development 125: 2963-71
Nakagawa S, Takeichi M (1997) N-cadherin is crucial for heart formation in the chick embryo. Dev Growth Differ 39: 451-5
Nakagawa S, Takeichi M (1995) Neural crest cell-cell adhesion controlled by sequential and subpopulation-specific expression of novel cadherins. Development 121: 1321-32
Collaborative studies
Yamazaki, T., Souquere, S., Chujo, T., Kobelke, S., Chong, Y.S., Fox, A.H., Bond, C.S., Nakagawa, S., Pierron, G. & Hirose, T. (2018) Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation. Mol Cell 70, 1038.
Lin, H., Miyauchi, K., Harada, T., Okita, R., Takeshita, E., Komaki, H., Fujioka, K., Yagasaki, H., Goto, Y.I., Yanaka, K., Nakagawa, S., Sakaguchi, Y. & Suzuki, T. CO2-sensitive tRNA modification associated with human mitochondrial disease. Nat Commun 9, 1875 (2018).
Gast, M., Rauch, B.H., Nakagawa, S., Haghikia, A., Jasina, A., Haas, J., Nath, N., Jensen, L., Stroux, A., Bohm, A., Friebel, J., Rauch, U., Skurk, C., Blankenberg, S., Zeller, T., Prasanth, K.V., Meder, B., Kuss, A., Landmesser, U. & Poller, W. (2018) Immune system-mediated atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in ApoE-/- mice. Cardiovasc Res.
Poller, W., Dimmeler, S., Heymans, S., Zeller, T., Haas, J., Karakas, M., Leistner, D.M., Jakob, P., Nakagawa, S., Blankenberg, S., Engelhardt, S., Thum, T., Weber, C., Meder, B., Hajjar, R. & Landmesser, U. (2017) Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J.
Mello, S.S., Sinow, C., Raj, N., Mazur, P.K., Bieging-Rolett, K., Broz, D.K., Imam, J.F.C., Vogel, H., Wood, L.D., Sage, J., Hirose, T., Nakagawa, S., Rinn, J. & Attardi, L.D.(2017) Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev 31, 1095-1108.
Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T. (2017) Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J. 36:1447-1462.
Quesnel-Vallière M,Dargaez Z, Irimia M, Gonatopoulos-Pournatzis T, Ip J, Wu M, Sterne-Weiler T, Nakagawa S, Woodin MA, Blencowe BJ, and Cordes SP (2016) Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders. Mol Cell 64(6):1023-1034
Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PW, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, van den Oord J, Nakagawa S, Hirose T, Sablina AA, Lambrechts D, Aerts S, Blanpain C, Marine JC. (2016) p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med. 22: 861-8.
Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV (2016) Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res 44: 2898-908
Peters T, Hermans-Beijnsberger S, Beqqali A, Bitsch N, Nakagawa S, Prasanth KV, de Windt LJ, van Oort RJ, Heymans S, Schroen B (2016) Long Non-Coding RNA Malat-1 Is Dispensable during Pressure Overload-Induced Cardiac Remodeling and Failure in Mice. PloS one 11: e0150236
Gast M, Schroen B, Voigt A, Haas J, Kuehl U, Lassner D, Skurk C, Escher F, Wang X, Kratzer A, Michalik K, Papageorgiou A, Peters T, Loebel M, Wilk S, Althof N, Prasanth KV, Katus H, Meder B, Nakagawa S et al. (2016) Long noncoding RNA MALAT1-derived mascRNA is involved in cardiovascular innate immunity. J Mol Cell Biol [open access]
Yamada N, Hasegawa Y, Yue M, Hamada T, Nakagawa S, Ogawa Y (2015) Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome. PLoS Genet 11: e1005430
Standaert L, Adriaens C, Radaelli E, Van Keymeulen A, Blanpain C, Hirose T, Nakagawa S, Marine JC (2014) The long noncoding RNA Neat1 is required for mammary gland development and lactation. RNA 20: 1844-9
Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H, Siomi MC (2014) Yb integrates piRNA intermediates and processing factors into perinuclear bodies to enhance piRISC assembly. Cell Rep 8: 103-13
Hirose T, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Benard M, Fox AH, Pierron G (2014) NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell 25: 169-83
Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM, Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, *Rubin MA. (2014) The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun 5: 5383
Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW, Nakagawa S, Rigo F, Taft RJ, Cairns MJ, Blackshaw S, Wolvetang EJ, Mattick JS (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular psychiatry 19: 486-94
Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T (2012) Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J.31:4020-34.
Redies C, Ast M, Nakagawa S, Takeichi M, Martinez-de-la-Torre M, Puelles L (2000) Morphologic fate of diencephalic prosomeres and their subdivisions revealed by mapping cadherin expression. J Comp Neurol 421: 481-514
Honjo Y, Nakagawa S, Takeichi M (2000) Blockade of cadherin-6B activity perturbs the distribution of PSD-95 family proteins in retinal neurones. Genes Cells 5: 309-18
Wohrn JC, Nakagawa S, Ast M, Takeichi M, Redies C (1999) Combinatorial expression of cadherins in the tectum and the sorting of neurites in the tectofugal pathways of the chicken embryo. Neuroscience 90: 985-1000
Aono S, Nakagawa S, Reynolds AB, Takeichi M (1999) p120(ctn) acts as an inhibitory regulator of cadherin function in colon carcinoma cells. J Cell Biol 145: 551-62
Wohrn JC, Puelles L, Nakagawa S, Takeichi M, Redies C (1998) Cadherin expression in the retina and retinofugal pathways of the chicken embryo. J Comp Neurol 396: 20-38
Arndt K, Nakagawa S, Takeichi M, Redies C (1998) Cadherin-defined segments and parasagittal cell ribbons in the developing chicken cerebellum. Mol Cell Neurosci 10: 211-28
Arndt K, Nakagawa S, Takeichi M, Redies C (1998) Cadherin-Defined Segments and Parasagittal Cell Ribbons in the Developing Chicken Cerebellum. Mol Cell Neurosci 10: 211-28
Hirai Y, Nakagawa S, Takeichi M (1993) Reexamination of the properties of epimorphin and its possible roles. Cell 73: 426-7
Review Articles
Nakagawa S (2016) Lessons from reverse-genetic studies of lncRNAs. Biochim Biophys Acta 1859: 177-83
Hirose T, Nakagawa S (2016) Clues to long noncoding RNA taxonomy. Biochim Biophys Acta 1859: 1-2
Nakagawa S, Kageyama Y (2014) Nuclear lncRNAs as epigenetic regulators-beyond skepticism. Biochim Biophys Acta 1839: 215-22
Nakagawa S, Hirano T (2014) Gathering around Firre. Nat Struct Mol Biol 21: 207-8
Nakagawa S, Hirose T (2012) Paraspeckle nuclear bodies--useful uselessness? Cell Mol Life Sci 69: 3027-36
Ip JY, Nakagawa S (2012) Long non-coding RNAs in nuclear bodies. Dev Growth Differ 54: 44-54
Nakagawa S, Prasanth KV (2011) eXIST with matrix-associated proteins. Trends Cell Biol 21: 321-7
Hasegawa Y, Nakagawa S (2011) Revisiting the function of nuclear scaffold/matrix binding proteins in X chromosome inactivation. RNA Biol 8: 735-9
Kubo F, Nakagawa S (2008) Wnt signaling in retinal stem cells and regeneration. Dev Growth Differ 50: 245-51
Protocols
Mito M, Kawaguchi T, Hirose T, Nakagawa S (2016) Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy. Methods 98: 158-65
Okada Y, Nakagawa S (2015) Super-resolution imaging of nuclear bodies by STED microscopy. Methods Mol Biol 1262: 21-35
Nakagawa S (2015) Analysis of the subcellular distribution of RNA by fluorescence in situ hybridization. Methods Mol Biol 1206: 107-22