Obuse C, Hirose T. Functional domains of nuclear long noncoding RNAs: Insights into gene regulation and intracellular architecture. Curr Opin Cell Biol. 85:102250.
Yamamoto T, Yamazaki T, Ninomiya K, Hirose T. Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus. Commun Biol. 6(1):1129.
Takakuwa H, Yamazaki T, Souquere S, Adachi S, Yoshino H, Fujiwara N, Yamamoto T, Natsume T, Nakagawa S, Pierron G, Hirose T. Shell protein composition specified by NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles. Nat. Cell Biol. 25:1664–1675.
Ninomiya K, Yamazaki T, Hirose T. Satellite RNAs: emerging players in subnuclear architecture and gene regulation. EMBO J. 42(18):e114331.
Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells.28(8):539-552.
Zeng C, Chujo T, Hirose T, Hamada M. Landscape of semi-extractable RNAs across five human cell lines. Nucleic Acids Res.51(15):7820-7831.
Hirose T, Ninomiya K, Nakagawa S, Yamazaki T. A guide to membraneless organelles and their various roles in gene regulation. Nat Rev Mol Cell Biol. 24(4):288-304.
Iwakiri J, Tanaka K, Chujo T, Takakuwa H, Yamazaki T, Terai G, Asai K, Hirose T. Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing. RNA. 29(2):170-177.
Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol.24(6):430-447.
2022
Gast M, Nageswaran V, Kuss AW, Tzvetkova A, Wang X, Mochmann LH, Rad PR, Weiss S, Simm S, Zeller T, Voelzke H, Hoffmann W, Völker U, Felix SB, Dörr M, Beling A, Skurk C, Leistner DM, Rauch BH, Hirose T, Heidecker B, Klingel K, Nakagawa S, Poller WC, Swirski FK, Haghikia A, Poller W. tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions. Cells. 11(24):3970.
Yamamoto T, Yamazaki T, Hirose T. Triblock copolymer micelle model of spherical paraspeckles. Front Mol Biosci. 9: 925058.
Yamazaki T, Yamamoto T, Hirose T. Micellization: A new principle in the formation of biomolecular condensates. Front Mol Biosci. 9: 974772.
Yamazaki T, Yamamoto T. Statistical Thermodynamics Approach for Intracellular Phase Separation. Methods Mol Biol. 2509: 361-393.
Wu Y, Li P, Liu L, Goodwin AJ, Halushka PV, Hirose T, Nakagawa S, Zhou J, Liu M, Fan H. lncRNA Neat1 regulates neuronal dysfunction post-sepsis via stabilization of hemoglobin subunit beta. Mol Ther. 30(7): 2618-2632.
2021
Park MK, Zhang L, Min KW, Cho JH, Yeh CC, Moon H, Hormaechea-Agulla D, Mun H, Ko S, Lee JW, Jathar S, Smith AS, Yao Y, Giang NT, Vu HH, Yan VC, Bridges MC, Kourtidis A, Muller F, Chang JH, Song SJ, Nakagawa S, Hirose T, Yoon JH, Song MS. NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis. Cell Metab. 33(12): 2380-2397.
Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 1506(1): 118-141.
Mannen T, Goto M, Yoshizawa T, Yamashita A, Hirose T, Hayano T. Distinct RNA polymerase transcripts direct the assembly of phase-separated DBC1 nuclear bodies in different cell lines. Mol Biol Cell. :mbc.E21-02.
Fukumura K, Yoshimoto R, Sperotto L, Kang HS, Hirose T, Inoue K, Sattler M, Mayeda A. SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns. Nat Commun. 12(1): 4910.
Yamamoto K, Goyama S, Asada S, Fujino T, Yonezawa T, Sato N, Takeda R, Tsuchiya A, Fukuyama T, Tanaka Y, Yokoyama A, Toya H, Kon A, Nannya Y, Onoguchi-Mizutani R, Nakagawa S, Hirose T, Ogawa S, Akimitsu N, Kitamura T. A histone modifier, ASXL1, interacts with NONO and is involved in paraspeckle formation in hematopoietic cells. Cell Rep. 36(8): 109576-109576.
Yamazaki T, Hirose T. Control of condensates dictates nucleolar architecture. Science. 373(6554): 486-487.
Ninomiya K, Iwakiri J, Aly MK, Sakaguchi Y, Adachi S, Natsume T, Terai G, Asai K, Suzuki T, Hirose T. m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing. EMBO J. 40(15) e107976.
Nakagawa S, Yamazaki T, Mannen T, Hirose T. ArcRNAs and the formation of nuclear bodies. Mamm genome. doi: 10.1007/s00335-021-09881-5
Yamazaki T, Yamamoto T, Yoshino H, Souquere S, Nakagawa S, Pierron G, Hirose T. Paraspeckles are constructed as block copolymer micelles. EMBO J. 40(12) e107270.
Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K. Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat Commun. 12(1): 236–236.
Yamazaki T, Hirose T. CRISPR-Mediated Mutagenesis of Long Noncoding RNAs. Methods Mol Biol. 2254: 283–303.
2020
Gidlöf O, Bader K, Celik S, Grossi M, Nakagawa S, Hirose T, Metzler B, Olde B, Erlinge D. Inhibition of the long non-coding RNA NEAT1 protects cardiomyocytes from hypoxia in vitro via decreased pri-miRNA processing. Cell Death Dis. 11(8). 677.
Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res. 30(7): 1060–1072.
Kukharsky MS, Ninkina NN, An H, Telezhkin V, Wei W, Meritens CR, Cooper-Knock J, Nakagawa S, Hirose T, Buchman VL, Shelkovnikova TA. Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice. Transl Psychiatry. 10(1): 171–171.
Isobe M, Toya H, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S. Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice. RNA. 26(3): 251-264.
Ninomiya K, Hirose T. Short Tandem Repeat-Enriched Architectural RNAs in Nuclear Bodies: Functions and Associated Diseases. Non-coding RNA. 6(1).
Yamazaki T, Nakagawa S, Hirose T. Architectural RNAs for Membraneless Nuclear Body Formation. Cold Spring Harb Symp Quant Biol. 84: 227-237.
Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J. 39(3): e102729.
Liang S, Takahashi H, Hirose T, Kuramitsu Y, Hatakeyama S, Yoshiyama H, Wang R, Hamada J, Iizasa H. NONO Is a Negative Regulator of SOX2 Promoter. Cancer Genomics Proteomics. 17(4): 359–367.
Yamamoto T, Yamazaki T, Hirose T. Phase separation driven by production of architectural RNA transcripts. Soft Matter. 16(19): 4692–4698.
2019
Adriaens C, Rambow F, Bervoets G, Silla T, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S, Jensen TH, Marine JC. The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth. RNA. 25(12): 1681-1695.
Gast M, Rauch B, Haghikia A, Nakagawa S, Haas J, Stroux A, Schmidt D, Schumann P, Weiss S, Jensen L, Kratzer A, Kraenkel N, Müller C, Börnigen D, Hirose T, Blankenberg S, Escher F, Kühl A, Kuss A, Meder B, Landmesser U, Zeller T, Poller W. Long noncoding RNA NEAT1 modulates immune cell functions and is suppressed in early onset myocardial infarction patients. Cardiovasc Res. 115(13): 1886-1906.
Hirose T, Yamazaki T, Nakagawa S. Molecular anatomy of the architectural NEAT1 noncoding RNA: the domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles. Wiley Interdiscip Rev RNA. 10(6): e1545.
Aly MK, Ninomiya K, Adachi S, Natsume T, Hirose T. Two distinct nuclear stress bodies containing different sets of RNA-binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure. Biochem Biophys Res Commun. 516(2): 419-423.
Modic M, Grosch M, Rot G, Engert S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-regulation between TDP-43 and paraspeckles promotes pluripotency differentiation transition. Mol Cell. 74(5): 951-965.e13.
Katsel P, Roussos P, Fam P, Khan S, Tan W, Hirose T, Nakagawa S, Pletnikov MV, Haroutunian V. The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription. NPJ Schizophr. 5(1): 3.
2018
Nakagawa S, Yamazaki T, Hirose T. Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu. Open Biol. 8(10) 180150.
Yamazaki T, Fujikawa C, Kubota A, Takahashi A, Hirose T. CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles. Biochem Biophys Res Commun. 504(1): 218-224.
Ahmed ASI, Dong K, Liu J, Wen T, Yu L, Xu F, Kang X, Osman I, Hu G, Bunting KM, Crethers D, Gao H, Zhang W, Liu Y, Wen K, Agarwal G, Hirose T, Nakagawa S, Vazdarjanova A, Zhou J. Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells. Proc Natl Acad Sci USA. 115(37): E8660-E8667.
Yamazaki T, Souquere S, Chujo T, Kobelke S, Chong YS, Fox AH, Bond CS, Nakagawa S, Pierron G, Hirose T. Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation. Mol Cell. 70(6): 1038-1053.e7.
Fox AH, Nakagawa S, Hirose T, Bond CS. Paraspeckles: Where Long Noncoding RNA Meets Phase Separation. Trends Biochem Sci. 43(2): 124-135.
2017
Chujo T, Hirose T. Nuclear bodies built on architectural long noncoding RNAs: unifying principles of their construction and function. Mol Cells. 40(12): 889-896.
Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T. Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J. 36(10): 1447-1462.
Mannen T, Hirose T. RNase sensitivity screening for nuclear bodies with RNA scaffolds in mammalian cells. Bio-protocol. 7.
2016
Anantharaman A, Jadaliha M, Tripathi V, Nakagawa S, Hirose T, Jantsch MF, Prasanth SG, Prasanth KV. Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA. Sci Rep. 6: 34043.
West JA, Mito M, Kurosaka S, Takumi T, Tanegashima C, Chujo T, Yanaka K, Kingston RE, Hirose T, Bond C, Fox A, Nakagawa S. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol. 214(7): 817-30.
Aly, MK, Hirose T. GAS5 Gene. In: eLS. John Wiley & Sons Ltd, Chichester.
Yamamoto K, Furukawa M, Fukumura K, Kawamura A, Yamada T, Suzuki H, Hirose T, Sakamoto H, Inoue K. Control of the heat stress-induced alternative splicing of a subset of genes by hnRNP K. Genes Cells. 21(9): 1006-14.
Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol. 214(1): 45-59.
Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PWG, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, ven den Oord J, Nakagawa S, Hirose T, Sablina AA, Lambrechts D, Aerts S, Blanpain C, Marine JC. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat. Med. 22(8): 861-8.
Hirose T, Nakagawa S. Clues to long noncoding RNA taxonomy. Biochim Biophys Acta. 1859(1): 1-2.
Chujo T, Yamazaki T, Hirose T. Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies. Biochim Biophys Acta. 1859(1): 139-46.
Mito M, Kawaguchi T, Hirose T, Nakagawa S. Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy. Methods. 98: 158-65.
2015
Kawaguchi T, Hirose T. Chromatin remodeling complexes in the assembly of long noncoding RNA-dependent nuclear bodies. Nucleus. 6(6): 462-7.
Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott GJ, Iyer KS, Ho D, Newcombe EA, Hosoki K, Goshima N, Kawaguchi T, Hatters D, Trinkle-Mulcahy L, Hirose T*, Bond CS*, Fox AH*. Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J Cell Biol. 210(4): 529-39. (* equally contributed)
Kawaguchi T, Tanigawa A, Naganuma T, Ohkawa Y, Souquere S, Pierron G, Hirose T. SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies. Proc Natl Acad Sci U S A. 112(14): 4304-9.
*Mannen T, *Chujo T, Hirose T. Long noncoding RNAs as structural and functional components of nuclear bodies. Long Noncoding RNAs: Structures and Functions.ed. Kurokawa. R.Springer.111-132. (* equally contributed)
Yamazaki T, Hirose T. The building process of the functional paraspeckle with long non-coding RNAs. Front Biosci (Elite Ed). 7: 1-41.
Hirose T, Goshima N. Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library. Methods Mol Biol. 1262: 155-63.
Hirose T, Mannen T. Rapid and efficient elimination of specific nuclear noncoding RNAs in mammalian cells with antisense oligonucleotides. Methods Mol Biol. 1206: 149-56.
2014
Nakagawa S, Shimada M, Yanaka K, Mito M, Arai T, Takahashi E, Fujita Y, Fujimori T, Standaert L, Marine JC, Hirose T. The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice. Development. 141(23): 4618-27.
Standaert L, Adriaens C, Radaelli E, Van Keymeulen A, Blanpain C, Hirose T, Nakagawa S, Marine JC. The long noncoding RNA Neat1 is required for mammary gland development and lactation. RNA. 20(12): 1844-9.
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. The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat. Commun. 5: 5383.
Hirose T, Mishima Y, Tomari Y. Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Rep. 15(5): 489-507.
Ono H, Motoi N, Nagano H, Miyauchi E, Ushijima M, Matsuura M, Okumura S, Nishio M, Hirose T, Inase N, Ishikawa Y. Long noncoding RNA HOTAIR is relevant to cellular proliferation, invasiveness, and clinical relapse in small-cell lung cancer. Cancer Med. 3(3): 632-42.
Hirose T*, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Benard M, Fox A*, Pierron G*. NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell. 25(1): 169-83. (*co-corresponding).
2013
Nishimoto Y, Nakagawa S, Hirose T, Okano HJ, Takao M, Shibata S, Suyama S, Kuwako K, Imai T, Murayama S, Suzuki N, Okano H. The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis. Mol Brain. 6: 31.
Naganuma T, Hirose T. Paraspeckle formation during the biogenesis of long non-coding RNAs. RNA Biol. 10(3): 456-61.
2012
Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T. Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J. 31(20): 4020-34.
Ideue T, Adachi S, Naganuma T, Tanigawa A, Natsume T, Hirose T. U7 small nuclear ribonucleoprotein represses histone gene transcription in cell cycle-arrested cells. Proc Natl Acad Sci U S A. 109(15): 5693-8.
Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X, Hirose T, Prasanth KV. Malat1 is not an essential component of nuclear speckles in mice. RNA. 18(8): 1487-99.
Hirose T, Nakagawa S. Paraspeckles: possible nuclear hubs by the RNA for the RNA. Biomol Concepts. 3(5): 415-28.
Nakagawa S, Hirose T. Paraspeckle nuclear bodies–useful uselessness? Cell Mol Life Sci. 69(18): 3027-36.
Kawaguchi T, Hirose T. Architectural roles of long noncoding RNAs in the intranuclear formation of functional paraspeckles. Front Biosci (Landmark Ed). 17: 1729-46.
Miyagawa R, Mizuno R, Nakamura Y, Ijiri K, Rakwal R, Shibato J, Masuo Y, Hirose T, Akimitsu N. Identification of the cis-acting and trans-acting determinants of noncoding RNA MALAT-1 for the nuclear speckles localization. RNA. 18(4): 738-51.
2011
Nakagawa S, Naganuma T, Shioi G, Hirose T. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol. 193(1): 31-9.
Hirose T. Gas5 gene. version 2. Encyclopedia on Human Genome. e1-5.
2010
Aoki K, Harashima A, Sano M, Yokoi T, Nakamura S, Kibata M, Hirose T. A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines. BMC Mol Biol. 11: 99.
Hirose T. Emerging roles of noncoding RNAs in subcellular architecture and gene expression. RNA technologies & Their applications. : 370-386 Springer.
2009
Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A. 106(8): 2525-30.
Ideue T, Hino K, Kitao S, Yokoi T, Hirose T. Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells. RNA. 15(8): 1578-87.
Kikuchi K, Fukuda M, Ito T, Inoue M, Yokoi T, Chiku S, Mitsuyama T, Asai K, Hirose T, Aizawa Y. Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation. Nucleic Acids Res. 37(15): 4987-5000.
Sasaki YT, Hirose T. How to build a paraspeckle. Genome Biol. 10(7): 227.
2007
Ideue T, Sasaki YT, Hagiwara M, Hirose T. Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes Dev. 21(16): 1993-8.
Fukumura K, Kato A, Jin Y, Ideue T, Hirose T, Kataoka N, Fujiwara T, Sakamoto H, Inoue K. Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1gamma gene. Nucleic Acids Res. 35(16): 5303-11.
Nojima T, Hirose T, Kimura H, Hagiwara M. The interaction between cap-binding complex and RNA export factor is required for intronless mRNA export. J Biol Chem. 282(21): 15645-51.
Sasaki YT, Sano M, Ideue T, Kin T, Asai K, Hirose T. Identification and characterization of human non-coding RNAs with tissue-specific expression. Biochem Biophys Res Commun. 357(4): 991-6.
Sasaki YT, Sano M, Kin T, Asai K, Hirose T. Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem Biophys Res Commun. 357(3): 724-30.
Kuroda H, Suzuki H, Kusumegi T, Hirose T, Yukawa Y, Sugiura M. Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts. Plant Cell Physiol. 48(9): 1374-8.
2006
Hirose T*, Ideue T, Nagai M, Hagiwara M, Shu M-D, Steitz JA*. A spliceosomal intron binding protein, IBP160, links position-dependent assembly of intron-encoded box C/D snoRNP to pre-mRNA splicing. Mol Cell. 23(5): 673-84. (*co-corresponding).
2004
Hirose T, Shu MD, Steitz JA. Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay. Proc Natl Acad Sci U S A. 101(52): 17976-81.
Hirose T, Sugiura M. Multiple elements required for translation of plastid atpB mRNA lacking the Shine-Dalgarno sequence. Nucleic Acids Res. 32(11): 3503-10.
Hirose T, Sugiura M. Functional Shine-Dalgarno-like sequences for translational initiation of chloroplast mRNAs. Plant Cell Physiol. 45(1): 114-7.
Hirose T, Miyamoto T, Obokata J, Sugiura M. In vitro RNA editing systems from higher plant chloroplasts. Methods Mol Biol. 265: 333-44.
Before 2003
Hirose T, Shu M-D, Steitz JA. Splicing-dependent and independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol. Cell.12: 113-123, 2003.
Hirose T, Steitz JA. gas5 gene. (Level 3 article). Encyclopedia on Human Genome. Nature Publishing group, 2003.
Hirose T, Steitz JA. Positions within host intron is critical for efficient processing of box C/D snoRNAs in mammalian cell. Proc. Natl. Acad. Sci. USA. 98: 12914-12919, 2001.
Hirose T, Sugiura M. Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J. 20: 1144-1152, 2001.
Hirose T, Kusumegi T, Tsudzuki T, Sugiura M. RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Mol. Gen. Genet. 262: 462-467, 1999.
Hirose T, Ideue T, Wakasugi T, Sugiura M. The chloroplast infA gene with a functional UUG initiation codon. FEBS Lett. 445: 169-172, 1999.
Hirose T, Kusumegi T, Sugiura M. Translation of tobacco chloroplast rps14 mRNA depends on a Shine-Dalgarno-like sequence in the 5′-untranslated region but not on internal RNA editing in the coding region. FEBS Lett. 430: 257-60, 1998.
Sugiura M, Hirose T, Sugita M. Evolution and mechanism of translation in chloroplasts. Annu. Rev. Genet. 32:437-459, 1998.
Sugiura M, Kusumegi T, Sugishita H, Murakami K, Ideue T, Hirose T. Translational control of photosynthetic genes in tobacco plastids. Photosynthesis: Mechanisms and Effects IV. : 2943-2946, 1998.
Mutsuda M, Hirose T, Sugiura M, Sugita M. The function of the cyanobacterial RNA-binding proteins. Photosynthesis: Mechanisms and Effects IV. : 2937-2940, 1998.
Tsudzuki T, Tsuduzki J, Nakashima K, Wakasugi T, Hirose T, Sugita M, Sugiura M. Newly identified genes in tobacco plastid genome. Photosynthesis: Mechanisms and Effects IV. : 2953-2956, 1998.
Hirose T, Sugiura M. Both RNA editing and RNA cleavage are required for translation of tobacco chloroplast ndhD mRNA : a possible regulatory mechanism for the expression of a chloroplast operon consisting of functionally unrelated gene. EMBO J. 16: 6804-6811, 1997.
Hirose T, Sugiura M. Cis-acting elements and trans-acting factor(s) for accurate translation of tobacco psbA mRNA in chloroplasts; development of a chloroplast in vitro translation system. EMBO J. 15: 1687-1695, 1996.
Wakasugi T, Hirose T, Horihata M, Tsudzuki T, Kossel H, Sugiura M. Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms. Proc. Natl. Acad. Sci. USA. 93: 8766-8770, 1996.
Vera A, Hirose T, Sugiura M. A ribosomal protein gene (rpl32) from tobacco chloroplast DNA is transcribed from alternative promoters: similarities in promoter region organization in plastid housekeeping genes. Mol. Gen. Genet. 251: 518-525, 1996.
Hirose T, Fan H, Suzuki JY, Wakasugi T, Tsudzuki T, Kossel H, Sugiura M. Occurrence of silent RNA editing in chloroplasts: its species specificity and the influence of environmental and developmental conditions. Plant Mol. Biol. 30: 667-672, 1996.
Hirose T, Sugita M, Sugiura M. In vivo and in vitro analysis of translation of psbA transcripts in tobacco chloroplasts. Photosynthesis: Mechanisms and Effects III. : 695-698, 1995.
Tsuzduki T, Hirose T, Fan H, Suzuki JY, Wakasugi T, Kossel H, Sugiura M. RNA editing in atpA and atpF transcripts from tobacco. Photosynthesis: Mechanisms and Effects III. : 687-690, 1995.
Hirose T, Wakasugi T, Sugiura M, Kossel H. RNA editing of tobacco petB mRNAs occurs both in chloroplasts and non-photosynthetic proplastids. Plant Mol. Biol. 26: 509-513, 1994.
Hirose T, Sugita M, Sugiura M. Characterization of a cDNA encoding a novel type of RNA-binding protein in tobacco: its expression and nucleic acid-binding properties. Mol. Gen. Genet. 244: 360-366, 1994.
Yokoyama R, Hirose T, Fujii N, Aspuria ET, Kato A, Uchimiya H. The rolC promoter of Agrobacterium rhizogenes Ri plasmid is activated by sucrose in transgenic tobacco plants. Mol. Gen. Genet. 244: 15-22, 1994.
Hirose T, Sugita M, Sugiura M. cDNA structure, expression and nucleic acid-binding properties of three RNA-binding proteins in tobacco. Nucleic Acids Res. 21: 3981-3987, 1993.