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1

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.

Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Lennartsson A, et al. Among authors: takahashi h. Epigenetics Chromatin. 2015 Dec 14;8:55. doi: 10.1186/s13072-015-0043-3. eCollection 2015. Epigenetics Chromatin. 2015. PMID: 26673794 Free PMC article.

2

The regulated retrotransposon transcriptome of mammalian cells.

Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. Faulkner GJ, et al. Among authors: takahashi h. Nat Genet. 2009 May;41(5):563-71. doi: 10.1038/ng.368. Epub 2009 Apr 19. Nat Genet. 2009. PMID: 19377475

3

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Hoskins RA, et al. Among authors: takahashi h. Genome Res. 2011 Feb;21(2):182-92. doi: 10.1101/gr.112466.110. Epub 2010 Dec 22. Genome Res. 2011. PMID: 21177961 Free PMC article.

4

CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks.

Takahashi H, Kato S, Murata M, Carninci P. Takahashi H, et al. Methods Mol Biol. 2012;786:181-200. doi: 10.1007/978-1-61779-292-2_11. Methods Mol Biol. 2012. PMID: 21938627 Free PMC article.

5

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Takahashi H, Lassmann T, Murata M, Carninci P. Takahashi H, et al. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. Nat Protoc. 2012. PMID: 22362160 Free PMC article.

6

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.

Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, Carninci P, Torres-Padilla ME. Fadloun A, et al. Among authors: takahashi h. Nat Struct Mol Biol. 2013 Mar;20(3):332-8. doi: 10.1038/nsmb.2495. Epub 2013 Jan 27. Nat Struct Mol Biol. 2013. PMID: 23353788

7

Widespread genome transcription: new possibilities for RNA therapies.

Takahashi H, Carninci P. Takahashi H, et al. Biochem Biophys Res Commun. 2014 Sep 19;452(2):294-301. doi: 10.1016/j.bbrc.2014.08.139. Epub 2014 Sep 1. Biochem Biophys Res Commun. 2014. PMID: 25193698 Free article. Review.

8

SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells.

Zucchelli S, Fasolo F, Russo R, Cimatti L, Patrucco L, Takahashi H, Jones MH, Santoro C, Sblattero D, Cotella D, Persichetti F, Carninci P, Gustincich S. Zucchelli S, et al. Among authors: takahashi h. Front Cell Neurosci. 2015 May 13;9:174. doi: 10.3389/fncel.2015.00174. eCollection 2015. Front Cell Neurosci. 2015. PMID: 26029048 Free PMC article.

9

Characterization of piRNAs across postnatal development in mouse brain.

Ghosheh Y, Seridi L, Ryu T, Takahashi H, Orlando V, Carninci P, Ravasi T. Ghosheh Y, et al. Among authors: takahashi h. Sci Rep. 2016 Apr 26;6:25039. doi: 10.1038/srep25039. Sci Rep. 2016. PMID: 27112104 Free PMC article.

10

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation.

Takahashi H, Kozhuharova A, Sharma H, Hirose M, Ohyama T, Fasolo F, Yamazaki T, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P. Takahashi H, et al. PLoS One. 2018 Feb 7;13(2):e0183229. doi: 10.1371/journal.pone.0183229. eCollection 2018. PLoS One. 2018. PMID: 29414979 Free PMC article.

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