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Article ; Online: m

Yoneda, Ryoma / Ueda, Naomi / Kurokawa, Riki

International journal of molecular sciences

2021 Volume 22, Issue 20

Abstract: Translocated in LipoSarcoma/Fused in Sarcoma (TLS/FUS) is a nuclear RNA binding protein whose mutations cause amyotrophic lateral sclerosis. TLS/FUS undergoes LLPS and forms membraneless particles with other proteins and nucleic acids. Interaction with ... ...

Abstract	Translocated in LipoSarcoma/Fused in Sarcoma (TLS/FUS) is a nuclear RNA binding protein whose mutations cause amyotrophic lateral sclerosis. TLS/FUS undergoes LLPS and forms membraneless particles with other proteins and nucleic acids. Interaction with RNA alters conformation of TLS/FUS, which affects binding with proteins, but the effect of m
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/chemistry ; Cell Line ; Cell Survival/drug effects ; Cytoplasm/metabolism ; Genetic Loci ; Humans ; Liquid-Liquid Extraction ; Mutagenesis, Site-Directed ; Protein Aggregates/drug effects ; Protein Binding ; RNA/chemistry ; RNA/metabolism ; RNA/pharmacology ; RNA, Long Noncoding/chemistry ; RNA-Binding Protein FUS/chemistry ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Sorbitol/pharmacology
Chemical Substances	Protein Aggregates ; RNA, Long Noncoding ; RNA-Binding Protein FUS ; Sorbitol (506T60A25R) ; RNA (63231-63-0) ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2021-10-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222011014
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Article ; Online: Long noncoding RNA

Yoneda, Ryoma / Ueda, Naomi / Uranishi, Kousuke / Hirasaki, Masataka / Kurokawa, Riki

The Journal of biological chemistry

2020 Volume 295, Issue 17, Page(s) 5626–5639

Abstract: ... pncRNA- ... ...

Abstract	pncRNA-D
MeSH term(s)	Cell Cycle Checkpoints ; Cyclin D1/genetics ; Down-Regulation ; Epigenesis, Genetic ; Genes, bcl-1 ; HeLa Cells ; Humans ; Methylation ; Promoter Regions, Genetic ; RNA, Long Noncoding/genetics
Chemical Substances	CCND1 protein, human ; RNA, Long Noncoding ; Cyclin D1 (136601-57-5)
Language	English
Publishing date	2020-03-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA119.011556
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Article ; Online: Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner.

Hamad, Nesreen / Yoneda, Ryoma / So, Masatomo / Kurokawa, Riki / Nagata, Takashi / Katahira, Masato

Scientific reports

2021 Volume 11, Issue 1, Page(s) 9523

Abstract: Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS ... ...

Abstract	Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.
MeSH term(s)	DNA-Binding Proteins/genetics ; Protein Aggregates/genetics ; RNA, Untranslated/genetics ; RNA-Binding Protein FUS/genetics ; RNA-Binding Proteins/genetics ; Shear Strength/physiology
Chemical Substances	DNA-Binding Proteins ; Protein Aggregates ; RNA, Untranslated ; RNA-Binding Protein FUS ; RNA-Binding Proteins
Language	English
Publishing date	2021-05-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-89075-w
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Article ; Online: Arginine methylation of translocated in liposarcoma (TLS) inhibits its binding to long noncoding RNA, abrogating TLS-mediated repression of CBP/p300 activity.

Cui, Wei / Yoneda, Ryoma / Ueda, Naomi / Kurokawa, Riki

The Journal of biological chemistry

2018 Volume 293, Issue 28, Page(s) 10937–10948

Abstract: Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A- ... ...

Abstract	Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A-binding protein P300 (p300) on the cyclin D1 (
MeSH term(s)	Arginine/chemistry ; Cyclin D1/genetics ; Cyclin D1/metabolism ; E1A-Associated p300 Protein/genetics ; E1A-Associated p300 Protein/metabolism ; Gene Expression Regulation ; Humans ; Methylation ; Promoter Regions, Genetic ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Transcription, Genetic
Chemical Substances	CCND1 protein, human ; RNA, Long Noncoding ; RNA-Binding Protein FUS ; Cyclin D1 (136601-57-5) ; Arginine (94ZLA3W45F) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; E1A-Associated p300 Protein (EC 2.3.1.48) ; EP300 protein, human (EC 2.3.1.48)
Language	English
Publishing date	2018-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA117.000598
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Article ; Online: A testis-specific serine protease, Prss41/Tessp-1, is necessary for the progression of meiosis during murine in vitro spermatogenesis.

Yoneda, Ryoma / Kimura, Atsushi P

Biochemical and biophysical research communications

2013 Volume 441, Issue 1, Page(s) 120–125

Abstract: The function of protease during male meiosis has not been well studied. We previously cloned and characterized four testis-specific serine proteases in the mouse testis. One of the proteases, Prss41/Tessp-1, was expressed in the germ and Sertoli cell. ... ...

Abstract	The function of protease during male meiosis has not been well studied. We previously cloned and characterized four testis-specific serine proteases in the mouse testis. One of the proteases, Prss41/Tessp-1, was expressed in the germ and Sertoli cell. This time, to examine the involvement of Prss41/Tessp-1 in spermatogenesis, we conducted the organ culture of testis fragments in the presence of the anti-Prss41/Tessp-1 antibody. Because in the Sertoli cell, the Prss41/Tessp-1 protein was mostly associated with the membrane of intracellular organelles by glycosylphosphatidylinositol, the antibody was expected to affect Prss41/Tessp-1 at the plasma membrane of spermatogonia. By adding the antibody, the number of germ cells was decreased in some seminiferous tubules. The marker genes expression strongly suggested that meiosis was arrested at spermatogonia, and the number of apoptotic germ cells increased by terminal deoxynucleotidyl transferase dUTP nick end labeling assay. These data indicated that Prss41/Tessp-1 was necessary for the progression of meiosis at the stage of spermatogonia during in vitro spermatogenesis. Together with our previous study, the current results suggest that the Prss/Tessp proteases are important for the progression of meiosis at each stage.
MeSH term(s)	Animals ; Antibodies/metabolism ; Apoptosis ; Male ; Meiosis ; Mice ; Mice, Inbred C57BL ; Models, Biological ; Organ Culture Techniques ; Organ Specificity ; Protein Transport ; Serine Endopeptidases/metabolism ; Sertoli Cells/cytology ; Sertoli Cells/enzymology ; Spermatogenesis ; Spermatogonia/cytology ; Spermatogonia/enzymology ; Subcellular Fractions/enzymology ; Testis/cytology ; Testis/enzymology
Chemical Substances	Antibodies ; Serine Endopeptidases (EC 3.4.21.-) ; TESSP-1 protein, mouse (EC 3.4.21.-)
Language	English
Publishing date	2013-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2013.10.028
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Article: A testis-specific serine protease, Prss41/Tessp-1, is necessary for the progression of meiosis during murine in vitro spermatogenesis

Yoneda, Ryoma / Kimura, Atsushi P

Biochemical and biophysical research communications. 2013 Nov. 8, v. 441, no. 1

2013

Abstract	The function of protease during male meiosis has not been well studied. We previously cloned and characterized four testis-specific serine proteases in the mouse testis. One of the proteases, Prss41/Tessp-1, was expressed in the germ and Sertoli cell. This time, to examine the involvement of Prss41/Tessp-1 in spermatogenesis, we conducted the organ culture of testis fragments in the presence of the anti-Prss41/Tessp-1 antibody. Because in the Sertoli cell, the Prss41/Tessp-1 protein was mostly associated with the membrane of intracellular organelles by glycosylphosphatidylinositol, the antibody was expected to affect Prss41/Tessp-1 at the plasma membrane of spermatogonia. By adding the antibody, the number of germ cells was decreased in some seminiferous tubules. The marker genes expression strongly suggested that meiosis was arrested at spermatogonia, and the number of apoptotic germ cells increased by terminal deoxynucleotidyl transferase dUTP nick end labeling assay. These data indicated that Prss41/Tessp-1 was necessary for the progression of meiosis at the stage of spermatogonia during in vitro spermatogenesis. Together with our previous study, the current results suggest that the Prss/Tessp proteases are important for the progression of meiosis at each stage.
Keywords	Sertoli cells ; antibodies ; apoptosis ; gene expression ; genetic markers ; males ; meiosis ; mice ; organ culture ; organelles ; plasma membrane ; seminiferous tubules ; serine proteinases ; spermatogenesis ; spermatogonia
Language	English
Dates of publication	2013-1108
Size	p. 120-125.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2013.10.028
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Article ; Online: RNA sequence and length contribute to RNA-induced conformational change of TLS/FUS.

Hamad, Nesreen / Mashima, Tsukasa / Yamaoki, Yudai / Kondo, Keiko / Yoneda, Ryoma / Oyoshi, Takanori / Kurokawa, Riki / Nagata, Takashi / Katahira, Masato

Scientific reports

2020 Volume 10, Issue 1, Page(s) 2629

Abstract: Translocated in liposarcoma (TLS)/fused in sarcoma (FUS) is a multitasking DNA/RNA binding protein implicated in cancer and neurodegenerative diseases. Upon DNA damage, TLS is recruited to the upstream region of the cyclin D1 gene (CCND1) through binding ...

Abstract	Translocated in liposarcoma (TLS)/fused in sarcoma (FUS) is a multitasking DNA/RNA binding protein implicated in cancer and neurodegenerative diseases. Upon DNA damage, TLS is recruited to the upstream region of the cyclin D1 gene (CCND1) through binding to the promotor associated non-coding RNA (pncRNA) that is transcribed from and tethered at the upstream region. Binding to pncRNA is hypothesized to cause the conformational change of TLS that enables its inhibitive interaction with histone acetyltransferases and resultant repression of CCND1 expression, although no experimental proof has been obtained. Here, the closed-to-open conformational change of TLS on binding pncRNA was implied by fluorescence resonance energy transfer. A small fragment (31 nucleotides) of the full-length pncRNA (602 nucleotides) was shown to be sufficient for the conformational change of TLS. Dissection of pncRNA identified the G-rich RNA sequence that is critical for the conformational change. The length of RNA was also revealed to be critical for the conformational change. Furthermore, it was demonstrated that the conformational change of TLS is caused by another target DNA and RNA, telomeric DNA and telomeric repeat-containing RNA. The conformational change of TLS on binding target RNA/DNA is suggested to be essential for biological functions.
MeSH term(s)	Base Sequence ; Binding Sites ; Fluorescence Resonance Energy Transfer ; Humans ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; RNA, Untranslated/chemistry ; RNA, Untranslated/metabolism ; RNA-Binding Protein FUS/chemistry ; RNA-Binding Protein FUS/metabolism
Chemical Substances	RNA, Untranslated ; RNA-Binding Protein FUS
Language	English
Publishing date	2020-02-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-59496-0
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Article ; Online: A Long Noncoding RNA, lncRNA-Amhr2, Plays a Role in Amhr2 Gene Activation in Mouse Ovarian Granulosa Cells.

Kimura, Atsushi P / Yoneda, Ryoma / Kurihara, Misuzu / Mayama, Shota / Matsubara, Shin

Endocrinology

2017 Volume 158, Issue 11, Page(s) 4105–4121

Abstract: Anti-Müllerian hormone (AMH) is critical to the regression of Müllerian ducts during mammalian male differentiation and targets ovarian granulosa cells and testicular Sertoli and Leydig cells of adults. Specific effects of AMH are exerted via its ... ...

Abstract	Anti-Müllerian hormone (AMH) is critical to the regression of Müllerian ducts during mammalian male differentiation and targets ovarian granulosa cells and testicular Sertoli and Leydig cells of adults. Specific effects of AMH are exerted via its receptor, AMH type II receptor (Amhr2), but the mechanism by which the Amhr2 gene is specifically activated is not fully understood. To see whether a proximal promoter was sufficient for Amhr2 gene activation, we generated transgenic mice that bore the enhanced green fluorescent protein (EGFP) gene driven by a 500-bp mouse Amhr2 gene promoter. None of the established 10 lines, however, showed appropriate EGFP expression, indicating that the 500-bp promoter was insufficient for Amhr2 gene activation. As a regulatory element, we found a long noncoding RNA, lncRNA-Amhr2, transcribed from upstream of the Amhr2 gene in ovarian granulosa cells and testicular Sertoli cells. In primary granulosa cells, knockdown of lncRNA-Amhr2 resulted in a decrease of Amhr2 messnger RNA level, and a transient reporter gene assay showed that lncRNA-Amhr2 activation increased Amhr2 promoter activity. The activity was correlated with lncRNA-Amhr2 transcription in stably transfected OV3121 cells derived from mouse granulosa cells. Moreover, by the Tet-on system, the induction of lncRNA-Amhr2 transcription dramatically increased Amhr2 promoter activity in OV3121 cells. These results indicate that lncRNA-Amhr2 plays a role in Amhr2 gene activation in ovarian granulosa cells by enhancing promoter activity, providing insight into Amhr2 gene regulation underlying the AMH signaling in the female reproductive system.
Language	English
Publishing date	2017-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	427856-2
ISSN	1945-7170 ; 0013-7227
ISSN (online)	1945-7170
ISSN	0013-7227
DOI	10.1210/en.2017-00619
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Article: The binding specificity of Translocated in LipoSarcoma/FUsed in Sarcoma with lncRNA transcribed from the promoter region of cyclin D1.

Yoneda, Ryoma / Suzuki, Shiho / Mashima, Tsukasa / Kondo, Keiko / Nagata, Takashi / Katahira, Masato / Kurokawa, Riki

Cell & bioscience

2016 Volume 6, Page(s) 4

Abstract: Background: Translocated in LipoSarcoma (TLS, also known as FUsed in Sarcoma) is an RNA/DNA binding protein whose mutation cause amyotrophic lateral sclerosis. In previous study, we demonstrated that TLS binds to long noncoding RNA, promoter-associated ... ...

Abstract	Background: Translocated in LipoSarcoma (TLS, also known as FUsed in Sarcoma) is an RNA/DNA binding protein whose mutation cause amyotrophic lateral sclerosis. In previous study, we demonstrated that TLS binds to long noncoding RNA, promoter-associated ncRNA-D (pncRNA-D), transcribed from the 5' upstream region of cyclin D1 (CCND1), and inhibits the expression of CCND1. Results: In order to elucidate the binding specificity between TLS and pncRNA-D, we divided pncRNA-D into seven fragments and examined the binding with full-length TLS, TLS-RGG2-zinc finger-RGG3, and TLS-RGG3 by RNA pull down assay. As a result, TLS was able to bind to all the seven fragments, but the fragments containing reported recognition motifs (GGUG and GGU) tend to bind more solidly. The full-length TLS and TLS-RGG2-zinc finger-RGG3 showed a similar interaction with pncRNA-D, but the binding specificity of TLS-RGG3 was lower compared to the full-length TLS and TLS-RGG2-zinc finger-RGG3. Mutation in GGUG and GGU motifs dramatically decreased the binding, and unexpectedly, we could only detect weak interaction with the RNA sequence with stem loop structure. Conclusion: The binding of TLS and pncRNA-D was affected by the presence of GGUG and GGU sequences, and the C terminal domains of TLS function in the interaction with pncRNA-D.
Language	English
Publishing date	2016-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2593367-X
ISSN	2045-3701
ISSN	2045-3701
DOI	10.1186/s13578-016-0068-8
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Article ; Online: A genomic region transcribed into a long noncoding RNA interacts with the Prss42/Tessp-2 promoter in spermatocytes during mouse spermatogenesis, and its flanking sequences can function as enhancers.

Yoneda, Ryoma / Satoh, Yui / Yoshida, Ikuya / Kawamura, Shohei / Kotani, Tomoya / Kimura, Atsushi P

Molecular reproduction and development

2016 Volume 83, Issue 6, Page(s) 541–557

Abstract: Spermatogenesis is regulated by many meiotic stage-specific genes, but how they coordinate the many individual processes is not fully understood. The Prss/Tessp gene cluster is located on mouse chromosome 9F2-F3, and the three genes at this site (Prss42/ ... ...

Abstract	Spermatogenesis is regulated by many meiotic stage-specific genes, but how they coordinate the many individual processes is not fully understood. The Prss/Tessp gene cluster is located on mouse chromosome 9F2-F3, and the three genes at this site (Prss42/Tessp-2, Prss43/Tessp-3, and Prss44/Tessp-4) are specifically activated during meiosis in pachytene spermatocytes. We searched for DNase I hypersensitive sites (HSs) and long noncoding RNAs (lncRNAs) at the Prss/Tessp locus to elucidate how they are activated. We found eight DNase I HSs, three of which were testis germ cell-specific at or close to the Prss42/Tessp-2 promoter, and a testis-specific lncRNA, lncRNA-HSVIII, that was transcribed from a region adjacent to the Prss42/Tessp-2 gene. lncRNA-HSVIII transcripts localized to nuclei of most pachytene spermatocytes and the cytosol of stage-X pachytene spermatocytes and spermatids. Chromosome conformation capture revealed that the lncRNA-HSVIII locus specifically interacted with the Prss42/Tessp-2 promoter in primary and secondary spermatocytes. A 5.8-kb genome sequence, encompassing the entire lncRNA-HSVIII sequence and its flanking regions, significantly increased Prss42/Tessp-2 promoter activity using a reporter-gene assay, yet this construct did not change lncRNA-HSVIII expression, indicating that the elevated promoter activity was likely through enhancer activity. Indeed, both upstream and downstream regions of the lncRNA-HSVIII sequence significantly increased Prss42/Tessp-2 promoter activity. Our data therefore identified the direct interaction of a genomic region in the lncRNA-HSVIII locus with the Prss42/Tessp-2 promoter in spermatocytes, and suggested that sequences adjacent to the lncRNA function as enhancers for the Prss42/Tessp-2 gene. Mol. Reprod. Dev. 83: 541-557, 2016. © 2016 Wiley Periodicals, Inc.
Language	English
Publishing date	2016-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	20321-x
ISSN	1098-2795 ; 1040-452X
ISSN (online)	1098-2795
ISSN	1040-452X
DOI	10.1002/mrd.22650
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