Article | Published:

Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy

Nature Geneticsvolume 50pages581590 (2018) | Download Citation


Epilepsy is a common neurological disorder, and mutations in genes encoding ion channels or neurotransmitter receptors are frequent causes of monogenic forms of epilepsy. Here we show that abnormal expansions of TTTCA and TTTTA repeats in intron 4 of SAMD12 cause benign adult familial myoclonic epilepsy (BAFME). Single-molecule, real-time sequencing of BAC clones and nanopore sequencing of genomic DNA identified two repeat configurations in SAMD12. Intriguingly, in two families with a clinical diagnosis of BAFME in which no repeat expansions in SAMD12 were observed, we identified similar expansions of TTTCA and TTTTA repeats in introns of TNRC6A and RAPGEF2, indicating that expansions of the same repeat motifs are involved in the pathogenesis of BAFME regardless of the genes in which the expanded repeats are located. This discovery that expansions of noncoding repeats lead to neuronal dysfunction responsible for myoclonic tremor and epilepsy extends the understanding of diseases with such repeat expansion.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Inazuki, G. et al. A clinical study and neuropathological findings of a familial disease with myoclonus and epilepsy–the nosological place of familial essential myoclonus and epilepsy (FEME). Psych. Neurol. Jpn. 92, 1–21 (1990).

  2. 2.

    Ikeda, A. et al. Cortical tremor: a variant of cortical reflex myoclonus. Neurology 40, 1561–1565 (1990).

  3. 3.

    Yasuda, T. Benign adult familial myoclonic epilepsy (BAFME). Kawasaki Med. J. 17, 1–13 (1991).

  4. 4.

    Plaster, N. M. et al. Genetic localization of the familial adult myoclonic epilepsy (FAME) gene to chromosome 8q24. Neurology 53, 1180–1183 (1999).

  5. 5.

    Mikami, M. et al. Localization of a gene for benign adult familial myoclonic epilepsy to chromosome 8q23.3-q24.1. Am. J. Hum. Genet. 65, 745–751 (1999).

  6. 6.

    Suzuki, T. Clinical genetics and linkage analysis of familial essential myoclonus and epilepsy (FEME). Niigata Igakkai Zasshi (in Japanese) 116, 535–545 (2002).

  7. 7.

    Uyama, E., Fu, Y. H. & Ptácek, L. J. Familial adult myoclonic epilepsy (FAME). in Advances in Neurology Vol. 95: Myoclonic Epilepsies (eds. A. V. Delgado-Escueta et al.) 281–288 (Lippincott Willams & Wilkins, Philadelphia, 1995). 

  8. 8.

    Mori, S. et al. Remapping and mutation analysis of benign adult familial myoclonic epilepsy in a Japanese pedigree. J. Hum. Genet. 56, 742–747 (2011).

  9. 9.

    Cen, Z. D. et al. Fine mapping and whole-exome sequencing of a familial cortical myoclonic tremor with epilepsy family. Am. J. Med. Genet. Part B 168, 595–599 (2015).

  10. 10.

    Guerrini, R. et al. Autosomal dominant cortical myoclonus and epilepsy (ADCME) with complex partial and generalized seizures: A newly recognized epilepsy syndrome with linkage to chromosome 2p11.1-q12.2. Brain 124, 2459–2475 (2001).

  11. 11.

    Depienne, C. et al. Familial cortical myoclonic tremor with epilepsy: the third locus (FCMTE3) maps to 5p. Neurology 74, 2000–2003 (2010).

  12. 12.

    Yeetong, P. et al. A newly identified locus for benign adult familial myoclonic epilepsy on chromosome 3q26.32-3q28. Eur. J. Hum. Genet. 21, 225–228 (2013).

  13. 13.

    Beck, J. et al. Large C9orf72 hexanucleotide repeat expansions are seen in multiple neurodegenerative syndromes and are more frequent than expected in the UK population. Am. J. Hum. Genet. 92, 345–353 (2013).

  14. 14.

    Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).

  15. 15.

    Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).

  16. 16.

    Hitomi, T. et al. Clinical anticipation in Japanese families of benign adult familial myoclonus epilepsy. Epilepsia 53, e33–e36 (2012).

  17. 17.

    Hitomi, T. et al. Increased clinical anticipation with maternal transmission in benign adult familial myoclonus epilepsy in Japan. Epileptic Disord. 15, 428–432 (2013).

  18. 18.

    Yoshida, K. et al. Distinctive features of degenerating Purkinje cells in spinocerebellar ataxia type 31. Neuropathology 34, 261–267 (2014).

  19. 19.

    Miyake, N. et al. Biallelic TBCD mutations cause early-onset neurodegenerative encephalopathy. Am. J. Hum. Genet. 99, 950–961 (2016).

  20. 20.

    Ameur, A. et al. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol. 18, 1435–1440 (2011).

  21. 21.

    Haeusler, A. R. et al. C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature 507, 195–200 (2014).

  22. 22.

    Doi, K. et al. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. Bioinformatics 30, 815–822 (2014).

  23. 23.

    Uhlén, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).

  24. 24.

    Arcot, S. S., Wang, Z., Weber, J. L., Deininger, P. L. & Batzer, M. A. Alu repeats: a source for the genesis of primate microsatellites. Genomics 29, 136–144 (1995).

  25. 25.

    Kurosaki, T., Matsuura, T., Ohno, K. & Ueda, S. Alu-mediated acquisition of unstable ATTCT pentanucleotide repeats in the human ATXN10 gene. Mol. Biol. Evol. 26, 2573–2579 (2009).

  26. 26.

    Sato, N. et al. Spinocerebellar ataxia type 31 is associated with “inserted” penta-nucleotide repeats containing (TGGAA)n. Am. J. Hum. Genet. 85, 544–557 (2009).

  27. 27.

    Taneja, K. L., McCurrach, M., Schalling, M., Housman, D. & Singer, R. H. Foci of trinucleotide repeat transcripts in nuclei of myotonic dystrophy cells and tissues. J. Cell Biol. 128, 995–1002 (1995).

  28. 28.

    Matsuura, T. et al. Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10. Nat. Genet. 26, 191–194 (2000).

  29. 29.

    Hagerman, R. J. et al. Intention tremor, parkinsonism, and generalized brain atrophy in male carriers of fragile X. Neurology 57, 127–130 (2001).

  30. 30.

    DeJesus-Hernandez, M. et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245–256 (2011).

  31. 31.

    Renton, A. E. et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72, 257–268 (2011).

  32. 32.

    Hitomi, T. et al. Increased cortical hyperexcitability and exaggerated myoclonus with aging in benign adult familial myoclonus epilepsy. Mov. Disord. 26, 1509–1514 (2011).

  33. 33.

    Charlet-B, N. et al. Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell 10, 45–53 (2002).

  34. 34.

    Mankodi, A. et al. Expanded CUG repeats trigger aberrant splicing of ClC-1 chloride channel pre-mRNA and hyperexcitability of skeletal muscle in myotonic dystrophy. Mol. Cell 10, 35–44 (2002).

  35. 35.

    Zu, T. et al. Non-ATG-initiated translation directed by microsatellite expansions. Proc. Natl. Acad. Sci. USA 108, 260–265 (2011).

  36. 36.

    Sanpei, K. et al. Identification of the spinocerebellar ataxia type 2 gene using a direct identification of repeat expansion and cloning technique, DIRECT. Nat. Genet. 14, 277–284 (1996).

  37. 37.

    Henden, L. et al. Identity by descent fine mapping of familial adult myoclonus epilepsy (FAME) to 2p11.2-2q11.2. Hum. Genet. 135, 1117–1125 (2016).

  38. 38.

    Fukuda, Y. et al. SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. BMC Bioinformatics 10, 121 (2009).

  39. 39.

    Gudbjartsson, D. F., Thorvaldsson, T., Kong, A., Gunnarsson, G. & Ingolfsdottir, A. Allegro version 2. Nat. Genet. 37, 1015–1016 (2005).

  40. 40.

    Regan, J. F. et al. A rapid molecular approach for chromosomal phasing. PLoS One 10, e0118270 (2015).

  41. 41.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

  42. 42.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

  43. 43.

    Zheng, G. X. Y. et al. Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat. Biotechnol. 34, 303–311 (2016).

  44. 44.

    Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

  45. 45.

    Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

Download references


We thank the patients and family members for participating in the study. We thank T. Sekiya (Department of Neurology, Sumitomo Hospital, Osaka, Japan), M. Kinoshita (Department of Neurology, Utano National Hospital, National Hospital Organization, Kyoto, Japan), M. Kanda (Department of Neurology, Ijinkai Takeda General Hospital, Kyoto, Japan), K. Hokkoku (Department of Neurology, Teikyo University School of Medicine, Tokyo, Japan) and others for kindly collecting and providing clinical information, and K. Hirayama, Zhenghong Wu, M. Takeyama, K. Wakabayashi, N. Maruyama, T. Sugai, and Y. Tsukamoto for technical support. This work was supported in part by KAKENHI (Grants-in-Aid for Scientific Research on Innovative Areas 22129001 and 22129002) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and Grants-in-Aid (H23-Jitsuyoka (Nanbyo)-Ippan-004 and H26-Jitsuyoka (Nanbyo)-Ippan-080) from the Ministry of Health, Welfare and Labour, Japan, and grants (15ek0109065h0002, 16kk0205001h0001, 17kk0205001h0002 and 17ek0109279h0001) from the Japan Agency for Medical Research and Development (AMED) to S.T. This work was also supported by KAKENHI (Grant-in-Aid for Young Scientists 17H05085) from the Japan Society for the Promotion of Science for H.I.

Author information

Author notes

  1. Deceased: Akira Ueki.


  1. Department of Neurology, The University of Tokyo Hospital, Tokyo, Japan

    • Hiroyuki Ishiura
    • , Jun Mitsui
    • , Miho Kawabe Matsukawa
    • , Shota Shibata
    • , Aki Mitsue
    • , Masaki Tanaka
    • , Hidetoshi Date
    • , Takashi Matsukawa
    • , Junko Kanda
    • , Fumiko Kusunoki Nakamoto
    • , Jun Shimizu
    • , Toshihiro Hayashi
    • , Satomi Inomata-Terada
    • , Masashi Hamada
    • , Yuichiro Shirota
    • , Akatsuki Kubota
    •  & Shoji Tsuji
  2. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    • Koichiro Doi
    • , Jun Yoshimura
    • , Wei Qu
    • , Kazuki Ichikawa
    •  & Shinichi Morishita
  3. Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan

    • Asao Fujiyama
  4. Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan

    • Yasuko Toyoshima
    • , Akiyoshi Kakita
    •  & Hitoshi Takahashi
  5. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    • Yutaka Suzuki
  6. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan

    • Sumio Sugano
  7. Department of Laboratory Medicine, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan

    • Hideaki Yurino
  8. Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan

    • Koichiro Higasa
  9. Department of Neurology, Kyorin University, Tokyo, Japan

    • Yaeko Ichikawa
  10. Department of Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan

    • Yuji Takahashi
  11. Department of Neurology, Tokyo Metropolitan Geriatric Hospital, Tokyo, Japan

    • Mana Higashihara
  12. Department of Neurology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan

    • Koji Abe
  13. Department of Neurology, Nishi-Niigata Chuo National Hospital, Niigata, Japan

    • Ryoko Koike
    •  & Yasuko Kuroha
  14. Department of Psychiatry, Toyosato Hospital, Ibaraki, Japan

    • Mutsuo Sasagawa
  15. Department of Epilepsy, Nishi-Niigata Chuo National Hospital, Niigata, Japan

    • Naoya Hasegawa
  16. Division of Cardiology, National Hospital Organization Takasaki General Medical Center, Gunma, Japan

    • Norio Kanesawa
  17. Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto, Japan

    • Takayuki Kondo
    •  & Takefumi Hitomi
  18. Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan

    • Takefumi Hitomi
  19. Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan

    • Masayoshi Tada
    •  & Osamu Onodera
  20. Department of Neurology, Tachikawa General Hospital, Niigata, Japan

    • Hiroki Takano
  21. Department of Neurology, Sannocho Hospital, Niigata, Japan

    • Yutaka Saito
  22. Department of Neurology, Sado General Hospital, Niigata, Japan

    • Kazuhiro Sanpei
  23. Department of Neurology, Niigata Medical Center, Niigata, Japan

    • Masatoyo Nishizawa
  24. Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan

    • Masayuki Nakamura
    •  & Akira Sano
  25. Department of Neurology, Kurashikikinen Hospital, Okayama, Japan

    • Takeshi Yasuda
  26. Department of Neurology, Jichi Medical University, Saitama Medical Center, Saitama, Japan

    • Yoshio Sakiyama
  27. Department of Neurology, International University of Health and Welfare, Tochigi, Japan

    • Mieko Otsuka
  28. Third Department of Internal Medicine, National Defense Medical College, Saitama, Japan

    • Ken-ichi Kaida
  29. Department of Neurology, School of Medicine, Kitasato University, Kanagawa, Japan

    • Ritsuko Hanajima
  30. Department of Cell Physiology, School of Medicine, Kyorin University, Tokyo, Japan

    • Yasuo Terao
  31. Department of Neurology, Fukushima Medical University, Fukushima, Japan

    • Yoshikazu Ugawa
  32. Department of Neurology, University of Yamanashi, Yamanashi, Japan

    • Kishin Koh
    •  & Yoshihisa Takiyama
  33. Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan

    • Natsumi Ohsawa-Yoshida
    •  & Shoichi Ishiura
  34. Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan

    • Shoichi Ishiura
  35. Department of Neurology, Neurological Institute, Faculty of Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan

    • Ryo Yamasaki
  36. Department of Neurology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan

    • Akira Tamaoka
  37. Hiratsuka Hospital, Kanagawa, Japan

    • Hiroshi Akiyama
  38. Epilepsy Hospital Bethel Japan, Miyagi, Japan

    • Taisuke Otsuki
  39. Department of Epilepsy, Movement Disorders and Physiology, Kyoto University Graduate School of Medicine, Kyoto, Japan

    • Akio Ikeda
  40. Department of Neurology, International University of Health and Welfare Mita Hospital, Tokyo, Japan

    • Jun Goto
  41. Medical Genome Center, The University of Tokyo Hospital, Tokyo, Japan

    • Shoji Tsuji
  42. International University of Health and Welfare, Chiba, Japan

    • Shoji Tsuji


  1. Search for Hiroyuki Ishiura in:

  2. Search for Koichiro Doi in:

  3. Search for Jun Mitsui in:

  4. Search for Jun Yoshimura in:

  5. Search for Miho Kawabe Matsukawa in:

  6. Search for Asao Fujiyama in:

  7. Search for Yasuko Toyoshima in:

  8. Search for Akiyoshi Kakita in:

  9. Search for Hitoshi Takahashi in:

  10. Search for Yutaka Suzuki in:

  11. Search for Sumio Sugano in:

  12. Search for Wei Qu in:

  13. Search for Kazuki Ichikawa in:

  14. Search for Hideaki Yurino in:

  15. Search for Koichiro Higasa in:

  16. Search for Shota Shibata in:

  17. Search for Aki Mitsue in:

  18. Search for Masaki Tanaka in:

  19. Search for Yaeko Ichikawa in:

  20. Search for Yuji Takahashi in:

  21. Search for Hidetoshi Date in:

  22. Search for Takashi Matsukawa in:

  23. Search for Junko Kanda in:

  24. Search for Fumiko Kusunoki Nakamoto in:

  25. Search for Mana Higashihara in:

  26. Search for Koji Abe in:

  27. Search for Ryoko Koike in:

  28. Search for Mutsuo Sasagawa in:

  29. Search for Yasuko Kuroha in:

  30. Search for Naoya Hasegawa in:

  31. Search for Norio Kanesawa in:

  32. Search for Takayuki Kondo in:

  33. Search for Takefumi Hitomi in:

  34. Search for Masayoshi Tada in:

  35. Search for Hiroki Takano in:

  36. Search for Yutaka Saito in:

  37. Search for Kazuhiro Sanpei in:

  38. Search for Osamu Onodera in:

  39. Search for Masatoyo Nishizawa in:

  40. Search for Masayuki Nakamura in:

  41. Search for Takeshi Yasuda in:

  42. Search for Yoshio Sakiyama in:

  43. Search for Mieko Otsuka in:

  44. Search for Akira Ueki in:

  45. Search for Ken-ichi Kaida in:

  46. Search for Jun Shimizu in:

  47. Search for Ritsuko Hanajima in:

  48. Search for Toshihiro Hayashi in:

  49. Search for Yasuo Terao in:

  50. Search for Satomi Inomata-Terada in:

  51. Search for Masashi Hamada in:

  52. Search for Yuichiro Shirota in:

  53. Search for Akatsuki Kubota in:

  54. Search for Yoshikazu Ugawa in:

  55. Search for Kishin Koh in:

  56. Search for Yoshihisa Takiyama in:

  57. Search for Natsumi Ohsawa-Yoshida in:

  58. Search for Shoichi Ishiura in:

  59. Search for Ryo Yamasaki in:

  60. Search for Akira Tamaoka in:

  61. Search for Hiroshi Akiyama in:

  62. Search for Taisuke Otsuki in:

  63. Search for Akira Sano in:

  64. Search for Akio Ikeda in:

  65. Search for Jun Goto in:

  66. Search for Shinichi Morishita in:

  67. Search for Shoji Tsuji in:


H.I. and S.T. designed the study; H.I., J.M., M.K.M., A.F., Y. Toyoshima, A. Kakita, H. Takahashi, Y. Suzuki, S. Sugano, H.Y., S. Shibata, A.M., M. Tanaka, Y.I., Y. Takahashi, H.D., T.M., J.S., N.O.-Y., S.I., J.G., S.M. and S.T. performed the experiments and analyzed the data; H.I., K.D., J.Y., Y. Suzuki, W.Q., K.I., K.H., H.D. and S.M. performed computational analysis; H.I., M.K.M., Y. Toyoshima, A.K., H. Takahashi and S.T. performed neuropathological analyses; H.I., J.M., M.K.M., Y. Toyoshima, A.K., H. Takahashi, M. Tanaka, Y.I., Y. Takahashi, T.M., S. Shibata., J.K., F.K.N., M. Higashihara, K.A., R.K., M.S., Y.K., N.H., N.K., T.K., T. Hitomi, M. Tada, H. Takano, Y. Saito, K.S., O.O., M. Nishizawa, M. Nakamura, T.Y., Y. Sakiyama, M.O., A.U., K. Kaida, R.H., T. Hayashi, Y. Terao, S.I.-T., M. Hamada, Y. Shirota, A. Kubota, Y.U., K. Koh, Y. Takiyama, R.Y., A.T., H.A., T.O., A.S. and A.I. collected and analyzed clinical data and provided patients’ samples; and H.I., M.K.M., A. Kakita, S.M. and S.T. wrote the manuscript, together with contributions from all authors.

Competing interests

The authors declare no competing financial interests. A.I. currently belongs to The Department of Epilepsy, Movement Disorders and Physiology, Graduate School of Medicine, Kyoto University, which is an endowment department supported with a grant from GlaxoSmithKline K.K., NIHON KOHDEN CORPORATION, Otsuka Pharmaceuticals Co., and UCB Japan Co., Ltd., but there is no financial relationship to this work.

Corresponding author

Correspondence to Shoji Tsuji.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1-17, Supplementary Tables 1, 2, 4-10 and Supplementary Note

  2. Life Sciences Reporting Summary

  3. Supplementary Table 3

    Differentially expressed genes

  4. Supplementary Data

    Uncropped blot images

About this article

Publication history




Issue Date


Further reading