Aki Ushiki, PhD
Associate Specialist
Bioengineering
School of Pharmacy

My research focus aims to understand how gene-regulatory elements control gene expression in mammals, as it relates to the genetic basis of development, evolution and disease. I am working on several projects: elucidating the mechanism of congenital limb malformation (acheiropodia), dissecting factors involved in bat wing development and understanding the genetic cause of scoliosis.

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I am also developing novel in vivo high-throughput technologies combining my skills in mouse embryo manipulation and genomic techniques. I apply these technologies to evaluate the function of enhancers and disease-associated variants in mice. Employing these novel tools, I will be able to directly connect DNA sequence changes to their phenotypic impact on an organism. This project is currently supported by NHGRI K99 award.

Awards

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• Reviewers’ Choice (the top 10% of all poster abstracts), American Society of Human Genetics (ASHG) 2020 Virtual Meeting, 2020
• Semi-Finalists of ASHG/Charles J. Epstein Trainee Awards, American Society of Human Genetics (ASHG) 2020 Virtual Meeting, 2020
• Dean’s Award for Excellence, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan, 2017
• Valedictorian award of the College of Biological Sciences, University of Tsukuba, Japan, 2012

Education & Training

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• Ph.D. University of Tsukuba 2017

Interests

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• Functional genomics
• Reproductive biology
• Limb development and evolution

Websites

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• Twitter (twitter.com)
• Ahituv Lab (pharm.ucsf.edu)
• Google scholar (scholar.google.co.jp)
• Linkedin (linkedin.com)

Grants and Projects

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• Development of functional genomic technologies in mice, NHGRI, 2023
• How limbs became wings -Identification of bat wing functional enhancer-, Japan Society for the Promotion of Science (JSPS), 2019-2021
• Identification of bat limb enhancers using comparative genomics, The Uehara Memorial Foundation, 2018-2019
• Identification of Renin gene hypertension responsive enhancer, Japan Society for the Promotion of Science (JSPS), 2017-2018
• Identification of Renin gene hypertension responsive enhancer, Japan Society for the Promotion of Science (JSPS), 2016-2017

Publications (14)

Top publication keywords:
Hand Deformities, CongenitalRNA, Long NoncodingFoot Deformities, CongenitalReninEnhancer Elements, GeneticCCCTC-Binding FactorGenomic ImprintingRenin-Angiotensin SystemLocus Control RegionGene Expression Regulation, DevelopmentalExtremitiesSequence DeletionHypertensionScoliosisInsulin-Like Growth Factor II

• Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
  Cell reports 2024 Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N
• Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis.
  eLife 2024 Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng RR, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, …
• Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis.
  bioRxiv : the preprint server for biology 2023 Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng R, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, …
• Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
  bioRxiv : the preprint server for biology 2023 Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N
• Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
  Nature communications 2021 Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL…

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• Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome.
  Human molecular genetics 2021 Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N
• The cartilage matrisome in adolescent idiopathic scoliosis.
  Bone research 2020 Wise CA, Sepich D, Ushiki A, Khanshour AM, Kidane YH, Makki N, Gurnett CA, Gray RS, Rios JJ, Ahituv N, Solnica-Krezel L
• Recapitulation of gametic DNA methylation and its post-fertilization maintenance with reassembled DNA elements at the mouse Igf2/H19 locus.
  Epigenetics & chromatin 2020 Matsuzaki H, Kuramochi D, Okamura E, Hirakawa K, Ushiki A, Tanimoto K
• Transvection-like interchromosomal interaction is not observed at the transcriptional level when tested in the Rosa26 locus in mouse.
  PloS one 2019 Tanimoto K, Matsuzaki H, Okamura E, Ushiki A, Fukamizu A, Engel JD
• Synthetic DNA fragments bearing ICR cis elements become differentially methylated and recapitulate genomic imprinting in transgenic mice.
  Epigenetics & chromatin 2018 Matsuzaki H, Okamura E, Kuramochi D, Ushiki A, Hirakawa K, Fukamizu A, Tanimoto K
• Homeostatic Response of Mouse renin Gene Transcription in a Hypertensive Environment Is Mediated by a Novel 5' Enhancer.
  Molecular and cellular biology 2018 Ushiki A, Matsuzaki H, Fukamizu A, Tanimoto K
• Long-Range Control of Renin Gene Expression in Tsukuba Hypertensive Mice.
  PloS one 2016 Ushiki A, Matsuzaki H, Ishida J, Fukamizu A, Tanimoto K
• De novo DNA methylation through the 5'-segment of the H19 ICR maintains its imprint during early embryogenesis.
  Development (Cambridge, England) 2015 Matsuzaki H, Okamura E, Takahashi T, Ushiki A, Nakamura T, Nakano T, Hata K, Fukamizu A, Tanimoto K
• A mouse renin distal enhancer is essential for blood pressure homeostasis in BAC-rescued renin-null mutant mice.
  Journal of receptor and signal transduction research 2014 Tanimoto K, Kanafusa S, Ushiki A, Matsuzaki H, Ishida J, Sugiyama F, Fukamizu A