| 1. |
Yasuyuki Ohkawa, Single-cell multi-targeted chromatin integration labeling technology for understanding chromatin dynamics, CSHA meeting on Integrative Epigenetics in Plants, 2022.12. |
| 2. |
Yasuyuki Ohkawa, Spatial multi-omics for understanding gene expression regulated by cell-cell interaction, Japan-UK Regulation through Chromatin Conference, 2022.08. |
| 3. |
Yasuyuki Ohkawa, Identification and Analysis of Minor Histone Variants, EMBO Workshop Physiology and function of histone variants, 2021.09. |
| 4. |
大川恭行, Chromatin integration labeling Technology for expanding multi-omics, 理研エピゲノム操作プロジェクトセミナー, 2020.06, Cell identity is determined by the selective activation or silencing of specific genes via transcription factor binding and epigenetic modifications on the genome. Chromatin immunoprecipitation (ChIP) has been the standard technique for mapping the sites of transcription factor binding and histone modification. Recently, alternative methods to ChIP have been developed for addressing the increasing demands for low-input epigenomic profiling. Chromatin integration labeling (ChIL) followed by sequencing (ChIL-seq) has been demonstrated to be particularly useful for epigenomic profiling of low-input samples or even single cells because the technique amplifies the target genomic sequence before cell lysis. After labeling the target protein or modification in situ with an oligonucleotide-conjugated antibody (ChIL probe), the nearby genome sequence is amplified by Tn5 transposase-mediated transposition followed by T7 RNA polymerase-mediated transcription. ChIL-seq enables the detection of the antibody target localization under a fluorescence microscope and at the genomic level. Here we describe the detailed protocol of ChIL-seq with assessment methods for the key steps, including ChIL probe reaction, transposition, in situ transcription and sequencing library preparation. The protocol usually takes 3 d to prepare the sequencing library, including overnight incubations for the ChIL probe reaction and in situ transcription. The ChIL probe can be separately prepared and stored for several months, and its preparation and evaluation protocols are also documented in detail. An optional analysis for multiple targets (multitarget ChIL-seq) is also described. We anticipate that the protocol presented here will make the ChIL technique more widely accessible for analyzing precious samples and facilitate further applications.. |
| 5. |
Yasuyuki Ohkawa, Chromatin integration labelling Technology for expanding multi-omics, EMBO Symposia: Multi-Omics, 2019.09. |
| 6. |
Yasuyuki Ohkawa, The Function of Histone H3.3 Subvariants in Skeletal Muscle Regeneration Approached from Spatial Transcriptomics , UPF招聘セミナー, 2019.09. |
| 7. |
大川 恭行, Transcriptional Plasticity regulated by novel Histone H3 Varigants, 理研連携プロジェクト「エピゲノム操作」, 2019.02. |
| 8. |
大川 恭行, Histone composition in chromatin regulates skeletal muscle regeneration, The 6th Society of Skeletal Muscle Cells, 2018.11. |
| 9. |
Ohkawa Yasuyuki, Tissue-specific Chromatin Structures According to Histone H3 Variants ., 研究セミナー, 2017.10. |
| 10. |
Ohkawa Yasuyuki, Myogenic chromatin structure is formed with the novel histone H3 variant., EMBO Workshop Histone Vriants, 2017.09. |
| 11. |
Ohkawa Yasuyuki, ChILT - an Immunoprecipitation-free Epigenome Profiling Technology., 1st München-Japan Mini Symposium “Chromatin Structure and Function”, 2017.09. |
| 12. |
Ohkawa Yasuyuki, Myogenic Chromatin Structure Is Formed with the Histone H3 Variant H3mm7, Gordon Research Conference, 2017.06. |
| 13. |
Ohkawa Yasuyuki, ChiLT-an Immunoprecipitation-free Epigenome Profiling Technology, Single Cell Omics (E3), 2017.05. |
| 14. |
大川 恭行, The baselines of transcription levels are determined by selective incorporation of histone H3 variants., Transcriptional and Epigenetic Control in Stem Cells (J1), 2017.01, Selective gene expression in cell differentiation is initiated by the binding of tissue-specific transcription factors (TFs).
Chromatin structure is known to tune the function of bound TFs by nucleosome positioning, histone modification, and the
incorporation of histone variants [1]. However the specific contribution of each component of chromatin has been
unclear.
We recently reported that we identified hitherto unknown fourteen histone H3 variants and that they were detected in a
variety of tissues [2]. Our functional analysis revealed that H3mm7, one of the newly discovered histone H3 variants, was
required for skeletal muscle differentiation. H3mm7 knockout in C2C12 myoblasts resulted in rigid chromatin structure
and in the reduction of transcription levels of a subset of the genes into which H3mm7 was incorporated. The data
suggest that H3mm7 and other variants contribute to set the baselines of transcription levels. I will discuss other recent
advances in understanding the novel histone H3 variants.
[1] Harada, A. et al. (2015) Nucleic Acids Res. 43, 775. Incorporation of histone H3.1 suppresses the lineage potential of
skeletal muscle.
[2] Maehara, K. et al. (2016) Epigenetics Chromatin. 8, 35. Tissue-specific expression of histone H3 variants diversified
after species separation.. |
| 15. |
大川 恭行, N6-methyladenosine is required for the processing of MyoD pre-mRNA for maintaining skeletal muscle differentiation potential., Keystone Symposia Chromatin and Epigenetics (C2), 2016.03. |
| 16. |
大川 恭行, Cell fate decision on chromatin by MyoD, BMB2010(第38回日本分子生物学会年会・第88回日本生化学会大会合同大会）, 2015.12. |
| 17. |
大川 恭行, The Diversity of Mouse Histone H3 Variants, International Symposium on Chromatin Structure, Dynamics, and Function, 2015.08. |
| 18. |
原田 哲仁, 前原 一満, 佐藤 優子, 木村 宏, 大川 恭行, Incorporation of Histone H3 Variants Dictates the Lineage Potential of Skeletal Muscle, FASEB;Science Research Conferences, 2014.07. |
| 19. |
前原 一満, 大川 恭行, Exploring nucleosome positioning patterns act as a functional component of chromatin structure, ENBO Workshop Histone varisnts, 2014.06. |
| 20. |
原田 哲仁, 前原 一満, 大川 恭行, Incorporation of Histone H3 Variants Dictates Myogenesis, ENBO Workshop Histone varisnts, 2014.06. |
| 21. |
大川 恭行, Diversity of histone H3 variants on mouse genome, ENBO Workshop Histone varisnts, 2014.06. |
| 22. |
原田 哲仁, 前原 一満, 大川 恭行, The balance of histone H3 variants around transcription start sites dictates cell differential potential, Keystone Symposia , 2014.02. |
| 23. |
前原 一満, 大川 恭行, The formation of nucleosome positioning patterns flanked by transcription factor binding site, Keystone Symposia , 2014.02. |
| 24. |
大川 恭行, Epigenomic approach unveils cell fate decision, 日本遺伝学会第85回大会, 2013.09. |
| 25. |
大川 恭行, High order chromatin regulation in skeletal muscle differentiation, 第86回日本生化学会大会, 2013.09. |
| 26. |
大川 恭行, Histone bariants determine the lineage potential of skeletal muscle, Fukuoka Internasional Symposium on Genomics & Epigenomics 2013, 2013.09. |
| 27. |
Genomic clustering accompanies cellular differentiation to temporally control gene expression. |
