Template Activating Factor-I α Regulates Retroviral Silencing during Reprogramming

Phuong Linh Bui; Ken Nishimura; Gonzalo Seminario Mondejar; Arun Kumar; Shiho Aizawa; Kensaku Murano; Kyosuke Nagata; Yohei Hayashi; Aya Fukuda; Yasuko Onuma; Yuzuru Ito; Mahito Nakanishi; Koji Hisatake

doi:10.1016/j.celrep.2019.10.010

Template Activating Factor-I α Regulates Retroviral Silencing during Reprogramming

Cell Rep. 2019 Nov 12;29(7):1909-1922.e5. doi: 10.1016/j.celrep.2019.10.010.

Authors

Affiliations

¹ Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
² Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan. Electronic address: ken-nishimura@md.tsukuba.ac.jp.
³ Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
⁴ Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
⁵ Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
⁶ Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
⁷ Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan. Electronic address: kojihisa@md.tsukuba.ac.jp.

PMID: 31722206
DOI: 10.1016/j.celrep.2019.10.010

Abstract

Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is accompanied by dramatic changes in epigenetic programs, including silencing of endogenous and exogenous retroviruses. Here, we utilized replication-defective and persistent Sendai virus (SeVdp)-based vectors to monitor retroviral silencing during reprogramming. We observed that retroviral silencing occurred at an early reprogramming stage without a requirement for KLF4 or the YY1-binding site in the retroviral genome. Insertional chromatin immunoprecipitation (iChIP) enabled us to isolate factors assembled on the silenced provirus, including components of inhibitor of histone acetyltransferase (INHAT), which includes the SET/TAF-I oncoprotein. Knockdown of SET/TAF-I in mouse embryonic fibroblasts (MEFs) diminished retroviral silencing during reprogramming, and overexpression of template activating factor-I α (TAF-Iα), a SET/TAF-I isoform predominant in embryonic stem cells (ESCs), reinforced retroviral silencing by an SeVdp-based vector that is otherwise defective in retroviral silencing. Our results indicate an important role for TAF-Iα in retroviral silencing during reprogramming.

Keywords: SeVdp vector; TAF-Iα; insertional chromatin immunoprecipitation; primer-binding site; reprogramming; retroviral silencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cellular Reprogramming Techniques*
Cellular Reprogramming*
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Endogenous Retroviruses* / genetics
Endogenous Retroviruses* / metabolism
Gene Silencing*
Histone Chaperones / genetics
Histone Chaperones / metabolism
Kruppel-Like Factor 4
Kruppel-Like Transcription Factors / genetics
Kruppel-Like Transcription Factors / metabolism
Mice
Mouse Embryonic Stem Cells* / cytology
Mouse Embryonic Stem Cells* / metabolism
Mouse Embryonic Stem Cells* / virology
Sendai virus / genetics
Sendai virus / metabolism
YY1 Transcription Factor / genetics
YY1 Transcription Factor / metabolism

Substances

DNA-Binding Proteins
Histone Chaperones
Klf4 protein, mouse
Kruppel-Like Factor 4
Kruppel-Like Transcription Factors
SET protein, mouse
YY1 Transcription Factor
Yy1 protein, mouse