The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers

Brianna J. Klein, Lianhua Piao, Yuanxin Xi, Hector Rincon-Arano, Scott B. Rothbart, Danni Peng, Hong Wen, Connie Larson, Xi Zhang, Zheng Xia, Michael A. Cortazar, Pedro V. Peña, Anthony Mangan, David L. Bentley, Brian D. Strahl, Mark Groudine, Wei Li, Xiaobing Shi, Tatiana G. Kutateladze

Research output: Contribution to journalArticle

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Abstract

The histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis. It contains multiple conserved chromatin-associated domains, including three PHD fingers of unknown function. Here, we show that the first and third, but not the second, PHD fingers of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3. RNA-seq analysis indicates that KDM5B functions as a transcriptional repressor for genes involved in inflammatory responses, cell proliferation, adhesion, and migration. Biochemical analysis reveals that KDM5B associates with components ofthe nucleosome remodeling and deacetylase (NuRD) complex and may cooperate with the histone deacetylase 1 (HDAC1) in gene repression. KDM5B is downregulated in triple-negative breast cancer relative to estrogen-receptor-positive breast cancer. Overexpression of KDM5B in the MDA-MB 231 breast cancer cells suppresses cell migration and invasion, and the PHD1-H3K4me0 interaction is essential for inhibiting migration. These findings highlight tumor-suppressive functions of KDM5B in triple-negative breast cancer cells and suggest a multivalent mechanism for KDM5B-mediated transcriptional regulation.

Original languageEnglish (US)
Pages (from-to)325-335
Number of pages11
JournalCell Reports
Volume6
Issue number2
DOIs
StatePublished - 2014
Externally publishedYes

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Histones
Fingers
Genes
Triple Negative Breast Neoplasms
Mi-2 Nucleosome Remodeling and Deacetylase Complex
Substrates
Histone Demethylases
Histone Deacetylase 1
Cells
Cell Movement
Histone Code
Cell proliferation
Transcription
Breast Neoplasms
Estrogen Receptors
Chromatin
Tumors
Adhesion
Cell Adhesion
RNA

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Klein, B. J., Piao, L., Xi, Y., Rincon-Arano, H., Rothbart, S. B., Peng, D., ... Kutateladze, T. G. (2014). The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers. Cell Reports, 6(2), 325-335. https://doi.org/10.1016/j.celrep.2013.12.021

The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers. / Klein, Brianna J.; Piao, Lianhua; Xi, Yuanxin; Rincon-Arano, Hector; Rothbart, Scott B.; Peng, Danni; Wen, Hong; Larson, Connie; Zhang, Xi; Xia, Zheng; Cortazar, Michael A.; Peña, Pedro V.; Mangan, Anthony; Bentley, David L.; Strahl, Brian D.; Groudine, Mark; Li, Wei; Shi, Xiaobing; Kutateladze, Tatiana G.

In: Cell Reports, Vol. 6, No. 2, 2014, p. 325-335.

Research output: Contribution to journalArticle

Klein, BJ, Piao, L, Xi, Y, Rincon-Arano, H, Rothbart, SB, Peng, D, Wen, H, Larson, C, Zhang, X, Xia, Z, Cortazar, MA, Peña, PV, Mangan, A, Bentley, DL, Strahl, BD, Groudine, M, Li, W, Shi, X & Kutateladze, TG 2014, 'The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers', Cell Reports, vol. 6, no. 2, pp. 325-335. https://doi.org/10.1016/j.celrep.2013.12.021
Klein, Brianna J. ; Piao, Lianhua ; Xi, Yuanxin ; Rincon-Arano, Hector ; Rothbart, Scott B. ; Peng, Danni ; Wen, Hong ; Larson, Connie ; Zhang, Xi ; Xia, Zheng ; Cortazar, Michael A. ; Peña, Pedro V. ; Mangan, Anthony ; Bentley, David L. ; Strahl, Brian D. ; Groudine, Mark ; Li, Wei ; Shi, Xiaobing ; Kutateladze, Tatiana G. / The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers. In: Cell Reports. 2014 ; Vol. 6, No. 2. pp. 325-335.
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AU - Rincon-Arano, Hector

AU - Rothbart, Scott B.

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AU - Wen, Hong

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AU - Cortazar, Michael A.

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AU - Bentley, David L.

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