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Nuclear localization signal region in nuclear receptor PXR governs the receptor association with mitotic chromatin

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Abstract

In recent years, some transcription factors have been observed to remain associated with mitotic chromatin. Based on these observations, it is suggested that these chromatin-bound transcription factors may serve as ‘epigenetic marks’ for transmission of pattern of gene expression from progenitor to progeny cells. In this context, our laboratory has reported that nuclear receptor PXR, a master regulator of xenobiotic metabolism, remains constitutively associated with mitotic chromatin. However, the region responsible for this interaction with chromatin remained unknown. In this study, we have shown, for the first time, that mitotic chromatin association of this factor is mediated by the combined action of two zinc fingers present in the DNA-binding domain of PXR. Overall, the nuclear localization signal (NLS) region appears to play a major role in this interaction with mitotic chromatin. Also, we have identified a sub-region of 11 amino acid residues within NLS region of PXR (R66-76R) essential for receptor interaction with the mitotic chromatin. Interestingly, this minimal region is sequence-specific and independent of its basic charge. We have termed this minimal sub-region as ‘mitotic chromatin binding-determining region’ (MCBR). It is suggested that this receptor region is essential for activation of its target genes. Additionally, we have shown that PXR remains associated with the everted repeat (ER6) region of its major target gene, CYP3A4 promoter during mitosis implying its suggested role in ‘gene bookmarking’.

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Abbreviations

AR:

Androgen receptor

BIOPIT:

Bimolecular imprints offered to progeny for inheritance of traits

Cdks:

Cyclin-dependent kinases

ChIP:

Chromatin immunoprecipitation

CTCF:

CCCTC-binding factor

DHT:

Dihydrotestosterone

ER6:

Everted repeat 6

ERα:

Estrogen receptor α

Esrrb:

Estrogen-related receptor beta

FACS:

Fluorescence-activated cell sorting

FLIM:

Fluorescence-lifetime imaging microscopy

FOX1:

Forkhead box 1

FRET:

Fluorescence resonance energy transfer

HMGA1a:

High-mobility group proteins A1

HMGB1:

High-mobility group box 1

HMGB2:

High-mobility group protein B2

hsp70:

70 kilodalton heat shock proteins

MCBR:

Mitotic chromatin binding-determining region

NLS:

Nuclear localization signal

PARP-1:

Poly (ADP-ribose) polymerase-1

PcG proteins:

Polycomb-group proteins

PXR:

Pregnane and xenobiotic receptor

RBPJ:

Recombining binding protein suppressor of hairless

Runx3:

Runt-related transcription factor 3

TBP:

TATA-box-binding protein

TFIID:

Transcription factor II D

TFIIH:

Transcription factor II Human

XREM:

Xenobiotic response element

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Acknowledgements

We acknowledge Dr. Amulya K. Panda, Director, and Dr. Vikash Kumar, Scientist at the National Institute of Immunology, New Delhi, for help with the cell cycle analysis and sorting of mitotic cells.

Funding

The research work presented in this paper was financially supported by a research grant to RKT from the UPE-II (University with Potential for Excellence phase II)- project ID 25 and UGC (University Grants Commission)- major project - F.No. 41-1294/2012(SR), Central financial support to our Centre by UGC-SAP (University Grants Commission-Special Assistance Programme) - F.No. 3-17/2015/DRS II (SAP-II), ICMR-CAR (Indian Council of Medical Research-Centre for Advanced Research) - F.No. 63/9/2010-BMS, DST-PURSE (Department of Science & Technology-Promotion of University Research and Scientific Excellence) - PAC-JNU-DST-PURSE-462 (Phase-II) is gratefully acknowledged. MR, AKD, and KP acknowledge UGC-BSR (University Grants Commission - Basic Scientific Research), DST-INSPIRE (Department of Science & Technology- Innovation in Science Pursuit for Inspired Research) and DST-SERB (Department of Science & Technology-Science and Engineering Research Board) respectively for the grant of doctoral research fellowships (MR and AKD) and post-doctoral research fellowship (KP).

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  1. Manjul Rana and Amit K. Dash contributed equally as first authors.

Authors and Affiliations

  1. Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India

    Manjul Rana, Amit K. Dash & Rakesh K. Tyagi

  2. Synthetic Biology Lab, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India

    Kalaiarasan Ponnusamy

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  1. Manjul Rana
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  2. Amit K. Dash
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  3. Kalaiarasan Ponnusamy
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  4. Rakesh K. Tyagi
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RKT conceived, designed, and supervised the project. MR and AKD designed and performed most of the experiments. RKT, MR, and AKD analyzed the data and wrote the paper. KP did the in silico experiments.

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Correspondence to Rakesh K. Tyagi.

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Rana, M., Dash, A.K., Ponnusamy, K. et al. Nuclear localization signal region in nuclear receptor PXR governs the receptor association with mitotic chromatin. Chromosome Res 26, 255–276 (2018). https://doi.org/10.1007/s10577-018-9583-2

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