Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor
Open accessAbstract
The roles of Plant Homeodomain (PHD) fingers in catalysis of histone modifications are unknown. We demonstrated that the PHD finger of Ubiquitin Protein Ligase E3 Component N-Recognin7 (UBR7) harbors E3 ubiquitin ligase activity toward monoubiquitination of histone H2B at lysine120 (H2BK120Ub). Purified PHD finger or full-length UBR7 monoubiquitinated H2BK120 in vitro, and loss of UBR7 drastically reduced H2BK120Ub genome-wide binding sites in MCF10A cells. Low UBR7 expression was correlated with occurrence of triple-negative breast cancer and metastatic tumors. Consistently, UBR7 knockdown enhanced the invasiveness, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 restored these cellular phenotypes and reduced tumor growth. Mechanistically, UBR7 loss reduced H2BK120Ub levels on cell adhesion genes, including CDH4, and upregulated the Wnt/β-Catenin signaling pathway. CDH4 overexpression could partially revert UBR7-dependent cellular phenotypes. Collectively, our results established UBR7 as a histone H2B monoubiquitin ligase that suppresses tumorigenesis and metastasis of triple-negative breast cancer.
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Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989 · see citing works
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219 · see citing works
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
Nishimura, R., Osako, T., Nishiyama, Y., Tashima, R., Nakano, M., Fujisue, M., Toyozumi, Y., & Arima, N. (2013) · Oncology · doi:10.1159/000353099 · Cited by 13,239 · see citing works
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro
Liang, C.-C., Park, A. Y., & Guan, J.-L. (2007) · Nature Protocols · doi:10.1038/nprot.2007.30 · Cited by 4,696 · see citing works
ChromHMM: automating chromatin-state discovery and characterization
Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works
The landscape of cancer genes and mutational processes in breast cancer
Stephens, P. J., Tarpey, P. S., Davies, H. R., Loo, P. V., Greenman, C., Wedge, D. C., Nik‐Zainal, S., Martin, S., Varela, I., Bignell, G. R., et al. (2012) · Nature · doi:10.1038/nature11017 · Cited by 1,686 · see citing works
Liu, H., & Naismith, J. H. (2008) · BMC Biotechnology · doi:10.1186/1472-6750-8-91 · Cited by 1,222 · see citing works
Cadherins in development: cell adhesion, sorting, and tissue morphogenesisPreprint
Halbleib, J. M., & Nelson, W. J. (2006) · Genes & Development · doi:10.1101/gad.1486806 · Cited by 1,063 · see citing works
Heterogeneity in breast cancer
Polyák, K. (2011) · Journal of Clinical Investigation · doi:10.1172/jci60534 · Cited by 1,012 · see citing works
SAMBLASTER : fast duplicate marking and structural variant read extraction
Faust, G. G., & Hall, I. M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu314 · Cited by 880 · see citing works
Shen, L., Shao, N., Liu, X., & Nestler, E. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-284 · Cited by 852 · see citing works
The PHD finger: Implications for chromatin-mediated transcriptional regulation
Aasland, R. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)88957-4 · Cited by 850 · see citing works
Cistrome: an integrative platform for transcriptional regulation studies
Liu, T., Ortiz, J. A., Taing, L., Meyer, C. A., Lee, B. T. K., Zhang, Y., Shin, H., Wong, S. S., Ma, J., Lei, Y., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-8-r83 · Cited by 705 · see citing works
Self-citationKi67, PCNA, and MCM proteins: Markers of proliferation in the diagnosis of breast cancer
Juríková, M., Danihel, Ľ., Polák, Š., & Varga, I. (2016) · Acta Histochemica · doi:10.1016/j.acthis.2016.05.002 · Cited by 609 · see citing works
Kim, J., Guermah, M., McGinty, R. K., Lee, J., Tang, Z., Milne, T. A., Shilatifard, A., Muir, T. W., & Roeder, R. G. (2009) · Cell · doi:10.1016/j.cell.2009.02.027 · Cited by 555 · see citing works
BRCA1 Is Associated with a Human SWI/SNF-Related Complex
Bochar, D. A., Wang, L., Beniya, H., Kinev, A. V., Xue, Y., Lane, W. S., Wang, W., Kashanchi, F., & Shiekhattar, R. (2000) · Cell · doi:10.1016/s0092-8674(00)00030-1 · Cited by 546 · see citing works
Elsheikh, S. E., Green, A. R., Rakha, E. A., Powe, D. G., Ahmed, R. A., Collins, H. M., Soria, D., Garibaldi, J. M., Paish, C. E., Ammar, A. A., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-3907 · Cited by 510 · see citing works
Epithelial–mesenchymal transition (EMT) and metastasis: yes, no, maybe?
Diepenbruck, M., & Christofori, G. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.06.002 · Cited by 473 · see citing works
The RING finger domain: a recent example of a sequence—structure family
Borden, K. L. B., & Freemont, P. S. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80060-1 · Cited by 472 · see citing works
Berx, G., & Roy, F. V. (2001) · Breast Cancer Research · doi:10.1186/bcr309 · Cited by 463 · see citing works
The PHD finger: a versatile epigenome reader
Sánchez, R., & Zhou, M. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.03.005 · Cited by 457 · see citing works
TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAs
Su, X., Chakravarti, D., Cho, M. S., Liu, L.-Z., Gi, Y. J., Lin, Y.-L., Leung, M. L., El‐Naggar, A. K., Creighton, C. J., Suraokar, M. B., et al. (2010) · Nature · doi:10.1038/nature09459 · Cited by 419 · see citing works
Self-citationCadherins and catenins in breast cancer
Cowin, P., Rowlands, T. M., & Hatsell, S. J. (2005) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2005.08.014 · Cited by 362 · see citing works
A Family of Mammalian E3 Ubiquitin Ligases That Contain the UBR Box Motif and Recognize N-Degrons
Tasaki, T., Mulder, L. C. F., Iwamatsu, A., Lee, M. J., Davydov, I. V., Varshavsky, A. J., Muesing, M. A., & Kwon, Y. T. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.16.7120-7136.2005 · Cited by 348 · see citing works
Is cancer a disease of self-seeding?
Norton, L., & Massagué, J. (2006) · Nature Medicine · doi:10.1038/nm0806-875 · Cited by 346 · see citing works
Li, J., & Zhou, B. P. (2011) · BMC Cancer · doi:10.1186/1471-2407-11-49 · Cited by 339 · see citing works
Kim, J., Hake, S. B., & Roeder, R. G. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.11.012 · Cited by 317 · see citing works
Histone Ubiquitination and Deubiquitination in Transcription, DNA Damage Response, and Cancer
Cao, J. P., & Yan, Q. (2012) · Frontiers in Oncology · doi:10.3389/fonc.2012.00026 · Cited by 317 · see citing works
Wnt signaling in triple-negative breast cancer
Pohl, S., Brook, N., Agostino, M., Arfuso, F., Kumar, A. P., & Dharmarajan, A. (2017) · Oncogenesis · doi:10.1038/oncsis.2017.14 · Cited by 296 · see citing works
Blecher-Gonen, R., Barnett-Itzhaki, Z., Jaitin, D., Amann-Zalcenstein, D., Lara-Astiaso, D., & Amit, I. (2013) · Nature Protocols · doi:10.1038/nprot.2013.023 · Cited by 289 · see citing works
Shema, E., Tirosh, I., Aylon, Y., Huang, J. L., Ye, C., Moskovits, N. B.-C., Raver-Shapira, N., Minsky, N., Pirngruber, J., Tarcic, G., et al. (2008) · Genes & Development · doi:10.1101/gad.1703008 · Cited by 288 · see citing works
Activation of the E3 ligase function of the BRCA1/BARD1 complex by polyubiquitin chains
Mallery, D. L., Vandenberg, C. J., & Hiom, K. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf691 · Cited by 280 · see citing works
Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation
Chatterjee, C., McGinty, R. K., Fierz, B., & Muir, T. W. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.315 · Cited by 249 · see citing works
EMT in Breast Carcinoma—A Review
Lima, J. F., Nofech‐Mozes, S., Bayani, J., et al. (2016) · Journal of Clinical Medicine · doi:10.3390/jcm5070065 · Cited by 231 · see citing works
The current state of breast cancer classification
Viale, G. (2012) · Annals of Oncology · doi:10.1093/annonc/mds326 · Cited by 218 · see citing works
RNF20 and USP44 Regulate Stem Cell Differentiation by Modulating H2B Monoubiquitylation
Fuchs, G., Shema, E., Vesterman, R., Kotler, E., Wolchinsky, Z., Wilder, S., Golomb, L., Pribluda, A., Zhang, F., Haj‐Yahya, M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.023 · Cited by 214 · see citing works
Enhancement of BRCA1 E3 Ubiquitin Ligase Activity through Direct Interaction with the BARD1 Protein
Xia, Y., Pao, G. M., Chen, H.-W., Verma, I. M., & Hunter, T. R. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m204591200 · Cited by 195 · see citing works
The mouse and human genes encoding the recognition component of the N-end rule pathway
Kwon, Y. T., Reiss, Y., Fried, V. A., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.14.7898 · Cited by 179 · see citing works
TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein
Bhatnagar, S., Gazin, C., Chamberlain, L., Ou, J., Zhu, X., Tushir, J. S., Virbasius, C.-M. A., Lin, L., Zhu, L. J., Wajapeyee, N., et al. (2014) · Nature · doi:10.1038/nature13955 · Cited by 177 · see citing works
The UCSC Cancer Genomics Browser
Zhu, J., Sanborn, Z., Benz, S. C., Szeto, C. W., Hsu, F., Kuhn, R. M., Karolchik, D., Archie, J. G., Lenburg, M. E., Esserman, L. J., et al. (2009) · Nature Methods · doi:10.1038/nmeth0409-239 · Cited by 171 · see citing works
Epigenome Mapping in Normal and Disease States
Maunakea, A. K., Chepelev, I., & Zhao, K. (2010) · Circulation Research · doi:10.1161/circresaha.110.222463 · Cited by 163 · see citing works
Histone modifications and cancer: biomarkers of prognosis?
Chervona, Y., & Costa, M. (2012) · Europe PMC (PubMed Central) · Cited by 155 · see citing works
The Substrate Recognition Domains of the N-end Rule Pathway
Tasaki, T., Zakrzewska, A., Dudgeon, D. D., Jiang, Y., Lazo, J. S., & Kwon, Y. T. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m803641200 · Cited by 149 · see citing works
IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo
Venkatanarayan, A., Raulji, P., Norton, W., Chakravarti, D., Coarfa, C., Su, X., Sandur, S. K., Ramirez, M. S., Lee, J., Kingsley, C. V., et al. (2014) · Nature · doi:10.1038/nature13910 · Cited by 131 · see citing works
Self-citationBiomarkers for EMT and MET in breast cancer: An update
Liu, F., Gu, L., Shan, B.-E., Geng, C., & Sang, M. (2016) · Oncology Letters · doi:10.3892/ol.2016.5369 · Cited by 130 · see citing works
Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition
Malouf, G. G., Taube, J. H., Lu, Y., Roysarkar, T., Panjarian, S. B., Estecio, M. R., Jelı́nek, J., Yamazaki, J., Raynal, N. J. ‐., Long, H., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-12-r144 · Cited by 92 · see citing works
Synthetic heterovalent inhibitors targeting recognition E3 components of the N-end rule pathway
Lee, M. J., Pal, K., Tasaki, T., Roy, S., Jiang, Y., An, J. Y., Banerjee, R., & Kwon, Y. T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708465105 · Cited by 82 · see citing works
Self-citationReply to Storey et al. : More DNA and dating studies needed for ancient El Arenal-1 chickens
Gongora, J., Rawlence, N. J., Mobegi, V. A., Jianlin, H., Alcalde, J. A., Matus, J. T., Hanotte, O., Moran, C., Austin, J. J., Ulm, S., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809681105 · Cited by 76 · see citing works
Adhikary, S., Sanyal, S., Basu, M., Sengupta, I., Sen, S., Srivastava, D. K., Roy, S., & Das, C. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.679985 · Cited by 71 · see citing works
Self-citationTaube, J. H., Sphyris, N., Johnson, K. S., Reisenauer, K. N., Nesbit, T. A., Joseph, R., Vijay, G. V., Sarkar, T. R., Bhangre, N., Song, J. J., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.19214 · Cited by 68 · see citing works
Engineering a Protein Scaffold from a PHD Finger
Kwan, A. H., Gell, D. A., Verger, A., Crossley, M., Matthews, J. M., & Mackay, J. P. (2003) · Structure · doi:10.1016/s0969-2126(03)00122-9 · Cited by 66 · see citing works
Dual Roles of RNF2 in Melanoma Progression
Rai, K., Akdemir, K. C., Kwong, L. N., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0493 · Cited by 66 · see citing works
Self-citationHistone H2B ubiquitination: the cancer connectionPreprint
Espinosa, J. M. (2008) · Genes & Development · doi:10.1101/gad.1732108 · Cited by 65 · see citing works
How integrins control breast biology
Glukhova, M. A., & Streuli, C. H. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.06.010 · Cited by 59 · see citing works
Loss of Retinal Cadherin Facilitates Mammary Tumor Progression and Metastasis
Agiostratidou, G., Li, M., Suyama, K., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-4007 · Cited by 51 · see citing works
The United States of Histone Ubiquitylation and Methylation
Werner, M. S., & Ruthenburg, A. J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.015 · Cited by 23 · see citing works
RNF20-SNF2H Pathway of Chromatin Relaxation in DNA Double-Strand Break Repair
Kato, A., & Komatsu, K. (2015) · Genes · doi:10.3390/genes6030592 · Cited by 17 · see citing works
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Manumycin polyketides act as molecular glues between UBR7 and P53
Isobe, Y., Okumura, M., McGregor, L. M., Brittain, S. M., Jones, M. D., Liang, X., White, R., Forrester, W., McKenna, J. M., Tallarico, J. A., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0557-2 · Cited by 124 · see citing works
- Authors
- Adhikary, S., Chakravarti, D., Terranova, C., Sengupta, I., Maitituoheti, M., Dasgupta, A., Srivastava, D. K., Ma, J., Raman, A. T., Tarco, E., Sahin, A. A., Bassett, R., Yang, F., Tapia, C., Roy, S., Rai, K., & Das, C.
- Affiliations
- Saha Institute of Nuclear Physics (IN)
- The University of Texas MD Anderson Cancer Center (US)
- Indian Institute of Chemical Biology (IN)
- Corresponding author
- Roy, Siddhartha
- Rai, Kunal
- Das, Chandrima
- ORCID
- Venue
- Nature Communications
- Published
- 2019-03-28
- Volume
- 10
- Issue
- 1
- Pages
- 1398-1398
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6438984
- OpenAlex
- W2923057516
- Cited by
- 57
- References
- 65
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 10 · 2023: 4 · 2022: 9 · 2021: 13 · 2020: 4 · 2019: 4
- FWCI
- 2.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Cancer Prevention and Research Institute of Texas (RP170067, CA160578)
- University Grants Commission
- University of Texas MD Anderson Cancer Center (RP170067, CA160578)
- National Cancer Institute (R00CA160578, K99CA160578, CA160578, P30CA016672)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- plant homeodomain finger, E3 ubiquitin ligase, histone H2B, triple-negative breast cancer, tumor suppressor, metastasis, epithelial-mesenchymal transition, CDH4, Wnt/β-catenin signaling, cell adhesion genes, MCF10A cells
- MeSH terms
- PHD Zinc Fingers, Animals, Cell Adhesion, Female, Histones, Humans, Mice, Nude, Neoplasm Metastasis, Neoplasm Transplantation, Transplantation, Heterologous, Cadherins, Histone Code, Ubiquitin-Protein Ligases, Cell Line, Tumor, Mice, Ubiquitination, Epithelial-Mesenchymal Transition, Wnt Signaling Pathway, Carcinogenesis, Triple Negative Breast Neoplasms
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