Phillip B. Carpenter, Ph.D

Associate Professor
BCB Graduate Program


Description of Research

EPIGENETICS AND THE NSD FAMILY IN DEVELOPMENT AND DISEASE

Our lab has been traditionally interested in the cellular response to DNA damage and more recently interested in the understanding the role of the nuclear receptor SET domain containing family, or “NSD” family in biological pathways that are relevant for health and disease. NSD proteins are very clinically relevant and have been found to be perturbed in various diseases including neuroblastoma, glioma, breast and prostate cancer. In fact, a recent, epigenetic gene expression profiling study identified a candidate gene signature that includes NSD1 (DNMT3A, MBD4,MLL2, MLL3, NSD1, and SRCAP), that can significantly discriminated nonmalignant from prostate tumor tissue (P = 0.0063) in an independent cohort.  Translocations in NSD1 are well established to be causal for the generation of acute myeloid leukemia and overexpression of NSD2 has been implicated in multiple myeloma. Moreover, haploinsufficiency in NSD1 is the major, if not only, cause of Sotos syndrome, a developmental abnormality marked by bone overgrowth, craniofacial defects, learning disabilities, and a spectrum of other disorders. Translocations at chromosome 4 can lead to defects in NSD2 and the developmental disorder known as Wolf Hirschhorn syndrome. Additional pathologies caused by perturbations in the NSD family have also been noted.

Although highly relevant to human health and disease, surprisingly only a few details have been published regarding the mechanism of NSD family action. NSD family members are large proteins that possess numerous domains, many of which have been implicated in chromatin biology. Notably, NSD family members possess a catalytic SET domain that has been shown to methylate histone side chains, particularly lysine 36 of histone H3 (H3-K36). Additional studies have revealed that in response to tumor necrosis factor α or interleukin-1, NSD1 is essential in mammals and methylates two lysine residues in the p65 subunit of NF-κB, a critical factor in numerous cell systems. Thus, NSD1, and by, extension additional family members, target non-histone proteins. The nature of these substrates and the pathways that they lie upon promise to be important in any of the numerous pathologies linked to the NSD family.

Our lab has created various research tools to understand the role of the NSD family in development and disease. Using a recently described “FLAG knock-in” strategy, we determined the global targets of NSD1. We found that NSD1 dependent methylation of H3-K36 recruits RNA Polymerase II to various promoter elements including that of bone morphogenic protein 4 (BMP4). We are currently examining the relationship between H3-K36 methylation and RNA Pol II activity.

philC_fig1

Structural relationship between members of the nuclear receptor binding SET domain containing protein (NSD) family. Major domains are highlighted: NID = nuclear receptor, ligand dependent (+L) or independent (-L) binding domains; HMG = high mobility group; PhD, C5HCH = chromatin associated Zinc fingers; PWWP= chromatin associated domains; SET = Set domain with pre- and post-motifs. Not drawn to scale.


4.2

Mutations in NSD1 cause the Sotos overgrowth syndrome.

philC_fig3

Strategy for engineering epitope tags at the 3′ end of human NSD1 gene.

Contact Information

phillip.b.carpenter@uth.tmc.edu

UTHealth Medical School
Department of Biochemistry and Molecular Biology
6431 Fannin Street, MSB 6.180
Houston, Texas 77030

713-500-6032 Direct  713-500-0652 Fax

Education

Ph.D. - University of Illinois

Postdoctoral Fellow - California Technical Institute

Research Interests

DNA repair, chromatin regulation

Publications

Understanding the language of Lys36 methylation at histone H3.

Wagner EJ, Carpenter PB.

Nat Rev Mol Cell Biol. 2012 Jan 23;13(2):115-26. doi: 10.1038/nrm3274. Review.

PMID: 22266761

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DNA damage-induced G2-M checkpoint activation by histone H2AX and 53BP1.

Fernandez-Capetillo O, Chen HT, Celeste A, Ward I, Romanienko PJ, Morales JC, Naka K, Xia Z, Camerini-Otero RD, Motoyama N, Carpenter PB, Bonner WM, Chen J, Nussenzweig A.

Nat Cell Biol. 2002 Dec;4(12):993-7.

PMID: 12447390

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Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function.

Lucio-Eterovic AK, Singh MM, Gardner JE, Veerappan CS, Rice JC, Carpenter PB.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16952-7. doi: 10.1073/pnas.1002653107. Epub 2010 Sep 13.

PMID: 20837538

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