Abstract: Cyclins encode regulatory subunits of holoenzymes that phosphorylate a variety of cellular substrates. Although the classic role of cyclins in cell cycle progression and tumorigenesis has been well characterized, new functions have been identified, including the induction of cellular migration and invasion, enhancement of angiogenesis, inhibition of mitochondrial metabolism, regulation of transcription factor signaling via a DNA-bound form, the induction of chromosomal instability, enhancement of DNA damage sensing and DNA damage repair, and feedback governing expression of the noncoding genome. This review describes the mechanisms of these new functions of cyclin D1. Cyclins encode regulatory subunits of holoenzymes that phosphorylate a variety of cellular substrates. Although the classic role of cyclins in cell cycle progression and tumorigenesis has been well characterized, new functions have been identified, including the induction of cellular migration and invasion, enhancement of angiogenesis, inhibition of mitochondrial metabolism, regulation of transcription factor signaling via a DNA-bound form, the induction of chromosomal instability, enhancement of DNA damage sensing and DNA damage repair, and feedback governing expression of the noncoding genome. This review describes the mechanisms of these new functions of cyclin D1. The family of D-type cyclins (D1, D2, and D3) regulates the G1/S-phase transition, and D cyclins bind and activate cyclin-dependent kinases (Cdk4 and Cdk6) to phosphorylate the retinoblastoma (pRb) protein, and through titration of the Cdk inhibitors p21Cip1 and p27Kip1, the cyclin D–Cdk4/6 complexes activate cyclin E/Cdk2.1Massague J. G1 cell-cycle control and cancer.Nature. 2004; 432: 298-306Crossref PubMed Scopus (960) Google Scholar Genetic analysis studies in mice have demonstrated an essential role for cyclin D1 in normal development of the retina, components of the nervous system, and terminal alveolar breast bud development.2Fantl V. Stamp G. Andrews A. Rosewell I. Dickson C. Mice lacking cyclin D1 are small and show defects in eye and mammary gland development.Genes Dev. 1995; 9: 2364-2372Crossref PubMed Scopus (604) Google Scholar, 3Sicinski P. Donaher J.L. Parker S.B. Li T. Fazeli A. Gardner H. Haslam S.Z. Bronson R.T. Elledge S.J. Weinberg R.A. Cyclin D1 provides a link between development and oncogenesis in the retina and breast.Cell. 1995; 82: 621-630Abstract Full Text PDF PubMed Scopus (890) Google Scholar Cyclin D1 promotes neural basal progenitors,4Lange C. Huttner W.B. Calegari F. 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Rescue of cyclin D1 deficiency by knockin cyclin E.Cell. 1999; 97: 767-777Abstract Full Text Full Text PDF PubMed Scopus (287) Google Scholar The kinase-defective cyclin D1 K112E binds p27Kip1, and, in conjunction with prior studies showing p27Kip1, is epistemic to cyclin D1 in the development of the retina and mammary epithelial cell proliferation, raises the possibility of a role for p27Kip1 binding in this stem cell differentiation function.7Geng Y. Yu Q. Sicinska E. Das M. Bronson R.T. Sicinski P. Deletion of the p27Kip1 gene restores normal development in cyclin D1-deficient mice.Proc Natl Acad Sci U S A. 2001; 98: 194-199Crossref PubMed Scopus (139) Google Scholar Studies of cyclin D1−/− bone marrow macrophages demonstrated an essential role for cyclin D1 in cellular adhesion and migration, a finding common to other cell types, including fibroblasts and mammary epithelial cells.8Neumeister P. Pixley F.J. Xiong Y. Xie H. Wu K. Ashton A. Cammer M. Chan A. Symons M. Stanley E.R. Pestell R.G. Cyclin D1 governs adhesion and motility of macrophages.Mol Biol Cell. 2003; 14: 2005-2015Crossref PubMed Scopus (130) Google Scholar, 9Li Z. Wang C. Jiao X. Lu Y. Fu M. Quong A.A. Dye C. Yang J. Dai M. Ju X. Zhang X. Li A. Burbelo P. Stanley E.R. Pestell R.G. Cyclin D1 regulates cellular migration through the inhibition of thrombospondin 1 and ROCK signaling.Mol Cell Biol. 2006; 26: 4240-4256Crossref PubMed Scopus (150) Google Scholar, 10Li Z. Jiao X. Wang C. Ju X. Lu Y. Yuan L. Lisanti M.P. Katiyar S. Pestell R.G. Cyclin D1 induction of cellular migration requires p27(KIP1).Cancer Res. 2006; 66: 9986-9994Crossref PubMed Scopus (112) Google Scholar Cyclin D1b, a common polymorphism at the exon-4 intron-4 boundary of the human cyclin D1 gene, did not enhance cell migration.11Li Z. Wang C. Jiao X. Katiyar S. Casimiro M.C. Prendergast G.C. Powell M.J. Pestell R.G. Alternate cyclin D1 mRNA splicing modulates p27KIP1 binding and cell migration.J Biol Chem. 2008; 283: 7007-7015Crossref PubMed Scopus (50) Google Scholar The mechanism by which cyclin D1a promotes cell migration has been examined in detail. Cyclin D1a stabilizes p27Kip1, inhibiting RhoA-inducing Rho-associated protein kinase and myosin light chain kinase.9Li Z. Wang C. Jiao X. Lu Y. Fu M. Quong A.A. Dye C. Yang J. Dai M. Ju X. Zhang X. Li A. Burbelo P. Stanley E.R. Pestell R.G. Cyclin D1 regulates cellular migration through the inhibition of thrombospondin 1 and ROCK signaling.Mol Cell Biol. 2006; 26: 4240-4256Crossref PubMed Scopus (150) Google Scholar, 10Li Z. Jiao X. Wang C. Ju X. Lu Y. Yuan L. Lisanti M.P. Katiyar S. Pestell R.G. Cyclin D1 induction of cellular migration requires p27(KIP1).Cancer Res. 2006; 66: 9986-9994Crossref PubMed Scopus (112) Google Scholar, 11Li Z. Wang C. Jiao X. Katiyar S. Casimiro M.C. Prendergast G.C. Powell M.J. Pestell R.G. Alternate cyclin D1 mRNA splicing modulates p27KIP1 binding and cell migration.J Biol Chem. 2008; 283: 7007-7015Crossref PubMed Scopus (50) Google Scholar Cyclin D1 also conveys an indirect effect to inhibit migration by inhibiting epithelial-mesenchymal transition,12Tobin N.P. Sims A.H. Lundgren K.L. Lehn S. Landberg G. Cyclin D1, Id1 and EMT in breast cancer.BMC Cancer. 2011; 11: 417Crossref PubMed Scopus (85) Google Scholar suggesting the effect of cyclin D1 on migration may vary by cell type and differentiation status.12Tobin N.P. Sims A.H. Lundgren K.L. Lehn S. Landberg G. Cyclin D1, Id1 and EMT in breast cancer.BMC Cancer. 2011; 11: 417Crossref PubMed Scopus (85) Google Scholar Mass spectrometry identified protein kinase C and casein kinase substrate in neurons 213Meng H. Tian L. Zhou J. Li Z. Jiao X. Li W.W. Plomann M. Xu Z. Lisanti M.P. Wang C. Pestell R.G. PACSIN 2 represses cellular migration through direct association with cyclin D1 but not its alternate splice form cyclin D1b.Cell Cycle. 2011; 10: 73-81Crossref PubMed Scopus (32) Google Scholar and filamin A13Meng H. Tian L. Zhou J. Li Z. Jiao X. Li W.W. Plomann M. Xu Z. Lisanti M.P. Wang C. Pestell R.G. PACSIN 2 represses cellular migration through direct association with cyclin D1 but not its alternate splice form cyclin D1b.Cell Cycle. 2011; 10: 73-81Crossref PubMed Scopus (32) Google Scholar as additional factors involved in cyclin D1–mediated migration. The effects of cyclin D1 to promote migration were observed in cyclin D1−/− cells that express cyclin D1 and cyclin A3; thus, the function appears to be specific to cyclin D1, which was necessary and sufficient for the promigratory function. Cyclin D1 deficiency in cells and in vivo is associated with increased mitochondrial size and activity (Figure 1).14Wang C. Li Z. Lu Y. Du R. Katiyar S. Yang J. Fu M. Leader J.E. Quong A. Novikoff P.M. Pestell R.G. Cyclin D1 repression of nuclear respiratory factor 1 integrates nuclear DNA synthesis and mitochondrial function.Proc Natl Acad Sci U S A. 2006; 103: 11567-11572Crossref PubMed Scopus (165) Google Scholar, 15Sakamaki T. Casimiro M.C. Ju X. Quong A.A. Katiyar S. Liu M. Jiao X. Li A. Zhang X. Lu Y. Wang C. Byers S. Nicholson R. Link T. Shemluck M. Yang J. Fricke S.T. Novikoff P.M. Papanikolaou A. Arnold A. Albanese C. Pestell R. Cyclin D1 determines mitochondrial function in vivo.Mol Cell Biol. 2006; 26: 5449-5469Crossref PubMed Scopus (144) Google Scholar Rescue of the cyclin D1−/− cells' mitochondrial phenotype required the Cdk function of cyclin D1. Nuclear respiratory factor 1 (NRF-1), which induces expression of nuclear-encoded mitochondrial genes, was repressed in expression and activity by cyclin D1, which phosphorylated NRF-1 at S47 (Figure 1A).14Wang C. Li Z. Lu Y. Du R. Katiyar S. Yang J. Fu M. Leader J.E. Quong A. Novikoff P.M. Pestell R.G. Cyclin D1 repression of nuclear respiratory factor 1 integrates nuclear DNA synthesis and mitochondrial function.Proc Natl Acad Sci U S A. 2006; 103: 11567-11572Crossref PubMed Scopus (165) Google Scholar By using cyclin D1 antisense mammary epithelial targeted transgenic mice, the role for cyclin D1 as an inhibitor of mitochondrial biogenesis and activity was confirmed in vivo. Endogenous cyclin D1 was shown to inhibit mitochondrial biogenesis and activity by gene expression signaling and in vivo imaging. Consistent with these findings, cyclin D1–induced mammary tumors showed inhibition of mitochondrial activity and aerobic glycolysis with enhanced cytosolic glycolysis.15Sakamaki T. Casimiro M.C. Ju X. Quong A.A. Katiyar S. Liu M. Jiao X. Li A. Zhang X. Lu Y. Wang C. Byers S. Nicholson R. Link T. Shemluck M. Yang J. Fricke S.T. Novikoff P.M. Papanikolaou A. Arnold A. Albanese C. Pestell R. Cyclin D1 determines mitochondrial function in vivo.Mol Cell Biol. 2006; 26: 5449-5469Crossref PubMed Scopus (144) Google Scholar In vivo measurements of relative use of amino acids from the tricarboxylic acid cycle using nuclear magnetic resonance in cyclin D1−/− mammary epithelium showed changes in the ratio of glutamate and glutamine/citrate, associated with the induction of mitochondrial metabolism and reduced cytosolic glycolysis, and the glutamate plus glutamine/citrate ratio was increased.15Sakamaki T. Casimiro M.C. Ju X. Quong A.A. Katiyar S. Liu M. Jiao X. Li A. Zhang X. Lu Y. Wang C. Byers S. Nicholson R. Link T. Shemluck M. Yang J. Fricke S.T. Novikoff P.M. Papanikolaou A. Arnold A. Albanese C. Pestell R. Cyclin D1 determines mitochondrial function in vivo.Mol Cell Biol. 2006; 26: 5449-5469Crossref PubMed Scopus (144) Google Scholar A similar change in cellular metabolism was observed in the mammary epithelium of ponasterone-inducible cyclin D1 antisense transgenic mice.15Sakamaki T. Casimiro M.C. Ju X. Quong A.A. Katiyar S. Liu M. Jiao X. Li A. Zhang X. Lu Y. Wang C. Byers S. Nicholson R. Link T. Shemluck M. Yang J. Fricke S.T. Novikoff P.M. Papanikolaou A. Arnold A. Albanese C. Pestell R. Cyclin D1 determines mitochondrial function in vivo.Mol Cell Biol. 2006; 26: 5449-5469Crossref PubMed Scopus (144) Google Scholar Cyclin D1 was also shown to inhibit mitochondrial function through binding to the mitochondrial voltage-dependent anion channel, thereby competing with hexokinase II.16Tchakarska G. Roussel M. Troussard X. Sola B. Cyclin D1 inhibits mitochondrial activity in B cells.Cancer Res. 2011; 71: 1690-1699Crossref PubMed Scopus (28) Google Scholar The cyclin D1–mediated inhibition of NRF-1 and, thereby mitochondrial transcription factor A, to reduce mitochondrial activity was observed in cells expressing cyclin E. Cyclin E is regulated by mitochondrial activity in that disruption of the mitochondrial electron transport chain activates a G1/S checkpoint that degrades cyclin E.17Mandal S. Freije W.A. Guptan P. Banerjee U. Metabolic control of G1-S transition: cyclin E degradation by p53-induced activation of the ubiquitin-proteasome system.J Cell Biol. 2010; 188: 473-479Crossref PubMed Scopus (64) Google Scholar Consistent with these findings, pRb was subsequently shown to couple cell cycle exit with mitochondrial biogenesis.18Sankaran V.G. Orkin S.H. Walkley C.R. Rb intrinsically promotes erythropoiesis by coupling cell cycle exit with mitochondrial biogenesis.Genes Dev. 2008; 22: 463-475Crossref PubMed Scopus (113) Google Scholar Inactivation of pRb, or p21 overexpression, also inhibits mitochondrial metabolism, thereby increasing cytosolic glycolysis, suggesting the effect of cyclin D1 is part of a broader role for the cyclin D1/Rb/CDK inhibitor pathway. Collectively, these studies demonstrated that increased abundance of cyclin D1 determines metabolic substrate prioritization toward amino acid synthesis from the tricarboxylic acid cycle, consistent with a known role for cyclin D1 in the induction of DNA synthesis and the known induction of cytosolic glycolysis in tumors. Whether the cyclin D1–dependent inhibition of mitochondrial biogenesis contributes to the glucose avidity of carcinomas remains to be determined. More than 35 distinct transcription factors are regulated by cyclin D1 expression.19Fu M. Wang C. Li Z. Sakamaki T. Pestell R.G. Minireview: cyclin D1: normal and abnormal functions.Endocrinology. 2004; 145: 5439-5447Crossref PubMed Scopus (811) Google Scholar The mechanism appears to involve recruitment to DNA of transcription factors and associated chromatin-modifying enzymes.19Fu M. Wang C. Li Z. Sakamaki T. Pestell R.G. Minireview: cyclin D1: normal and abnormal functions.Endocrinology. 2004; 145: 5439-5447Crossref PubMed Scopus (811) Google Scholar By using cyclin D1−/− mice, it was shown that cyclin D1 plays a critical role in the recruitment of transcription factors in the context of local chromatin to their cognate DNA-binding site.20Hulit J. Wang C. Li Z. Albanese C. Rao M. Di Vizio D. Shah S. Byers S.W. Mahmood R. Augenlicht L.H. Russell R. Pestell R.G. Cyclin D1 genetic heterozygosity regulates colonic epithelial cell differentiation and tumor number in ApcMin mice.Mol Cell Biol. 2004; 24: 7598-7611Crossref PubMed Scopus (134) Google Scholar Peroxisome proliferator-activated receptor (PPAR)γ recruitment to the murine lipoprotein lipase promoter, characterized in chromatin immunoprecipitation (ChIP) assays, was dependent on the relative abundance of endogenous cyclin D1. These original studies by Hulit et al20Hulit J. Wang C. Li Z. Albanese C. Rao M. Di Vizio D. Shah S. Byers S.W. Mahmood R. Augenlicht L.H. Russell R. Pestell R.G. Cyclin D1 genetic heterozygosity regulates colonic epithelial cell differentiation and tumor number in ApcMin mice.Mol Cell Biol. 2004; 24: 7598-7611Crossref PubMed Scopus (134) Google Scholar demonstrated the essential role for cyclin D1 in the recruitment of transcription factors in the context of local chromatin. Although it was known that cyclin D1 inhibited PPARγ reporter gene activity in a Cdk-independent manner, and that endogenous cyclin D1 played an important role in fat metabolism in vivo, these studies by Hulit and coworkers,21Wang C. Pattabiraman N. Zhou J.N. Fu M. Sakamaki T. Albanese C. Li Z. Wu K. Hulit J. Neumeister P. Novikoff P.M. Brownlee M. Scherer P.E. Jones J.G. Whitney K.D. Donehower L.A. Harris E.L. Rohan T. Johns D.C. Pestell R.G. Cyclin D1 repression of peroxisome proliferator-activated receptor gamma expression and transactivation.Mol Cell Biol. 2003; 23: 6159-6173Crossref PubMed Scopus (177) Google Scholar were the first to demonstrate the critical role for cyclin D1 in recruiting a transcription factor to target genes in vivo. Subsequent studies using ChIP analysis provided a framework demonstrating that cyclin D1 was recruited in the context of local chromatin to target genes. Fu et al22Fu M. Rao M. Bouras T. Wang C. Wu K. Zhang X. Li Z. Yao T.P. Pestell R.G. Cyclin D1 inhibits peroxisome proliferator-activated receptor gamma-mediated adipogenesis through histone deacetylase recruitment.J Biol Chem. 2005; 280: 16934-16941Crossref PubMed Scopus (232) Google Scholar conducted ChIP analysis of cyclin D1−/− mouse embryo fibroblasts (MEFs), demonstrating that the recruitment of cyclin D1, in turn, recruited PPARγ, histone deacetylase (HDAC), and HDAC3 in the context of local chromatin. Fu et al22Fu M. Rao M. Bouras T. Wang C. Wu K. Zhang X. Li Z. Yao T.P. Pestell R.G. Cyclin D1 inhibits peroxisome proliferator-activated receptor gamma-mediated adipogenesis through histone deacetylase recruitment.J Biol Chem. 2005; 280: 16934-16941Crossref PubMed Scopus (232) Google Scholar, 23Fu M. Wang C. Rao M. Wu X. Bouras T. Zhang X. Li Z. Jiao X. Yang J. Li A. Perkins N.D. Thimmapaya B. Kung A.L. Munoz A. Giordano A. Lisanti M.P. Pestell R.G. Cyclin D1 represses p300 transactivation through a cyclin-dependent kinase-independent mechanism.J Biol Chem. 2005; 280: 29728-29742Crossref PubMed Scopus (78) Google Scholar showed that the recruitment of cyclin D1 was associated with the corecruitment of Su (Var) 39H1 and heterochromatin protein 1α (Figure 2) and an induction of dimethylation of H3K9. Cyclins E and D regulate transcription factor activity through several mechanisms.24Pestell R.G. Albanese C. Reutens A.T. Segall J.E. Lee R.J. Arnold A. The cyclins and cyclin-dependent kinase inhibitors in hormonal regulation of proliferation and differentiation.Endocr Rev. 1999; 20: 501-534Crossref PubMed Scopus (318) Google Scholar First, CDK activity regulates the function of a variety of transcription factors, including p53, E2 transcription factor, B lymphoma Mo-MLV insertion region 1 homolog, and inhibitor of DNA-binding protein 2, in a Cdk-dependent manner. In addition, cyclins regulate the activity of the basal transcription apparatus and co-activators. Thus, the RNA polymerase II large subunit contains the essential carboxyl terminal domain, which is phosphorylated by the general transcription factor, TFIIH. The co-activator proteins p300/calcium-binding protein (CBP) undergo phosphorylation during the cell cycle, and the activity of p300 is directly regulated by cyclin D1.23Fu M. Wang C. Rao M. Wu X. Bouras T. Zhang X. Li Z. Jiao X. Yang J. Li A. Perkins N.D. Thimmapaya B. Kung A.L. Munoz A. Giordano A. Lisanti M.P. Pestell R.G. Cyclin D1 represses p300 transactivation through a cyclin-dependent kinase-independent mechanism.J Biol Chem. 2005; 280: 29728-29742Crossref PubMed Scopus (78) Google Scholar The repression of p300 by cyclin D1 involved distinct domains from those regulated by p21Cip1. Recent studies demonstrated the association of p300/CBP with cyclin D1 and the co-occupancy of p300 and cyclin D1 in the context of local chromatin using ChIP-ChIP on a −5.5- to 2.5-kb ChIP-ChIP microarray containing approximately 17,000 genes. At the p21Cip1/Waf1 promoter, cyclin D1 reduced the recruitment of CBP,25Bienvenu F. Barre B. Giraud S. Avril S. Coqueret O. Transcriptional regulation by a DNA-associated form of cyclin D1.Mol Biol Cell. 2005; 16: 1850-1858Crossref PubMed Scopus (44) Google Scholar whereas cyclin D1 enhanced recruitment of the related p300 to the murine LPL promoter,23Fu M. Wang C. Rao M. Wu X. Bouras T. Zhang X. Li Z. Jiao X. Yang J. Li A. Perkins N.D. Thimmapaya B. Kung A.L. Munoz A. Giordano A. Lisanti M.P. Pestell R.G. Cyclin D1 represses p300 transactivation through a cyclin-dependent kinase-independent mechanism.J Biol Chem. 2005; 280: 29728-29742Crossref PubMed Scopus (78) Google Scholar suggesting cyclin D1 conveys gene-specific co-integrator recruitment function. Cyclin D1 inhibits p300-mediated acetylation of histones and autoacetylation, providing an alternative mechanism by which cyclin D1 may regulate gene transcription (Figure 2).23Fu M. Wang C. Rao M. Wu X. Bouras T. Zhang X. Li Z. Jiao X. Yang J. Li A. Perkins N.D. Thimmapaya B. Kung A.L. Munoz A. Giordano A. Lisanti M.P. Pestell R.G. Cyclin D1 represses p300 transactivation through a cyclin-dependent kinase-independent mechanism.J Biol Chem. 2005; 280: 29728-29742Crossref PubMed Scopus (78) Google Scholar In addition to binding histone acetyltransferases (p300, CBP, and p300/CBP-associated factor)26Reutens A.T. Fu M. Wang C. Albanese C. McPhaul M.J. Sun Z. Balk S.P. Janne O.A. Palvimo J.J. Pestell R.G. 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Cyclin D1 genetic heterozygosity regulates colonic epithelial cell differentiation and tumor number in ApcMin mice.Mol Cell Biol. 2004; 24: 7598-7611Crossref PubMed Scopus (134) Google Scholar Cyclin D1 expression enhanced ERα recruitment in the context of local chromatin to an estrogen-responsive element in ChIP assays, and cyclin D1 interacted with ERα and BRCA1 at the pS2 gene promoter. ChIP-ChIP and ChIP-Sequencing analyses have revealed the complexity of genomic binding by the DNA-associated form of cyclin D1. ChIP of cyclin D1, followed by ChIP-Sequencing, mapped at high resolution the entire genomic region bound by cyclin D1. The genome-wide distribution of binding sites in relation to the transcriptional start site showed that peak values of active regions within the promoter are comparable to those at 10 kb and beyond, suggesting that cyclin D1 localizes to both promoter-proximal elements and distant elements (Figure 2). The transcription factor–binding sites enriched in the cyclin D1 peak interval sequences of ChIP-ChIP identified several top hit transcription factors that correlated in function with the previous studies by Sicinski using promoter ChIP analysis, including mitochondrial metabolism, cellular division, and RNA processing (Figure 2). The cis elements included Ctcf, Zfx, Sp1, Mizf, Esr1, ERα, E2f1, and Creb1. Subsequent studies identified cyclin D3 in ChIP at PPARγ target promoters, much like cyclin D1.40Sarruf D.A. Iankova I. Abella A. Assou S. Miard S. Fajas L. 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