51
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Abstract
Pioneer factors such as FoxA target nucleosomal DNA and initiate cooperative interactions at silent genes during development, cellular reprogramming, and steroid hormone induction. Biophysical studies previously showed that the nuclear mobility of FoxA1 is slower than for many other transcription factors, whereas a new single molecule study (Swinstead et al., 2016, Cell) shows comparable chromatin residence times for FoxA1 and steroid receptors. Despite that steroid receptors engage nucleosome-remodeling complexes, the vast majority of co-bound sites with FoxA are dependent upon FoxA, not vice versa. Taken together, the distinguishing feature of pioneer factors remains nucleosomal access rather than an exceptional residence time in chromatin.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
| | - Jonathan Lerner
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
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52
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Lu R, Mucaki EJ, Rogan PK. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs. Nucleic Acids Res 2017; 45:e27. [PMID: 27899659 PMCID: PMC5389469 DOI: 10.1093/nar/gkw1036] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes.
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Affiliation(s)
- Ruipeng Lu
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada
| | - Peter K Rogan
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada.,Department of Oncology, Western University, London, Ontario, N6A 4L6, Canada.,Cytognomix Inc., London, Ontario, N5X 3X5, Canada
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53
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Fisher JB, Pulakanti K, Rao S, Duncan SA. GATA6 is essential for endoderm formation from human pluripotent stem cells. Biol Open 2017; 6:1084-1095. [PMID: 28606935 PMCID: PMC5550920 DOI: 10.1242/bio.026120] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protocols have been established that direct differentiation of human pluripotent stem cells into a variety of cell types, including the endoderm and its derivatives. This model of differentiation has been useful for investigating the molecular mechanisms that guide human developmental processes. Using a directed differentiation protocol combined with shRNA depletion we sought to understand the role of GATA6 in regulating the earliest switch from pluripotency to definitive endoderm. We reveal that GATA6 depletion during endoderm formation results in apoptosis of nascent endoderm cells, concomitant with a loss of endoderm gene expression. We show by chromatin immunoprecipitation followed by DNA sequencing that GATA6 directly binds to several genes encoding transcription factors that are necessary for endoderm differentiation. Our data support the view that GATA6 is a central regulator of the formation of human definitive endoderm from pluripotent stem cells by directly controlling endoderm gene expression. Summary: Using the differentiation of huESCs as a model for endoderm formation, we reveal that the transcription factor GATA6 regulates the onset of endoderm gene expression and is required for its viability.
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Affiliation(s)
- J B Fisher
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - K Pulakanti
- Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - S Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Blood Center of Wisconsin, Milwaukee, WI 53226, USA.,Division of Pediatric Hematology, Oncology, and Blood and Marrow Transplant, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - S A Duncan
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA .,Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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54
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Simon CS, Downes DJ, Gosden ME, Telenius J, Higgs DR, Hughes JR, Costello I, Bikoff EK, Robertson EJ. Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo. Development 2017; 144:1249-1260. [PMID: 28174238 PMCID: PMC5399628 DOI: 10.1242/dev.147322] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/25/2017] [Indexed: 12/28/2022]
Abstract
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue-specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable, and only VPE is required for optimal Eomes expression in vivo. Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation. Chromosome conformation capture experiments reveal VPE-promoter interactions in embryonic stem cells (ESCs), prior to gene activation. The locus resides in a large (500 kb) pre-formed compartment in ESCs and activation during DE differentiation occurs in the absence of 3D structural changes. ATAC-seq analysis reveals that VPE, PSE_a and four additional putative enhancers display increased chromatin accessibility in DE that is associated with Smad2/3 binding coincident with transcriptional activation. By contrast, activation of the Eomes target genes Foxa2 and Lhx1 is associated with higher order chromatin reorganisation. Thus, diverse regulatory mechanisms govern activation of lineage specifying TFs during early development. Summary: Expression of the mouse T-box factor Eomes is controlled by a key gene-proximal enhancer-like element, with changes in chromatin accessibility influencing its activity in definitive endoderm.
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Affiliation(s)
- Claire S Simon
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthew E Gosden
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Ita Costello
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Elizabeth K Bikoff
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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55
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Hettiarachchi N, Saitou N. GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates. Genome Biol Evol 2016; 8:3377-3392. [PMID: 28040773 PMCID: PMC5203776 DOI: 10.1093/gbe/evw231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs.
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Affiliation(s)
- Nilmini Hettiarachchi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan.,Division of Population Genetics, National institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan .,Division of Population Genetics, National institute of Genetics, Mishima, Japan
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56
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Swinstead EE, Paakinaho V, Presman DM, Hager GL. Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective: Multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factors. Bioessays 2016; 38:1150-1157. [PMID: 27633730 DOI: 10.1002/bies.201600137] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transcription factor (TF) signaling regulates gene transcription and requires a complex network of proteins. This network includes co-activators, co-repressors, multiple TFs, histone-modifying complexes, and the basal transcription machinery. It has been widely appreciated that pioneer factors, such as FoxA1 and GATA1, play an important role in opening closed chromatin regions, thereby allowing binding of a secondary factor. In this review we will focus on a newly proposed model wherein multiple TFs, such as steroid receptors (SRs), can function in a pioneering role. This model, termed dynamic assisted loading, integrates data from widely divergent methodologies, including genome wide ChIP-Seq, digital genomic footprinting, DHS-Seq, live cell protein dynamics, and biochemical studies of ATP-dependent remodeling complexes, to present a real time view of TF chromatin interactions. Under this view, many TFs can act as initiating factors for chromatin landscape programming. Furthermore, enhancer and promoter states are more accurately described as energy-dependent, non-equilibrium steady states.
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Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA.
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57
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Zhang Y, Zhang D, Li Q, Liang J, Sun L, Yi X, Chen Z, Yan R, Xie G, Li W, Liu S, Xu B, Li L, Yang J, He L, Shang Y. Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering. Nat Genet 2016; 48:1003-13. [PMID: 27500525 DOI: 10.1038/ng.3635] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/01/2016] [Indexed: 12/14/2022]
Abstract
FOXA1 functions in epigenetic reprogramming and is described as a 'pioneer factor'. However, exactly how FOXA1 achieves these remarkable biological functions is not fully understood. Here we report that FOXA1 associates with DNA repair complexes and is required for genomic targeting of DNA polymerase β (POLB) in human cells. Genome-wide DNA methylomes demonstrate that the FOXA1 DNA repair complex is functionally linked to DNA demethylation in a lineage-specific fashion. Depletion of FOXA1 results in localized reestablishment of methylation in a large portion of FOXA1-bound regions, and the regions with the most consistent hypermethylation exhibit the greatest loss of POLB and are represented by active promoters and enhancers. Consistently, overexpression of FOXA1 commits its binding sites to active DNA demethylation in a POLB-dependent manner. Finally, FOXA1-associated DNA demethylation is tightly coupled with estrogen receptor genomic targeting and estrogen responsiveness. Together, these results link FOXA1-associated DNA demethylation to transcriptional pioneering by FOXA1.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Di Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Qian Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xia Yi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhe Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ruorong Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Guojia Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bosen Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Hormones and Development (Ministry of Health), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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58
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Tanaka K, Tokunaga E, Yamashita N, Sagara Y, Ohi Y, Taguchi K, Ohno S, Okano S, Oda Y, Maehara Y. The relationship between the expression of FOXA1 and GATA3 and the efficacy of neoadjuvant endocrine therapy. Breast Cancer 2016; 24:384-392. [PMID: 27473079 DOI: 10.1007/s12282-016-0714-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/21/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Estrogen receptor (ER)/GATA3/Forkhead box A1 (FOXA1) network is necessary for the ERα functional signature. High FOXA1 expression indicates a good prognosis in ER-positive breast cancer. However, little is known about the significance of FOXA1 and GATA3 expression in neoadjuvant endocrine therapy (NAE). The aim of this study is to investigate their predictive potential for NAE and their expression changes after NAE. METHODS FOXA1 and GATA3 expression was evaluated using immunohistochemistry in 66 patients with ER-positive/HER2-negative breast cancer who had been treated with NAE. The association between biological marker expressions and the efficacy of NAE and their expression changes after NAE were analyzed. RESULTS The median pre-treatment FOXA1 and GATA3 expressions were 94.6 and 90 %. Pre-treatment FOXA1 expression was positively correlated with GATA3 (P = 0.0003) and progesterone receptor (PgR) (P = 0.0138). There was no correlation between pre- or post-treatment FOXA1 and GATA3 expressions and the efficacy of NAE. Post-treatment Ki67 expression was significantly lower in tumors with partial response (PR) (P = 0.0007). In terms of the changes of the expression, PgR, Ki67, and FOXA1 expression significantly decreased after NAE (P < 0.0001, P < 0.0001, and P < 0.0001, respectively). CONCLUSIONS FOXA1 and GATA3 expression was not correlated with the efficacy of NAE, but FOXA1 expression was significantly reduced after NAE.
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Affiliation(s)
- Kimihiro Tanaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eriko Tokunaga
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan. .,Department of Breast Oncology, National Hospital Organization Kyushu Cancer Center, 3-1-1 Notame, Minami-ku, Fukuoka, 811-1395, Japan.
| | - Nami Yamashita
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuaki Sagara
- Department of Breast Surgical Oncology, Sagara Hospital, Kagoshima, Japan
| | - Yasuyo Ohi
- Department of Pathology, Sagara Hospital, Kagoshima, Japan
| | - Kenichi Taguchi
- Department of Pathology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Shinji Ohno
- Department of Breast Oncology, National Hospital Organization Kyushu Cancer Center, 3-1-1 Notame, Minami-ku, Fukuoka, 811-1395, Japan
| | - Shinji Okano
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Pathological Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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59
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Carroll JS. Mechanisms of oestrogen receptor (ER) gene regulation in breast cancer. Eur J Endocrinol 2016; 175:R41-9. [PMID: 26884552 PMCID: PMC5065078 DOI: 10.1530/eje-16-0124] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 12/24/2022]
Abstract
Most breast cancers are driven by a transcription factor called oestrogen receptor (ER). Understanding the mechanisms of ER activity in breast cancer has been a major research interest and recent genomic advances have revealed extraordinary insights into how ER mediates gene transcription and what occurs during endocrine resistance. This review discusses our current understanding on ER activity, with an emphasis on several evolving, but important areas of ER biology.
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Affiliation(s)
- J S Carroll
- Cancer Research UKCambridge Institute, University of Cambridge, Cambridge, UK
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60
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Matcovitch-Natan O, Winter DR, Giladi A, Vargas Aguilar S, Spinrad A, Sarrazin S, Ben-Yehuda H, David E, Zelada González F, Perrin P, Keren-Shaul H, Gury M, Lara-Astaiso D, Thaiss CA, Cohen M, Bahar Halpern K, Baruch K, Deczkowska A, Lorenzo-Vivas E, Itzkovitz S, Elinav E, Sieweke MH, Schwartz M, Amit I. Microglia development follows a stepwise program to regulate brain homeostasis. Science 2016; 353:aad8670. [PMID: 27338705 DOI: 10.1126/science.aad8670] [Citation(s) in RCA: 802] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
Microglia, the resident myeloid cells of the central nervous system, play important roles in life-long brain maintenance and in pathology. Despite their importance, their regulatory dynamics during brain development have not been fully elucidated. Using genome-wide chromatin and expression profiling coupled with single-cell transcriptomic analysis throughout development, we found that microglia undergo three temporal stages of development in synchrony with the brain--early, pre-, and adult microglia--which are under distinct regulatory circuits. Knockout of the gene encoding the adult microglia transcription factor MAFB and environmental perturbations, such as those affecting the microbiome or prenatal immune activation, led to disruption of developmental genes and immune response pathways. Together, our work identifies a stepwise microglia developmental program integrating immune response pathways that may be associated with several neurodevelopmental disorders.
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Affiliation(s)
- Orit Matcovitch-Natan
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah R Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Stephanie Vargas Aguilar
- Centre d'Immunologie de Marseille-Luminy (CIML), Université Aix-Marseille, UM2, Campus de Luminy, Marseille, France. Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France. Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France. Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Straß 10, 13125 Berlin, Germany
| | - Amit Spinrad
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Sarrazin
- Centre d'Immunologie de Marseille-Luminy (CIML), Université Aix-Marseille, UM2, Campus de Luminy, Marseille, France. Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France. Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - Hila Ben-Yehuda
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Fabiola Zelada González
- Centre d'Immunologie de Marseille-Luminy (CIML), Université Aix-Marseille, UM2, Campus de Luminy, Marseille, France. Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France. Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - Pierre Perrin
- Centre d'Immunologie de Marseille-Luminy (CIML), Université Aix-Marseille, UM2, Campus de Luminy, Marseille, France. Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France. Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Meital Gury
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - David Lara-Astaiso
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Cohen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Kuti Baruch
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Shalev Itzkovitz
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael H Sieweke
- Centre d'Immunologie de Marseille-Luminy (CIML), Université Aix-Marseille, UM2, Campus de Luminy, Marseille, France. Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France. Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France. Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Straß 10, 13125 Berlin, Germany.
| | - Michal Schwartz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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61
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Palierne G, Fabre A, Solinhac R, Le Péron C, Avner S, Lenfant F, Fontaine C, Salbert G, Flouriot G, Arnal JF, Métivier R. Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment. Mol Endocrinol 2016; 30:709-32. [PMID: 27164166 DOI: 10.1210/me.2015-1311] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulation by the estrogen receptor-α (ER) has been investigated mainly in breast cancer cell lines, but estrogens such as 17β-estradiol (E2) exert numerous extrareproductive effects, particularly in the liver, where E2 exhibits both protective metabolic and deleterious thrombotic actions. To analyze the direct and early transcriptional effects of estrogens in the liver, we determined the E2-sensitive transcriptome and ER cistrome in mice after acute administration of E2 or placebo. These analyses revealed the early induction of genes involved in lipid metabolism, which fits with the crucial role of ER in the prevention of liver steatosis. Characterization of the chromatin state of ER binding sites (BSs) in mice expressing or not ER demonstrated that ER is not required per se for the establishment and/or maintenance of chromatin modifications at the majority of its BSs. This is presumably a consequence of a strong overlap between ER and hepatocyte nuclear factor 4α BSs. In contrast, 40% of the BSs of the pioneer factor forkhead box protein a (Foxa2) were dependent upon ER expression, and ER expression also affected the distribution of nucleosomes harboring dimethylated lysine 4 of Histone H3 around Foxa2 BSs. We finally show that, in addition to a network of liver-specific transcription factors including CCAAT/enhancer-binding protein and hepatocyte nuclear factor 4α, ER might be required for proper Foxa2 function in this tissue.
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Affiliation(s)
- Gaëlle Palierne
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Aurélie Fabre
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Romain Solinhac
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Christine Le Péron
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Stéphane Avner
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Françoise Lenfant
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Coralie Fontaine
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Salbert
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Flouriot
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Jean-François Arnal
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Raphaël Métivier
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
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62
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Amit I, Winter DR, Jung S. The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis. Nat Immunol 2016; 17:18-25. [PMID: 26681458 DOI: 10.1038/ni.3325] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Abstract
Macrophages provide a critical systemic network cells of the innate immune system. Emerging data suggest that in addition, they have important tissue-specific functions that range from clearance of surfactant from the lungs to neuronal pruning and establishment of gut homeostasis. The differentiation and tissue-specific activation of macrophages require precise regulation of gene expression, a process governed by epigenetic mechanisms such as DNA methylation, histone modification and chromatin structure. We argue that epigenetic regulation of macrophages is determined by lineage- and tissue-specific transcription factors controlled by the built-in programming of myeloid development in combination with signaling from the tissue environment. Perturbation of epigenetic mechanisms of tissue macrophage identity can affect normal macrophage tissue function and contribute to pathologies ranging from obesity and autoimmunity to neurodegenerative diseases.
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Affiliation(s)
- Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah R Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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63
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Yalley A, Schill D, Hatta M, Johnson N, Cirillo LA. Loss of Interdependent Binding by the FoxO1 and FoxA1/A2 Forkhead Transcription Factors Culminates in Perturbation of Active Chromatin Marks and Binding of Transcriptional Regulators at Insulin-sensitive Genes. J Biol Chem 2016; 291:8848-61. [PMID: 26929406 DOI: 10.1074/jbc.m115.677583] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 01/04/2023] Open
Abstract
FoxO1 binds to insulin response elements located in the promoters of insulin-like growth factor-binding protein 1 (IGFBP1) and glucose-6-phosphatase (G6Pase), activating their expression. Insulin-mediated phosphorylation of FoxO1 promotes cytoplasmic translocation, inhibiting FoxO1-mediated transactivation. We have previously demonstrated that FoxO1 opens and remodels chromatin assembled from the IGFBP1 promoter via a highly conserved winged helix motif. This finding, which established FoxO1 as a "pioneer" factor, suggested a model whereby FoxO1 chromatin remodeling at regulatory targets facilitates binding and recruitment of additional regulatory factors. However, the impact of FoxO1 phosphorylation on its ability to bind chromatin and the effect of FoxO1 loss on recruitment of neighboring transcription factors at its regulatory targets in liver chromatin is unknown. In this study, we demonstrate that an amino acid substitution that mimics insulin-mediated phosphorylation of a serine in the winged helix DNA binding motif curtails FoxO1 nucleosome binding. We also demonstrate that shRNA-mediated loss of FoxO1 binding to the IGFBP1 and G6Pase promoters in HepG2 cells significantly reduces binding of RNA polymerase II and the pioneer factors FoxA1/A2. Knockdown of FoxA1 similarly reduced binding of RNA polymerase II and FoxO1. Reduction in acetylation of histone H3 Lys-27 accompanies loss of FoxO1 and FoxA1/A2 binding. Interdependent binding of FoxO1 and FoxA1/A2 possibly entails cooperative binding because FoxO1 and FoxA1/A2 facilitate one another's binding to IGFPB1 promoter DNA. These results illustrate how transcription factors can nucleate transcriptional events in chromatin in response to signaling events and suggest a model for regulation of hepatic glucose metabolism through interdependent FoxO/FoxA binding.
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Affiliation(s)
- Akua Yalley
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Daniel Schill
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Mitsutoki Hatta
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Nicole Johnson
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Lisa Ann Cirillo
- From the Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
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64
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Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol 2016; 17:36. [PMID: 26922637 PMCID: PMC4769547 DOI: 10.1186/s13059-016-0897-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022] Open
Abstract
Background Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells. This process typically requires pioneer transcription factors (TFs) to induce de novo formation of enhancers at previously closed chromatin. Mechanistic information on this process is currently sparse. Results Here we explore the mechanistic basis by which GATA3 functions as a pioneer TF in a cellular reprogramming event relevant to breast cancer, the mesenchymal to epithelial transition (MET). In some instances, GATA3 binds previously inaccessible chromatin, characterized by stable, positioned nucleosomes where it induces nucleosome eviction, alters local histone modifications, and remodels local chromatin architecture. At other loci, GATA3 binding induces nucleosome sliding without concomitant generation of accessible chromatin. Deletion of the transactivation domain retains the chromatin binding ability of GATA3 but cripples chromatin reprogramming ability, resulting in failure to induce MET. Conclusions These data provide mechanistic insights into GATA3-mediated chromatin reprogramming during MET, and suggest unexpected complexity to TF pioneering. Successful reprogramming requires stable binding to a nucleosomal site; activation domain-dependent recruitment of co-factors including BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex; and appropriate genomic context. The resulting model provides a new conceptual framework for de novo enhancer establishment by a pioneer TF. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0897-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sara A Grimm
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lalith Perera
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Roberta Menafra
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, Netherlands
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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65
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Dell'Orso S, Wang AH, Shih HY, Saso K, Berghella L, Gutierrez-Cruz G, Ladurner AG, O'Shea JJ, Sartorelli V, Zare H. The Histone Variant MacroH2A1.2 Is Necessary for the Activation of Muscle Enhancers and Recruitment of the Transcription Factor Pbx1. Cell Rep 2016; 14:1156-1168. [PMID: 26832413 DOI: 10.1016/j.celrep.2015.12.103] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/10/2015] [Accepted: 12/23/2015] [Indexed: 01/21/2023] Open
Abstract
Histone variants complement and integrate histone post-translational modifications in regulating transcription. The histone variant macroH2A1 (mH2A1) is almost three times the size of its canonical H2A counterpart, due to the presence of an ∼25 kDa evolutionarily conserved non-histone macro domain. Strikingly, mH2A1 can mediate both gene repression and activation. However, the molecular determinants conferring these alternative functions remain elusive. Here, we report that mH2A1.2 is required for the activation of the myogenic gene regulatory network and muscle cell differentiation. H3K27 acetylation at prospective enhancers is exquisitely sensitive to mH2A1.2, indicating a role of mH2A1.2 in imparting enhancer activation. Both H3K27 acetylation and recruitment of the transcription factor Pbx1 at prospective enhancers are regulated by mH2A1.2. Overall, our findings indicate a role of mH2A1.2 in marking regulatory regions for activation.
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Affiliation(s)
- Stefania Dell'Orso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - A Hongjun Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Kayoko Saso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Libera Berghella
- Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Gustavo Gutierrez-Cruz
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Andreas G Ladurner
- Butenandt Institute, LMU Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
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66
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Schulz KN, Bondra ER, Moshe A, Villalta JE, Lieb JD, Kaplan T, McKay DJ, Harrison MM. Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo. Genome Res 2015; 25:1715-26. [PMID: 26335634 PMCID: PMC4617967 DOI: 10.1101/gr.192682.115] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/20/2015] [Indexed: 01/24/2023]
Abstract
The transition from a specified germ cell to a population of pluripotent cells occurs rapidly following fertilization. During this developmental transition, the zygotic genome is largely transcriptionally quiescent and undergoes significant chromatin remodeling. In Drosophila, the DNA-binding protein Zelda (also known as Vielfaltig) is required for this transition and for transcriptional activation of the zygotic genome. Open chromatin is associated with Zelda-bound loci, as well as more generally with regions of active transcription. Nonetheless, the extent to which Zelda influences chromatin accessibility across the genome is largely unknown. Here we used formaldehyde-assisted isolation of regulatory elements to determine the role of Zelda in regulating regions of open chromatin in the early embryo. We demonstrate that Zelda is essential for hundreds of regions of open chromatin. This Zelda-mediated chromatin accessibility facilitates transcription-factor recruitment and early gene expression. Thus, Zelda possesses some key characteristics of a pioneer factor. Unexpectedly, chromatin at a large subset of Zelda-bound regions remains open even in the absence of Zelda. The GAGA factor-binding motif and embryonic GAGA factor binding are specifically enriched in these regions. We propose that both Zelda and GAGA factor function to specify sites of open chromatin and together facilitate the remodeling of the early embryonic genome.
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Affiliation(s)
- Katharine N Schulz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - Eliana R Bondra
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - Arbel Moshe
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jacqueline E Villalta
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daniel J McKay
- Departments of Biology and Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
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67
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Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat Rev Immunol 2015; 15:585-94. [DOI: 10.1038/nri3884] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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68
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Abstract
In immune cells, as in all mammalian cells, nuclear DNA is wrapped around histones to form nucleosomes. The positioning and modifications of nucleosomes throughout the genome defines the chromatin state of the cell and has a large impact on gene regulation. Chromatin state is dynamic throughout immune cell development and activation. High-throughput open chromatin assays, such as DNase-seq, can be used to find regulatory element across the genome and, when combined with histone modifications, can specify their function. During hematopoiesis, distal regulatory elements, known as enhancers, are established by pioneer factors that alter chromatin state. Some of these enhancers are lost, some are gained, and some are maintained as a memory of the cell's developmental origin. The enhancer landscape is unique to the cell lineage-with different enhancers regulating the same promoter-and determines the mechanism of cell type-specific activation after exposure to stimuli. Histone modification and promoter architecture govern the diverse responses to stimulation. Furthermore, chromatin dynamics may explain the high plasticity of certain tissue-resident immune cell types. Future epigenomic research will depend on the development of more efficient experiments and better methods to associate enhancers with genes. The ultimate goal of mapping genome-wide chromatin state throughout the hematopoietic tree will help illuminate the mechanisms behind immune cell development and function.
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Affiliation(s)
- Deborah R Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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69
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Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 2015; 161:555-568. [PMID: 25892221 DOI: 10.1016/j.cell.2015.03.017] [Citation(s) in RCA: 537] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/24/2014] [Accepted: 02/15/2015] [Indexed: 12/23/2022]
Abstract
Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin. Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency. Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes. Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface. Such partial motif recognition can occur by coordinate binding between factors. Our findings provide insight into how pioneer factors can target naive chromatin sites.
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70
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Affiliation(s)
- Taketaro Sadahiro
- From the Department of Cardiology, Keio University School of Medicine, Japan Science and Technology CREST, Tokyo, Japan (T.S., M.I.); Japan Science and Technology CREST, Tokyo, Japan (M.I.); Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan (S.Y.); and Gladstone Institute of Cardiovascular Disease, San Francisco, CA (S.Y.)
| | - Shinya Yamanaka
- From the Department of Cardiology, Keio University School of Medicine, Japan Science and Technology CREST, Tokyo, Japan (T.S., M.I.); Japan Science and Technology CREST, Tokyo, Japan (M.I.); Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan (S.Y.); and Gladstone Institute of Cardiovascular Disease, San Francisco, CA (S.Y.)
| | - Masaki Ieda
- From the Department of Cardiology, Keio University School of Medicine, Japan Science and Technology CREST, Tokyo, Japan (T.S., M.I.); Japan Science and Technology CREST, Tokyo, Japan (M.I.); Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan (S.Y.); and Gladstone Institute of Cardiovascular Disease, San Francisco, CA (S.Y.)
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71
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Abstract
Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. This review by Iwafuchi-Doi and Zaret focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatin-binding properties, and facilitators and impediments to chromatin binding. A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in “closed” chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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72
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Edlund RK, Birol O, Groves AK. The role of foxi family transcription factors in the development of the ear and jaw. Curr Top Dev Biol 2015; 111:461-95. [PMID: 25662269 DOI: 10.1016/bs.ctdb.2014.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mammalian outer, middle, and inner ears have different embryonic origins and evolved at different times in the vertebrate lineage. The outer ear is derived from first and second branchial arch ectoderm and mesoderm, the middle ear ossicles are derived from neural crest mesenchymal cells that invade the first and second branchial arches, whereas the inner ear and its associated vestibule-acoustic (VIIIth) ganglion are derived from the otic placode. In this chapter, we discuss recent findings in the development of these structures and describe the contributions of members of a Forkhead transcription factor family, the Foxi family to their formation. Foxi transcription factors are critical for formation of the otic placode, survival of the branchial arch neural crest, and developmental remodeling of the branchial arch ectoderm.
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Affiliation(s)
- Renée K Edlund
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Onur Birol
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.
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73
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Harrison MM, Eisen MB. Transcriptional Activation of the Zygotic Genome in Drosophila. Curr Top Dev Biol 2015; 113:85-112. [DOI: 10.1016/bs.ctdb.2015.07.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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74
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Hu DG, Meech R, McKinnon RA, Mackenzie PI. Transcriptional regulation of human UDP-glucuronosyltransferase genes. Drug Metab Rev 2014; 46:421-58. [PMID: 25336387 DOI: 10.3109/03602532.2014.973037] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Glucuronidation is an important metabolic pathway for many small endogenous and exogenous lipophilic compounds, including bilirubin, steroid hormones, bile acids, carcinogens and therapeutic drugs. Glucuronidation is primarily catalyzed by the UDP-glucuronosyltransferase (UGT) 1A and two subfamilies, including nine functional UGT1A enzymes (1A1, 1A3-1A10) and 10 functional UGT2 enzymes (2A1, 2A2, 2A3, 2B4, 2B7, 2B10, 2B11, 2B15, 2B17 and 2B28). Most UGTs are expressed in the liver and this expression relates to the major role of hepatic glucuronidation in systemic clearance of toxic lipophilic compounds. Hepatic glucuronidation activity protects the body from chemical insults and governs the therapeutic efficacy of drugs that are inactivated by UGTs. UGT mRNAs have also been detected in over 20 extrahepatic tissues with a unique complement of UGT mRNAs seen in almost every tissue. This extrahepatic glucuronidation activity helps to maintain homeostasis and hence regulates biological activity of endogenous molecules that are primarily inactivated by UGTs. Deciphering the molecular mechanisms underlying tissue-specific UGT expression has been the subject of a large number of studies over the last two decades. These studies have shown that the constitutive and inducible expression of UGTs is primarily regulated by tissue-specific and ligand-activated transcription factors (TFs) via their binding to cis-regulatory elements (CREs) in UGT promoters and enhancers. This review first briefly summarizes published UGT gene transcriptional studies and the experimental models and tools utilized in these studies, and then describes in detail the TFs and their respective CREs that have been identified in the promoters and/or enhancers of individual UGT genes.
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Affiliation(s)
- Dong Gui Hu
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University School of Medicine, Flinders Medical Centre , Bedford Park, SA , Australia
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75
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Beck S, Lee BK, Kim J. Multi-layered global gene regulation in mouse embryonic stem cells. Cell Mol Life Sci 2014; 72:199-216. [PMID: 25227241 PMCID: PMC4284393 DOI: 10.1007/s00018-014-1734-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 02/05/2023]
Abstract
Embryonic stem (ES) cells derived from the inner cell mass of developing embryos have tremendous potential in regenerative medicine due to their unique properties: ES cells can be maintained for a prolonged time without changes in their cellular characteristics in vitro (self-renewal), while sustaining the capacity to give rise to all cell types of adult organisms (pluripotency). In addition to the development of protocols to manipulate ES cells for therapeutic applications, understanding how such unique properties are maintained has been one of the key questions in stem cell research. During the past decade, advances in high-throughput technologies have enabled us to systematically monitor multiple layers of gene regulatory mechanisms in ES cells. In this review, we briefly summarize recent findings on global gene regulatory modes in ES cells, mainly focusing on the regulatory factors responsible for transcriptional and epigenetic regulations as well as their modular regulatory patterns throughout the genome.
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Affiliation(s)
- Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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76
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Tangen IL, Krakstad C, Halle MK, Werner HMJ, Øyan AM, Kusonmano K, Petersen K, Kalland KH, Akslen LA, Trovik J, Hurtado A, Salvesen HB. Switch in FOXA1 status associates with endometrial cancer progression. PLoS One 2014; 9:e98069. [PMID: 24849812 PMCID: PMC4029819 DOI: 10.1371/journal.pone.0098069] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/18/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The transcription factor Forkhead box A1 (FOXA1) is suggested to be important in hormone dependent cancers, although with little data for endometrial cancer. We investigated expression levels of FOXA1 in primary and metastatic endometrial cancer in relation to clinical phenotype, and transcriptional alterations related to FOXA1 status. METHODS Protein expression of FOXA1 was explored by immunohistochemistry in 529 primary and 199 metastatic endometrial carcinoma lesions. mRNA levels from corresponding 158 fresh frozen primary and 42 metastatic lesions were analyzed using Agilent Microarrays (44k) in parallel. RESULTS Low FOXA1 protein expression in primary tumors significantly correlated with low FOXA1 mRNA, high age, non-endometrioid histology, high grade, loss of ERα and PR and poor survival (all p-values <0.05). Through a Connectivity Map search, HDAC inhibitors were suggested as potential treatment for patients with low FOXA1 expression. An increase in FOXA1 expression was observed from primary to metastatic lesions and it correlated with CDKN2A expression in metastases. CONCLUSION Low FOXA1 is associated with poor survival and suggests a potential for HDAC inhibitors in endometrial carcinoma. A switch in FOXA1 expression from primary to metastatic lesions is observed and gene expression indicates a link between FOXA1 and CDKN2A in metastatic lesions.
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Affiliation(s)
- Ingvild Løberg Tangen
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- * E-mail:
| | - Camilla Krakstad
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Mari K. Halle
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Henrica M. J. Werner
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Anne M. Øyan
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Kanthida Kusonmano
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Kjell Petersen
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Karl Henning Kalland
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Lars A. Akslen
- Center for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Jone Trovik
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Antoni Hurtado
- Breast Cancer Research group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Helga B. Salvesen
- Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
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Paul F, Amit I. Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function. Curr Opin Immunol 2014; 30:1-8. [PMID: 24820527 DOI: 10.1016/j.coi.2014.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/09/2014] [Indexed: 12/23/2022]
Abstract
Dendritic cells (DC) are critical and functionally versatile innate immune sentinels. Here, we coarsely partition the adult DC lineage into three developmental subtypes and argue that pioneer transcription factors and chromatin remodeling are responsible for specification and plasticity between the DC subsets. Subsequently, intricate signaling-dependent transcription factor networks generate different functional states in response to pathogen stimuli within a specified DC subtype. To expand our understanding of lineage heterogeneity and functional activation states, we discuss the use of single cell genomics approaches in the context of a newly emerging systems immunology era, complementing the dichotomous definition of immune cells based solely on their surface marker expression. Rapid developments in single cell genomics are beginning to provide us with robust tools to potentially revise the working models of DC specification and the common hematopoietic tree.
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Affiliation(s)
- Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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78
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DeVilbiss AW, Sanalkumar R, Johnson KD, Keles S, Bresnick EH. Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points. Exp Hematol 2014; 42:618-29. [PMID: 24816274 DOI: 10.1016/j.exphem.2014.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/04/2014] [Indexed: 12/12/2022]
Abstract
Hematopoiesis is an exquisitely regulated process in which stem cells in the developing embryo and the adult generate progenitor cells that give rise to all blood lineages. Master regulatory transcription factors control hematopoiesis by integrating signals from the microenvironment and dynamically establishing and maintaining genetic networks. One of the most rudimentary aspects of cell type-specific transcription factor function, how they occupy a highly restricted cohort of cis-elements in chromatin, remains poorly understood. Transformative technologic advances involving the coupling of next-generation DNA sequencing technology with the chromatin immunoprecipitation assay (ChIP-seq) have enabled genome-wide mapping of factor occupancy patterns. However, formidable problems remain; notably, ChIP-seq analysis yields hundreds to thousands of chromatin sites occupied by a given transcription factor, and only a fraction of the sites appear to be endowed with critical, non-redundant function. It has become en vogue to map transcription factor occupancy patterns genome-wide, while using powerful statistical tools to establish correlations to inform biology and mechanisms. With the advent of revolutionary genome editing technologies, one can now reach beyond correlations to conduct definitive hypothesis testing. This review focuses on key discoveries that have emerged during the path from single loci to genome-wide analyses, specifically in the context of hematopoietic transcriptional mechanisms.
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Affiliation(s)
- Andrew W DeVilbiss
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Rajendran Sanalkumar
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Kirby D Johnson
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Sunduz Keles
- University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H Bresnick
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA.
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Abstract
The nuclear receptor (NR) family comprises 48 transcription factors (TFs) with essential and diverse roles in development, metabolism and disease. Differently from other TFs, NRs engage with well-defined DNA-regulatory elements, mostly after ligand-induced structural changes. However, NR binding is not stochastic, and only a fraction of the cognate regulatory elements within the genome actively engage with NRs. In this review, we summarize recent advances in the understanding of the interactions between NRs and DNA. We discuss how chromatin accessibility and epigenetic modifications contribute to the recruitment and transactivation of NRs. Lastly, we present novel evidence of the interplay between non-coding RNA and NRs in the mediation of the assembly of the transcriptional machinery.
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Affiliation(s)
- Raffaella Maria Gadaleta
- Division of Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, W12 0NN, UK
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80
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Soufi A. Mechanisms for enhancing cellular reprogramming. Curr Opin Genet Dev 2014; 25:101-9. [PMID: 24607881 DOI: 10.1016/j.gde.2013.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/26/2013] [Indexed: 01/23/2023]
Abstract
During development, the genome adopts specific chromatin states to establish and maintain functionally distinct cell types in a well-controlled environment. A select group of transcription factors have the ability to drive the transition of the genome from a pluripotent to a more specialized chromatin state. The same set of factors can be used as reprogramming factors to reset the already established chromatin state back to pluripotency or directly to an alternative cell type. However, under the suboptimal reprogramming conditions, these factors fall short in guiding the majority of cells to their new fate. In this review, we visit the recent findings addressing the manipulation of chromatin structure to enhance the performance of transcription factors in reprogramming. The main emphasis is on the mechanisms underlying the conversion of somatic cells to pluripotency using OSKM. This review is intended to highlight the windows of opportunities for developing mechanistically based approaches to replace the phenotypically guided methods currently employed in reprogramming, in an attempt to move the field of cell conversion towards using next generation technologies.
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Affiliation(s)
- Abdenour Soufi
- Institute for Regenerative Medicine, Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
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81
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Qiu M, Bao W, Wang J, Yang T, He X, Liao Y, Wan X. FOXA1 promotes tumor cell proliferation through AR involving the Notch pathway in endometrial cancer. BMC Cancer 2014; 14:78. [PMID: 24512546 PMCID: PMC3926330 DOI: 10.1186/1471-2407-14-78] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/06/2014] [Indexed: 12/17/2022] Open
Abstract
Background Increasing evidence suggests that forkhead box A1 (FOXA1) is frequently dysregulated in many types of human cancers. However, the exact function and mechanism of FOXA1 in human endometrial cancer (EC) remains unclear. Methods FOXA1 expression, androgen receptor (AR) expression, and the relationships of these two markers with clinicopathological factors were determined by immunohistochemistry analysis. FOXA1 and AR were up-regulated by transient transfection with plasmids, and were down-regulated by transfection with siRNA or short hairpin RNA (shRNA). The effects of FOXA1 depletion and FOXA1 overexpression on AR-mediated transcription as well as Notch pathway and their impact on EC cell proliferation were examined by qRT-PCR, western blotting, co-immunoprecipitation, ChIP-PCR, MTT, colony-formation, and xenograft tumor–formation assays. Results We found that the expression of FOXA1 and AR in ECs was significantly higher than that in a typical hyperplasia and normal tissues. FOXA1 expression was significantly correlated with AR expression in clinical tissues. High FOXA1 levels positively correlated with pathological grade and depth of myometrial invasion in EC. High AR levels also positively correlated with pathological grade in EC. Moreover, the expression of XBP1, MYC, ZBTB16, and UHRF1, which are downstream targets of AR, was promoted by FOXA1 up-regulation or inhibited by FOXA1 down-regulation. Co-immunoprecipitation showed that FOXA1 interacted with AR in EC cells. ChIP-PCR assays showed that FOXA1 and AR could directly bind to the promoter and enhancer regions upstream of MYC. Mechanistic investigation revealed that over-expression of Notch1 and Hes1 proteins by FOXA1 could be reversed by AR depletion. In addition, we showed that down-regulation of AR attenuated FOXA1-up-regulated cell proliferation. However, AR didn’t influence the promotion effect of FOXA1 on cell migration and invasion. In vivo xenograft model, FOXA1 knockdown reduced the rate of tumor growth. Conclusions These results suggest that FOXA1 promotes cell proliferation by AR and activates Notch pathway. It indicated that FOXA1 and AR may serve as potential gene therapy in EC.
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Affiliation(s)
| | | | | | | | | | | | - Xiaoping Wan
- Department of Obstetrics and Gynecology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Xinsongjiang Road, Shanghai, China.
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82
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Delacher M, Schreiber L, Richards DM, Farah C, Feuerer M, Huehn J. Transcriptional control of regulatory T cells. Curr Top Microbiol Immunol 2014; 381:83-124. [PMID: 24831347 DOI: 10.1007/82_2014_373] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Regulatory T cells (Tregs) constitute unique T cell lineage that plays a key role for immunological tolerance. Tregs are characterized by the expression of the forkhead box transcription factor Foxp3, which acts as a lineage-specifying factor by determining the unique suppression profile of these immune cells. Here, we summarize the recent progress in understanding how Foxp3 expression itself is epigenetically and transcriptionally controlled, how the Treg-specific signature is achieved and how unique properties of Treg subsets are defined by other transcription factors. Finally, we will discuss recent studies focusing on the molecular targeting of Tregs to utilize the specific properties of this unique cell type in therapeutic settings.
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Affiliation(s)
- Michael Delacher
- Immune Tolerance, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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83
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Cui F, Zhurkin VB. Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res 2013; 42:836-47. [PMID: 24153113 PMCID: PMC3902933 DOI: 10.1093/nar/gkt943] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The tumor suppressor protein p53 exhibits high affinity to the response elements regulating cell cycle arrest genes (CCA-sites), but relatively low affinity to the sites associated with apoptosis (Apo-sites). This in vivo tendency cannot be explained solely by the p53-DNA binding constants measured in vitro. Since p53 can bind nucleosomal DNA, we sought to understand if the two groups of p53 sites differ in their accessibility when embedded in nucleosomes. To this aim, we analyzed the sequence-dependent bending anisotropy of human genomic DNA containing p53 sites. For the 20 CCA-sites, we calculated rotational positioning patterns predicting that most of the sites are exposed on the nucleosomal surface. This is consistent with experimentally observed positioning of human nucleosomes. Remarkably, the sequence-dependent DNA anisotropy of both the p53 sites and flanking DNA work in concert producing strong positioning signals. By contrast, both the predicted and observed rotational settings of the 38 Apo-sites in nucleosomes suggest that many of these sites are buried inside, thus preventing immediate p53 recognition and delaying gene induction. The distinct chromatin organization of the CCA response elements appears to be one of the key factors facilitating p53-DNA binding and subsequent activation of genes associated with cell cycle arrest.
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Affiliation(s)
- Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive Rochester, NY 14623, USA and Laboratory of Cell Biology, National Cancer Institute, NIH Bg. 37, Room 3035A, Convent Dr., Bethesda, MD 20892, USA
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Li Q, Zhang Y, Fu J, Han L, Xue L, Lv C, Wang P, Li G, Tong T. FOXA1 mediates p16(INK4a) activation during cellular senescence. EMBO J 2013; 32:858-73. [PMID: 23443045 DOI: 10.1038/emboj.2013.35] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Mechanisms governing the transcription of p16(INK4a), one of the master regulators of cellular senescence, have been extensively studied. However, little is known about chromatin dynamics taking place at its promoter and distal enhancer. Here, we report that Forkhead box A1 protein (FOXA1) is significantly upregulated in both replicative and oncogene-induced senescence, and in turn activates transcription of p16(INK4a) through multiple mechanisms. In addition to acting as a classic sequence-specific transcriptional activator, FOXA1 binding leads to a decrease in nucleosome density at the p16(INK4a) promoter in senescent fibroblasts. Moreover, FOXA1, itself a direct target of Polycomb-mediated repression, antagonizes Polycomb function at the p16(INK4a) locus. Finally, a systematic survey of putative FOXA1 binding sites in the p16(INK4a) genomic region revealed an ∼150 kb distal element that could loop back to the promoter and potentiate p16(INK4a) expression. Overall, our findings establish several mechanisms by which FOXA1 controls p16(INK4a) expression during cellular senescence.
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Affiliation(s)
- Qian Li
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
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85
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Bernardo GM, Bebek G, Ginther CL, Sizemore ST, Lozada KL, Miedler JD, Anderson LA, Godwin AK, Abdul-Karim FW, Slamon DJ, Keri RA. FOXA1 represses the molecular phenotype of basal breast cancer cells. Oncogene 2013; 32:554-63. [PMID: 22391567 PMCID: PMC3371315 DOI: 10.1038/onc.2012.62] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 12/12/2022]
Abstract
Breast cancer is a heterogeneous disease that comprises multiple subtypes. Luminal subtype tumors confer a more favorable patient prognosis, which is, in part, attributed to estrogen receptor (ER)-α positivity and antihormone responsiveness. Expression of the forkhead box transcription factor, FOXA1, similarly correlates with the luminal subtype and patient survival, but is also present in a subset of ER-negative tumors. FOXA1 is also consistently expressed in luminal breast cancer cell lines even in the absence of ER. In contrast, breast cancer cell lines representing the basal subtype do not express FOXA1. To delineate an ER-independent role for FOXA1 in maintaining the luminal phenotype, and hence a more favorable prognosis, we performed expression microarray analyses on FOXA1-positive and ER-positive (MCF7, T47D), or FOXA1-positive and ER-negative (MDA-MB-453, SKBR3) luminal cell lines in the presence or absence of transient FOXA1 silencing. This resulted in three FOXA1 transcriptomes: (1) a luminal signature (consistent across cell lines), (2) an ER-positive signature (restricted to MCF7 and T47D) and (3) an ER-negative signature (restricted to MDA-MB-453 and SKBR3). Gene set enrichment analyses revealed FOXA1 silencing causes a partial transcriptome shift from luminal to basal gene expression signatures. FOXA1 binds to a subset of both luminal and basal genes within luminal breast cancer cells, and loss of FOXA1 increases enhancer RNA transcription for a representative basal gene (CD58). These data suggest FOXA1 directly represses a subset of basal signature genes. Functionally, FOXA1 silencing increases migration and invasion of luminal cancer cells, both of which are characteristics of basal subtype cells. We conclude FOXA1 controls plasticity between basal and luminal breast cancer cells, not only by inducing luminal genes but also by repressing the basal phenotype, and thus aggressiveness. Although it has been proposed that FOXA1-targeting agents may be useful for treating luminal tumors, these data suggest that this approach may promote transitions toward more aggressive cancers.
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Affiliation(s)
- Gina M. Bernardo
- Departments of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Gurkan Bebek
- Departments of Case Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Charles L. Ginther
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Steven T. Sizemore
- Departments of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kristen L. Lozada
- Departments of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - John D. Miedler
- Department of Pathology, University Hospitals-Case Medical Center, Cleveland, OH, 44106, USA
| | - Lee A. Anderson
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Fadi W. Abdul-Karim
- Departments of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Pathology, University Hospitals-Case Medical Center, Cleveland, OH, 44106, USA
| | - Dennis J. Slamon
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Ruth A. Keri
- Departments of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Departments of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Division of General Medical Sciences-Oncology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS. Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 2013; 27:251-60. [PMID: 23355396 DOI: 10.1101/gad.206458.112] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
While most transcription factors exit the chromatin during mitosis and the genome becomes silent, a subset of factors remains and "bookmarks" genes for rapid reactivation as cells progress through the cell cycle. However, it is unknown whether such bookmarking factors bind to chromatin similarly in mitosis and how different binding capacities among them relate to function. We compared a diverse set of transcription factors involved in liver differentiation and found markedly different extents of mitotic chromosome binding. Among them, the pioneer factor FoxA1 exhibits the greatest extent of mitotic chromosome binding. Genomically, ~15% of the FoxA1 interphase target sites are bound in mitosis, including at genes that are important for liver differentiation. Biophysical, genome mapping, and mutagenesis studies of FoxA1 reveals two different modes of binding to mitotic chromatin. Specific binding in mitosis occurs at sites that continue to be bound from interphase. Nonspecific binding in mitosis occurs across the chromosome due to the intrinsic chromatin affinity of FoxA1. Both specific and nonspecific binding contribute to timely reactivation of target genes post-mitosis. These studies reveal an unexpected diversity in the mechanisms by which transcription factors help retain cell identity during mitosis.
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Affiliation(s)
- Juan Manuel Caravaca
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Smilow Center for Translation Research, Philadelphia, PA 19104, USA
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87
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Morris SA, Daley GQ. A blueprint for engineering cell fate: current technologies to reprogram cell identity. Cell Res 2013; 23:33-48. [PMID: 23277278 DOI: 10.1038/cr.2013.1] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Human diseases such as heart failure, diabetes, neurodegenerative disorders, and many others result from the deficiency or dysfunction of critical cell types. Strategies for therapeutic tissue repair or regeneration require the in vitro manufacture of clinically relevant quantities of defined cell types. In addition to transplantation therapy, the generation of otherwise inaccessible cells also permits disease modeling, toxicology testing and drug discovery in vitro. In this review, we discuss current strategies to manipulate the identity of abundant and accessible cells by differentiation from an induced pluripotent state or direct conversion between differentiated states. We contrast these approaches with recent advances employing partial reprogramming to facilitate lineage switching, and discuss the mechanisms underlying the engineering of cell fate. Finally, we address the current limitations of the field and how the resulting cell types can be assessed to ensure the production of medically relevant populations.
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Affiliation(s)
- Samantha A Morris
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, MA, USA
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88
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Serrano F, Calatayud CF, Blazquez M, Torres J, Castell JV, Bort R. Gata4 Blocks Somatic Cell Reprogramming By Directly Repressing Nanog. Stem Cells 2012; 31:71-82. [DOI: 10.1002/stem.1272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/04/2012] [Indexed: 12/31/2022]
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89
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Abstract
Pioneer factors are a special class of transcription factor that can associate with compacted chromatin to facilitate the binding of additional transcription factors. The function of pioneer factors was originally described during development; more recently, they have been implicated in hormone-dependent cancers, such as oestrogen receptor-positive breast cancer and androgen receptor-positive prostate cancer. We discuss the importance of pioneer factors in these specific cancers, the discovery of new putative pioneer factors and the interplay between these proteins in mediating nuclear receptor function in cancer.
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Affiliation(s)
- Kamila M Jozwik
- Cancer Research UK, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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90
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FOXA1: a transcription factor with parallel functions in development and cancer. Biosci Rep 2012; 32:113-30. [PMID: 22115363 DOI: 10.1042/bsr20110046] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
When aberrant, factors critical for organ morphogenesis are also commonly involved in disease progression. FOXA1 (forkhead box A1), also known as HNF3α (hepatocyte nuclear factor 3α), is required for postnatal survival due to its essential role in controlling pancreatic and renal function. In addition to regulating a variety of tissues during embryogenesis and early life, rescue experiments have revealed a specific role for FOXA1 in the postnatal development of the mammary gland and prostate. Activity of the nuclear hormone receptors ERα (oestrogen receptor α) and AR (androgen receptor) is also required for proper development of the mammary gland and prostate respectively. FOXA1 modulates ER and AR function in breast and prostate cancer cells, supporting the postulate that FOXA1 is involved in ER and AR signalling under normal conditions, and that some carcinogenic processes in these tissues stem from hormonally regulated developmental pathways gone awry. In addition to broadly reviewing the function of FOXA1 in various aspects of development and cancer, this review focuses on the interplay of FOXA1/ER and FOXA1/AR, in normal and cancerous mammary and prostate epithelial cells. Given the hormone dependency of both breast and prostate cancer, a thorough understanding of FOXA1's role in both cancer types is critical for battling hormone receptor-positive disease and acquired anti-hormone resistance.
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91
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Belikov S, Holmqvist PH, Åstrand C, Wrange Ö. FoxA1 and glucocorticoid receptor crosstalk via histone H4K16 acetylation at a hormone regulated enhancer. Exp Cell Res 2012; 318:61-74. [DOI: 10.1016/j.yexcr.2011.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/02/2011] [Accepted: 09/29/2011] [Indexed: 12/17/2022]
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92
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A matter of packaging: influence of nucleosome positioning on heterologous gene expression. Methods Mol Biol 2012; 824:51-64. [PMID: 22160893 DOI: 10.1007/978-1-61779-433-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The organization of DNA into the various levels of chromatin compaction is the main obstacle that restricts the access of transcriptional machinery to genes. Genome-wide chromatin analyses have shown that there are common chromatin organization patterns for most genes but have also revealed important differences in nucleosome positioning throughout the genome. Such chromatin heterogeneity is one of the reasons why recombinant gene expression is highly dependent on integration sites. Different solutions have been tested for this problem, including artificial targeting of chromatin-modifying factors or the addition of DNA elements, which efficiently counteract the influence of the chromatin environment.An influence of the chromatin configuration of the recombinant gene itself on its transcriptional behavior has also been established. This view is especially important for heterologous genes since the general parameters of chromatin organization change from one species to another. The chromatin organization of bacterial DNA proves particularly dramatic when introduced into eukaryotes. The nucleosome positioning of recombinant genes is the result of the interaction between the machinery of the hosting cell and the sequences of both the recombinant genes and the promoter regions. We discuss the key aspects of this phenomenon from the heterologous gene expression perspective.
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93
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Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227-41. [PMID: 22056668 DOI: 10.1101/gad.176826.111] [Citation(s) in RCA: 1145] [Impact Index Per Article: 88.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special "pioneer transcription factors" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.
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Affiliation(s)
- Kenneth S Zaret
- Epigenetics Program, Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, USA.
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94
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Hirai H, Tani T, Kikyo N. Structure and functions of powerful transactivators: VP16, MyoD and FoxA. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2011; 54:1589-96. [PMID: 21404180 DOI: 10.1387/ijdb.103194hh] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Induced pluripotent stem cell (iPSC) technology is a promising approach for converting one type of a differentiated cell into another type of differentiated cell through a pluripotent state as an intermediate step. Recent studies, however, indicate the possibility of directly converting one cell type to another without going through a pluripotent state. This direct reprogramming approach is dependent on a combination of highly potent transcription factors for cell-type conversion, presumably skipping more physiological and multi-step differentiation processes. A trial-and-error strategy is commonly used to screen many candidate transcription factors to identify the correct combination of factors. We speculate, however, that a better understanding of the functional mechanisms of exemplary transcriptional activators will facilitate the identification of novel factor combinations capable of direct reprogramming. The purpose of this review is to critically examine the literature on three highly potent transcriptional activators: the herpes virus protein, VP16; the master regulator of skeletal muscle differentiation, MyoD and the "pioneer" factor for hepatogenesis, FoxA. We discuss the roles of their functional protein domains, interacting partners and chromatin remodeling mechanisms during gene activation to understand how these factors open the chromatin of inactive genes and reset the transcriptional pattern during cell type conversion.
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95
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FOXA1: master of steroid receptor function in cancer. EMBO J 2011; 30:3885-94. [PMID: 21934649 DOI: 10.1038/emboj.2011.340] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 08/29/2011] [Indexed: 12/15/2022] Open
Abstract
FOXA transcription factors are potent, context-specific mediators of development that hold specialized functions in hormone-dependent tissues. Over the last several years, FOXA1 has emerged as a critical mediator of nuclear steroid receptor signalling, manifest at least in part through regulation of androgen receptor and oestrogen receptor activity. Recent findings point towards a major role for FOXA1 in modulating nuclear steroid receptor activity in breast and prostate cancer, and suggest that FOXA1 may significantly contribute to pro-tumourigenic phenotypes. The present review article will focus on the mechanisms, consequence, and clinical relevance of FOXA1-mediated steroid nuclear receptor signalling in human malignancy.
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96
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Nagaoka M, Duncan SA. Transcriptional control of hepatocyte differentiation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 97:79-101. [PMID: 21074730 DOI: 10.1016/b978-0-12-385233-5.00003-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The liver is the largest glandular organ in the body and plays a central role in controlling metabolism. During hepatogenesis, complex developmental processes must generate an array of cell types that are spatially arranged to generate a hepatic architecture that is essential to support liver function. The processes that control the ultimate formation of the liver are diverse and complex and in many cases poorly defined. Much of the focus of research during the past three decades has been on understanding how hepatocytes, which are the predominant liver parenchymal cells, differentiate during embryogenesis. Through a combination of mouse molecular genetics, embryology, and molecular biochemistry, investigators have defined a myriad of transcription factors that combine to control formation and function of hepatocytes. Here, we will review the major discoveries that underlie our current understanding of transcriptional regulation of hepatocyte differentiation.
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Affiliation(s)
- Masato Nagaoka
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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97
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Kim SW, Yoon SJ, Chuong E, Oyolu C, Wills AE, Gupta R, Baker J. Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs. Dev Biol 2011; 357:492-504. [PMID: 21741376 DOI: 10.1016/j.ydbio.2011.06.009] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 11/15/2022]
Abstract
The first stages of embryonic differentiation are driven by signaling pathways hardwired to induce particular fates. Endoderm commitment is controlled by the TGF-β superfamily member, Nodal, which utilizes the transcription factors, SMAD2/3, SMAD4 and FOXH1, to drive target gene expression. While the role of Nodal is well defined within the context of endoderm commitment, mechanistically it is unknown how this signal interacts with chromatin on a genome wide scale to trigger downstream responses. To elucidate the Nodal transcriptional network that governs endoderm formation, we used ChIP-seq to identify genomic targets for SMAD2/3, SMAD3, SMAD4, FOXH1 and the active and repressive chromatin marks, H3K4me3 and H3K27me3, in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that while SMAD2/3, SMAD4 and FOXH1 associate with DNA in a highly dynamic fashion, there is an optimal bivalent signature at 32 gene loci for driving endoderm commitment. Initially, this signature is marked by both H3K4me3 and H3K27me3 as a very broad bivalent domain in hESCs. Within the first 24h, SMAD2/3 accumulation coincides with H3K27me3 reduction so that these loci become monovalent marked by H3K4me3. JMJD3, a histone demethylase, is simultaneously recruited to these promoters, suggesting a conservation of mechanism at multiple promoters genome-wide. The correlation between SMAD2/3 binding, monovalent formation and transcriptional activation suggests a mechanism by which SMAD proteins coordinate with chromatin at critical promoters to drive endoderm specification.
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Affiliation(s)
- Si Wan Kim
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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98
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Abstract
Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.
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99
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Mansour AA, Nissim-Eliraz E, Zisman S, Golan-Lev T, Schatz O, Klar A, Ben-Arie N. Foxa2 regulates the expression of Nato3 in the floor plate by a novel evolutionarily conserved promoter. Mol Cell Neurosci 2010; 46:187-99. [PMID: 20849957 DOI: 10.1016/j.mcn.2010.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 11/24/2022] Open
Abstract
The development of the neural tube into a complex central nervous system involves morphological, cellular and molecular changes, all of which are tightly regulated. The floor plate (FP) is a critical organizing center located at the ventral-most midline of the neural tube. FP cells regulate dorsoventral patterning, differentiation and axon guidance by secreting morphogens. Here we show that the bHLH transcription factor Nato3 (Ferd3l) is specifically expressed in the spinal FP of chick and mouse embryos. Using in ovo electroporation to understand the regulation of the FP-specific expression of Nato3, we have identified an evolutionarily conserved 204 bp genomic region, which is necessary and sufficient to drive expression to the chick FP. This promoter contains two Foxa2-binding sites, which are highly conserved among distant phyla. The two sites can bind Foxa2 in vitro, and are necessary for the expression in the FP in vivo. Gain and loss of Foxa2 function in vivo further emphasize its role in Nato3 promoter activity. Thus, our data suggest that Nato3 is a direct target of Foxa2, a transcription activator and effector of Sonic hedgehog, the hallmark regulator of FP induction and spinal cord development. The identification of the FP-specific promoter is an important step towards a better understanding of the molecular mechanisms through which Nato3 transcription is regulated and for uncovering its function during nervous system development. Moreover, the promoter provides us with a powerful tool for conditional genetic manipulations in the FP.
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Affiliation(s)
- Abed AlFatah Mansour
- Department of Cell and Developmental Biology, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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100
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Samaan G, Yugo D, Rajagopalan S, Wall J, Donnell R, Goldowitz D, Gopalakrishnan R, Venkatachalam S. Foxn3 is essential for craniofacial development in mice and a putative candidate involved in human congenital craniofacial defects. Biochem Biophys Res Commun 2010; 400:60-5. [DOI: 10.1016/j.bbrc.2010.07.142] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 07/31/2010] [Indexed: 12/12/2022]
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