101
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Kaestner KH. The FoxA factors in organogenesis and differentiation. Curr Opin Genet Dev 2010; 20:527-32. [PMID: 20591647 DOI: 10.1016/j.gde.2010.06.005] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/01/2010] [Accepted: 06/02/2010] [Indexed: 11/26/2022]
Abstract
The genetic analysis of the Foxa genes in both total and conditional mutant mice has clearly established that organogenesis of multiple systems is controlled by this subfamily of winged helix transcription factors. These discoveries followed the establishment of the conceptional framework of the mechanism of action of the FoxA proteins as 'pioneer factors' that can engage chromatin before other transcription factors. Recent molecular and genomic studies have also shown that FoxA proteins can facilitate binding of several nuclear receptors to their respective targets in a context-dependent manner, greatly increasing the range and importance of FoxA factors in biology.
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Affiliation(s)
- Klaus H Kaestner
- Department of Genetics & Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6145, United States.
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102
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Abstract
Embryonic development of the liver has been studied intensely, yielding insights that impact diverse areas of developmental and cell biology. Understanding the fundamental mechanisms that control hepatogenesis has also laid the basis for the rational differentiation of stem cells into cells that display many hepatic functions. Here, we review the basic molecular mechanisms that control the formation of the liver as an organ.
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103
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Stevenson KS, McGlynn L, Hodge M, McLinden H, George WD, Davies RW, Shiels PG. Isolation, characterization, and differentiation of thy1.1-sorted pancreatic adult progenitor cell populations. Stem Cells Dev 2010; 18:1389-98. [PMID: 19326970 DOI: 10.1089/scd.2008.0301] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have isolated a novel progenitor cell population from adult rat pancreatic ducts, termed pancreatic-derived progenitor cells (PDPCs). Here, we report the in vitro culture, selection, and characterization of Thy1.1-positive and Thy1.1-negative PDPC subpopulations. These cells exhibit bipotentiality for differentiation into both pancreatic and hepatic cell types. Significantly, they express Pdx-1. Using a serum-free FGF-4-containing differentiation protocol, we have observed a time course of both morphological and gene expression changes indicative of hepatic lineage differentiation for the Thy1.1-positive subpopulation. These cells express albumin and store glycogen, typical features of mature hepatocytes. The Thy1.1-positive subpopulation could also readily be induced to differentiate into a pancreatic lineage with characteristic morphological changes resulting in three-dimensional islet-like structures and the transcriptional expression of insulin and glucagon in addition to Pdx-1. No morphological evidence of islet-like clusters was observed using the Thy1.1-negative population. However, Thy1.1-negative cells grown in pancreatic differentiation medium did show insulin gene transcription. Glucagon was not expressed in the undifferentiated Thy1.1-negative cells, nor was it induced in vitro after differentiation. The detection of Pdx-1 transcriptional expression in both populations indicates their potential as a novel source of non-beta-cell-derived insulin.
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Affiliation(s)
- Karen S Stevenson
- Division of Cancer Sciences and Molecular Pathology, Department of Surgery, University of Glasgow, Glasgow G31 2ER, Scotland, United Kingdom
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104
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Le Lay J, Kaestner KH. The Fox genes in the liver: from organogenesis to functional integration. Physiol Rev 2010; 90:1-22. [PMID: 20086072 DOI: 10.1152/physrev.00018.2009] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation and function of the liver are highly controlled, essential processes. Multiple signaling pathways and transcriptional regulatory networks cooperate in this complex system. The evolutionarily conserved FOX, for Forkhead bOX, class of transcriptional regulators is critical to many aspects of liver development and function. The FOX proteins are small, mostly monomeric DNA binding factors containing the so-called winged helix DNA binding motif that distinguishes them from other classes of transcription factors. We discuss the biochemical and genetic roles of Foxa, Foxl1, Foxm1, and Foxo, as these have been shown to regulate many processes throughout the life of the organ, controlling both formation and function of the liver.
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Affiliation(s)
- John Le Lay
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6145, USA
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105
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Kohler S, Cirillo LA. Stable chromatin binding prevents FoxA acetylation, preserving FoxA chromatin remodeling. J Biol Chem 2010; 285:464-72. [PMID: 19897491 PMCID: PMC2804194 DOI: 10.1074/jbc.m109.063149] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/05/2009] [Indexed: 12/22/2022] Open
Abstract
FoxA1-3 (formerly HNF3alpha, -beta, and -gamma), members of the FoxA subfamily of forkhead transcription factors, function as initial chromatin-binding and chromatin-remodeling factors in a variety of tissues, including liver and pancreas. Despite essential roles in development and metabolism, regulation of FoxA factors is not well understood. This study examines a potential role for acetylation in the regulation of FoxA chromatin binding and remodeling. Using in silico analysis, we have identified 11 putative p300 acetylation sites within FoxA1, five of which are located within wings 1 and 2 of its winged-helix DNA-binding domain. These polypeptide structures stabilize FoxA DNA and chromatin binding, and we have demonstrated that acetylation attenuates FoxA binding to DNA and diminishes its ability to remodel chromatin. FoxA acetylation is inhibited by chromatin binding. We propose a model whereby stable chromatin binding protects the FoxA DNA-binding domain from acetylation to preserve chromatin binding and remodeling by FoxA factors in the absence of extracellular cues.
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Affiliation(s)
- Sarah Kohler
- 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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106
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Sahu G, Wang D, Chen CB, Zhurkin VB, Harrington RE, Appella E, Hager GL, Nagaich AK. p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J Biol Chem 2009; 285:1321-32. [PMID: 19887449 DOI: 10.1074/jbc.m109.081182] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sequence-specific binding to DNA is crucial for the p53 tumor suppressor function. To investigate the constraints imposed on p53-DNA recognition by nucleosomal organization, we studied binding of the p53 DNA binding domain (p53DBD) and full-length wild-type p53 protein to a single p53 response element (p53RE) placed near the nucleosomal dyad in six rotational settings. We demonstrate that the strongest p53 binding occurs when the p53RE in the nucleosome is bent in the same direction as observed for the p53-DNA complexes in solution and in co-crystals. The p53RE becomes inaccessible, however, if its orientation in the core particle is changed by approximately 180 degrees. Our observations indicate that the orientation of the binding sites on a nucleosome may play a significant role in the initial p53-DNA recognition and subsequent cofactor recruitment.
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Affiliation(s)
- Geetaram Sahu
- Laboratory of Chemistry, Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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107
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Kappen C, Salbaum JM. Identification of regulatory elements in the Isl1 gene locus. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2009; 53:935-46. [PMID: 19598113 DOI: 10.1387/ijdb.082819ck] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Isl1 is a LIM/homeodomain transcription factor with critical roles for the development of the heart, the nervous system and the pancreas. Both deficiency and mis-expression of Isl1 cause profound developmental defects, demonstrating the importance of proper regulation of Isl1 gene expression during development. In order to understand the mechanisms that control Isl1 expression during embryogenesis and in tissue differentiation, we initiated a screen for gene regulatory elements in the Isl1 locus using a novel dual reporter gene vector that allows screens of large genomic regions through reporter gene assays in vitro and in vivo. We identified regions from the Isl1 gene locus that confer transcriptional activity in pancreatic cell lines in vitro. Using transgenic mice, we furthermore discovered an enhancer with in vivo specificity for the developing heart, as well as visceral and posterior mesoderm. Our findings further suggest that Foxo1 as well as Gata4 contribute to the activity of this enhancer in the developing embryo. We conclude that Isl1 gene expression is controlled in modular fashion by several elements with distinct functionality. Embryonic Isl1 expression in several tissues of mesodermal origin is driven by a specific enhancer that is located 3-6kb downstream of the gene.
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Affiliation(s)
- Claudia Kappen
- Pennington Biomedical Research Center, Baton Rouge, LA 71010, USA.
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108
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Nock A, Ascano JM, Jones T, Barrero MJ, Sugiyama N, Tomita M, Ishihama Y, Malik S. Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2. J Biol Chem 2009; 284:19915-26. [PMID: 19478084 PMCID: PMC2740417 DOI: 10.1074/jbc.m109.016295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Indexed: 11/06/2022] Open
Abstract
Forkhead factors are important regulators of animal development and homeostasis. They are among the earliest to bind quiescent genes, which they activate in conjunction with other transcription factors. Many liver-specific genes are under the control of FoxA2, a liver-enriched forkhead protein. Here we confirmed by chromatin immunoprecipitation that FoxA2 is one of the factors bound to the promoter-proximal enhancer of the gene encoding apolipoprotein AI (a component of high density lipoprotein) and that it functions in synergy with the nuclear receptor hepatocyte nuclear factor-4alpha. Furthermore, toward identifying additional cofactors that could potentially regulate FoxA2 activity, we identified DNA-dependent protein kinase (DNA-PK) as a FoxA2-associated factor upon affinity purification of epitope-tagged FoxA2. We show that FoxA2, found to be a phosphoprotein in vivo, is also an efficient substrate for DNA-PK, which targets serine 283. This residue is contained within a conserved serine-glutamine phosphorylation signal for DNA-PK, located within the C-terminal third of the polypeptide, just distal to its winged-helix DNA binding domain. We establish that this residue is critical for FoxA2 function because FoxA2 bearing a mutation at this site is severely compromised in its ability to activate a reporter gene under the control of its cognate DNA-binding site (apoAI site B). Complementary experiments rule out that this mutation compromises the ability of FoxA2 to either translocate to the nucleus or to bind site B. We therefore conclude that DNA-PK-dependent phosphorylation of FoxA2 plays a critical role in its transcriptional activation function per se.
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Affiliation(s)
- Adam Nock
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Janice M. Ascano
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Tara Jones
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Maria J. Barrero
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Naoyuki Sugiyama
- the Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan, and
| | - Masaru Tomita
- the Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan, and
| | - Yasushi Ishihama
- the Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan, and
- PRESTO, Japan Science and Technology Agency, Sanbancho Building, 5-Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
| | - Sohail Malik
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
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109
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Kang J, Nathan E, Xu SM, Tzahor E, Black BL. Isl1 is a direct transcriptional target of Forkhead transcription factors in second-heart-field-derived mesoderm. Dev Biol 2009; 334:513-22. [PMID: 19580802 DOI: 10.1016/j.ydbio.2009.06.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 06/27/2009] [Indexed: 10/20/2022]
Abstract
The cells of the second heart field (SHF) contribute to the outflow tract and right ventricle, as well as to parts of the left ventricle and atria. Isl1, a member of the LIM-homeodomain transcription factor family, is expressed early in this cardiac progenitor population and functions near the top of a transcriptional pathway essential for heart development. Isl1 is required for the survival and migration of SHF-derived cells into the early developing heart at the inflow and outflow poles. Despite this important role for Isl1 in early heart formation, the transcriptional regulation of Isl1 has remained largely undefined. Therefore, to identify transcription factors that regulate Isl1 expression in vivo, we screened the conserved noncoding sequences from the mouse Isl1 locus for enhancer activity in transgenic mouse embryos. Here, we report the identification of an enhancer from the mouse Isl1 gene that is sufficient to direct expression to the SHF and its derivatives. The Isl1 SHF enhancer contains three consensus Forkhead transcription factor binding sites that are efficiently and specifically bound by Forkhead transcription factors. Importantly, the activity of the enhancer is dependent on these three Forkhead binding sites in transgenic mouse embryos. Thus, these studies demonstrate that Isl1 is a direct transcriptional target of Forkhead transcription factors in the SHF and establish a transcriptional pathway upstream of Isl1 in the SHF.
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Affiliation(s)
- Jione Kang
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94158-2517, USA
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110
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Expression of Pit-1 in nonsomatotrope cell lines induces human growth hormone locus control region histone modification and hGH-N transcription. J Mol Biol 2009; 390:26-44. [PMID: 19427323 DOI: 10.1016/j.jmb.2009.04.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 04/29/2009] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
The POU domain transcription factor Pit-1 is expressed in somatotropes, lactotropes, and thyrotropes of the anterior pituitary. Pit-1 is essential for the establishment of these lineages during development and regulates the expression of genes encoding the peptide hormones secreted by each cell type, including the growth hormone gene expressed in somatotropes. In contrast to rodent growth hormone loci, the human growth hormone (hGH) locus is regulated by a distal locus control region (LCR), which is required in cis for the proper expression of the hGH gene cluster in transgenic mice. The hGH LCR mediates a domain of histone acetylation targeted to the hGH locus that is associated with distal hGH-N activation, and the discrete determinants of this activity coincide with DNaseI hypersensitive site (HS) I of the LCR. The identification of three in vitro Pit-1 binding sites within the HS-I region suggested a model in which Pit-1 binding at HS-I initiates the chromatin modification mechanism associated with hGH LCR activity. To test this hypothesis directly and to determine whether Pit-1 expression is sufficient to confer hGH locus histone acetylation and activate hGH-N transcription from an inactive locus, we expressed Pit-1 in nonpituitary cell types. We show that Pit-1 expression established a domain of histone hyperacetylation at the LCR and hGH-N promoter in these cells similar to that observed in pituitary chromatin. This was accompanied by the activation of hGH-N transcription and an increase in intergenic and CD79b transcripts proximal to HS-I. These effects were coincident with Pit-1 occupancy at HS-I and the hGH-N promoter and were observed irrespective of the basal histone modification status of HS-I in the heterologous cell line. These findings are consistent with a role for Pit-1 as an initiating factor in hGH locus activation during somatotrope ontogeny, acting through binding sites at HS-I of the hGH LCR.
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111
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Sekiya T, Muthurajan UM, Luger K, Tulin AV, Zaret KS. Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA. Genes Dev 2009; 23:804-9. [PMID: 19339686 DOI: 10.1101/gad.1775509] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
FoxA proteins are pioneer transcription factors, among the first to bind chromatin domains in development and enable gene activity. The Fox DNA-binding domain structurally resembles linker histone and binds nucleosomes stably. Using fluorescence recovery after photobleaching, we found that FoxA1 and FoxA2 move much more slowly in nuclei than other transcription factor types, including c-Myc, GATA-4, NF-1, and HMGB1. We find that slower nuclear mobility correlates with high nonspecific nucleosome binding, and point mutations that disrupt nonspecific binding markedly increase nuclear mobility. FoxA's distinct nuclear mobility is consistent with its pioneer activity in chromatin.
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Affiliation(s)
- Takashi Sekiya
- Epigenetics and Progenitor Cells Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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112
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Ishii H, Du H, Zhang Z, Henderson A, Sen R, Pazin MJ. Mi2beta shows chromatin enzyme specificity by erasing a DNase I-hypersensitive site established by ACF. J Biol Chem 2009; 284:7533-41. [PMID: 19158090 DOI: 10.1074/jbc.m807617200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent remodeling enzymes ACF and Mi2beta can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding to chromatin. In a second step, PU.1 directs Mi2beta to erase an established DNase I-hypersensitive site, in an ATP-dependent reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site. Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively. Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure.
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Affiliation(s)
- Haruhiko Ishii
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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113
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Zaret KS, Watts J, Xu J, Wandzioch E, Smale ST, Sekiya T. Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 73:119-26. [PMID: 19028990 DOI: 10.1101/sqb.2008.73.040] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The endoderm is a multipotent progenitor cell population in the embryo that gives rise to the liver, pancreas, and other cell types and provides paradigms for understanding cell-type specification. Studies of isolated embryo tissue cells and genetic approaches in vivo have defined fibroblast growth factor/mitogen-activated protein kinase (FGF/MAPK) and bone morphogenetic protein (BMP) signaling pathways that induce liver and pancreatic fates in the endoderm. In undifferentiated endoderm cells, the FoxA and GATA transcription factors are among the first to engage silent genes, helping to endow competence for cell-type specification. FoxA proteins can bind their target sites in highly compacted chromatin and open up the local region for other factors to bind; hence, they have been termed "pioneer factors." We recently found that FoxA proteins remain bound to chromatin in mitosis, as an epigenetic mark. In embryonic stem cells, which lack FoxA, FoxA target sites can be occupied by FoxD3, which in turn helps to maintain a local demethylation of chromatin. By these means, a cascade of Fox factors helps to endow progenitor cells with the competence to activate genes in response to tissue-inductive signals. Understanding such epigenetic mechanisms for transcriptional competence coupled with knowledge of the relevant signals for cell-type specification should greatly facilitate efforts to predictably differentiate stem cells to liver and pancreatic fates.
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Affiliation(s)
- K S Zaret
- Epigenetics and Progenitor Cells Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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114
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Lukin K, Fields S, Hartley J, Hagman J. Early B cell factor: Regulator of B lineage specification and commitment. Semin Immunol 2008; 20:221-7. [PMID: 18722139 DOI: 10.1016/j.smim.2008.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/02/2008] [Accepted: 07/10/2008] [Indexed: 12/21/2022]
Abstract
B lymphocytes are generated from hematopoietic stem cells in a series of steps controlled by transcription factors. One of the most important regulators of this process is early B cell factor (EBF). Multiple lines of evidence indicate that expression of EBF is a principle determinant of the B cell fate. In the absence of EBF, progenitor cells fail to express classical markers of B cells, including immunoglobulins. EBF drives B cell differentiation by activating the Pax5 gene and other genes required for the pre-B and B cell receptors. New evidence suggests that expression of EBF in common lymphoid progenitors directs B cell fate decisions. Specification and commitment of cells to the B cell lineage are further established by Pax5, which increases expression of EBF. Recently, it was demonstrated that both EBF and Pax5 contribute to the commitment of cells to the B lineage. Together, these studies confirm that EBF is a keystone in the regulatory network that coordinates B cell lineage specification and commitment.
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Affiliation(s)
- Kara Lukin
- Integrated Department of Immunology, National Jewish Medical and Research Center, 1400 Jackson Street, K516B, Denver, CO 80206, USA
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115
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How transcription factors program chromatin—Lessons from studies of the regulation of myeloid-specific genes. Semin Immunol 2008; 20:257-63. [DOI: 10.1016/j.smim.2008.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 05/15/2008] [Indexed: 12/21/2022]
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116
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Verzi MP, Khan AH, Ito S, Shivdasani RA. Transcription factor foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells. Gastroenterology 2008; 135:591-600. [PMID: 18558092 PMCID: PMC2955860 DOI: 10.1053/j.gastro.2008.04.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 04/08/2008] [Accepted: 04/13/2008] [Indexed: 01/12/2023]
Abstract
BACKGROUND & AIMS The gastric mucosa provides a stringent epithelial barrier and produces acid and enzymes that initiate digestion. In this regenerating tissue, progenitors differentiate continually into 4 principal specialized cell types, yet underlying mechanisms of differentiation are poorly understood. We identified stomach-restricted expression of the forkhead transcription factor FOXQ1. METHODS We used a combination of genetic, histochemical, ultrastructural, and molecular analysis to study gastric cell lineages with respect to FOXQ1. RESULTS Within the developing and adult gastrointestinal tract, Foxq1 messenger RNA (mRNA) is restricted to the stomach and expressed predominantly in foveolar (pit) cells, the abundant mucin-producing cells that line the mucosal surface. Mice carrying Foxq1 coding mutations show virtual absence of mRNA and protein for the backbone of the major stomach mucin MUC5AC. These observations correspond to a paucity of foveolar cell secretory vesicles and notable loss of stomach but not intestinal mucus. Transcriptional profiling identified a surprisingly restricted set of genes with altered expression in Foxq1 mutant stomachs. MUC5AC is a highly tissue-restricted product that similarly depends on FOXQ1 in its other major site of expression, conjunctival goblet cells. CONCLUSIONS Taken together, these observations imply that promotion of gastric MUC5AC synthesis is a primary, cell-autonomous function of FOXQ1. This study is the first to implicate a transcription factor in terminal differentiation of foveolar cells and begins to define the requirements to assemble highly specialized organelles and cells in the gastric mucosa.
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Affiliation(s)
- Michael P. Verzi
- Dana-Farber Cancer Institute and Departments of Medicine, Boston, MA, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Abdul H. Khan
- Dana-Farber Cancer Institute and Departments of Medicine, Boston, MA, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Susumu Ito
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Ramesh A. Shivdasani
- Dana-Farber Cancer Institute and Departments of Medicine, Boston, MA, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA,Corresponding author: Ramesh A. Shivdasani, MD, PhD, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Tel. (617) 632-5746 Fax (617) 582-8490,
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117
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Plachetka A, Chayka O, Wilczek C, Melnik S, Bonifer C, Klempnauer KH. C/EBPbeta induces chromatin opening at a cell-type-specific enhancer. Mol Cell Biol 2008; 28:2102-12. [PMID: 18195047 PMCID: PMC2268399 DOI: 10.1128/mcb.01943-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/16/2007] [Accepted: 01/01/2008] [Indexed: 12/16/2022] Open
Abstract
We have used the chicken mim-1 gene as a model to study the mechanisms by which transcription factors gain initial access to their target sites in compacted chromatin. The expression of mim-1 is restricted to the myelomonocytic lineage of the hematopoietic system where it is regulated synergistically by the Myb and CCAAT/enhancer binding protein (C/EBP) factors. Myb and C/EBPbeta cooperate at two distinct cis elements of mim-1, the promoter and a cell-type-specific enhancer, both of which are associated with DNase I hypersensitive sites in myelomonocytic cells but not in mim-1-nonexpressing cells. Previous work has shown that ectopic expression of Myb and C/EBPbeta activates the endogenous mim-1 gene in a nonhematopoietic cell type (fibroblasts), where the gene is normally completely silent. Here, we investigated the molecular details of this finding and show that the activation of mim-1 occurs by two independent mechanisms. In the absence of Myb, C/EBPbeta triggers the initial steps of chromatin opening at the mim-1 enhancer without inducing transcription of the gene. mim-1 transcription occurs only in the presence of Myb and is associated with chromatin opening at the promoter. Our work identifies a novel function for C/EBPbeta in the initial steps of a localized chromatin opening at a specific, physiologically relevant target region.
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Affiliation(s)
- Annette Plachetka
- Institut für Biochemie, Westfälische-Wilhelms-Universität Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster, Germany
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118
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Repression by Groucho/TLE/Grg proteins: genomic site recruitment generates compacted chromatin in vitro and impairs activator binding in vivo. Mol Cell 2008; 28:291-303. [PMID: 17964267 DOI: 10.1016/j.molcel.2007.10.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 07/13/2007] [Accepted: 08/12/2007] [Indexed: 11/21/2022]
Abstract
Groucho-related (Gro/TLE/Grg) corepressors meditate embryonic segmentation, dorsal-ventral patterning, neurogenesis, and Notch and Wnt signaling. Although Gro/TLE/Grgs disrupt activator complexes and recruit histone deacetylases (HDAC), activator complexes can be disrupted in various ways, HDAC recruitment does not account for full corepressor activity, and a direct role for Gro/TLE/Grg binding and altering chromatin structure has not been explored. Using diverse chromatin substrates in vitro, we show that Grg3 creates higher-order, condensed complexes of polynucleosome arrays. Surprisingly, such complexes are in an open, exposed configuration. We find that chromatin binding enables Grg3 recruitment by a transcription factor and the creation of a closed, poorly accessible domain spanning three to four nucleosomes. Targeted recruitment of Grg3 blankets a similar-sized region in vivo, impairing activator recruitment and repressing transcription. These activities of a Groucho protein represent a newly discovered mechanism which differs from that of other classes of corepressors.
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119
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Zeng J, Yan J, Wang T, Mosbrook-Davis D, Dolan KT, Christensen R, Stormo GD, Haussler D, Lathrop RH, Brachmann RK, Burgess SM. Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic Acids Res 2007; 36:e8. [PMID: 18086703 PMCID: PMC2248728 DOI: 10.1093/nar/gkm1117] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Knowledge of all binding sites for transcriptional activators and repressors is essential for computationally aided identification of transcriptional networks. The techniques developed for defining the binding sites of transcription factors tend to be cumbersome and not adaptable to high throughput. We refined a versatile yeast strategy to rapidly and efficiently identify genomic targets of DNA-binding proteins. Yeast expressing a transcription factor is mated to yeast containing a library of genomic fragments cloned upstream of the reporter gene URA3. DNA fragments with target-binding sites are identified by growth of yeast clones in media lacking uracil. The experimental approach was validated with the tumor suppressor protein p53 and the forkhead protein FoxI1 using genomic libraries for zebrafish and mouse generated by shotgun cloning of short genomic fragments. Computational analysis of the genomic fragments recapitulated the published consensus-binding site for each protein. Identified fragments were mapped to identify the genomic context of each binding site. Our yeast screening strategy, combined with bioinformatics approaches, will allow both detailed and high-throughput characterization of transcription factors, scalable to the analysis of all putative DNA-binding proteins.
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Affiliation(s)
- Jue Zeng
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA, USA
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120
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Hatta M, Cirillo LA. Chromatin Opening and Stable Perturbation of Core Histone:DNA Contacts by FoxO1. J Biol Chem 2007; 282:35583-93. [DOI: 10.1074/jbc.m704735200] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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121
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Development of the mammalian liver and ventral pancreas is dependent on GATA4. BMC DEVELOPMENTAL BIOLOGY 2007; 7:37. [PMID: 17451603 PMCID: PMC1877807 DOI: 10.1186/1471-213x-7-37] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/23/2007] [Indexed: 01/05/2023]
Abstract
BACKGROUND In the mouse, the parenchyma of both the liver and ventral pancreas is specified from adjacent domains of the ventral foregut endoderm. GATA4, a zinc finger transcription factor, is strongly expressed in these endodermal domains and molecular analyses have implicated GATA4 in potentiating liver gene expression during the onset of hepatogenesis. We therefore hypothesized that GATA4 has an integral role in controlling the early stages of pancreatic and liver development. RESULTS To determine whether GATA4 contributes to development of either the pancreas or liver we characterized the formation of pancreatic and hepatic tissues in embryos derived from Gata4-/- ES cells by tetraploid embryo complementation. In the absence of GATA4, development of the liver and ventral pancreas was disrupted. At embryonic day (E) 9.5, the liver bud failed to expand although, contrary to expectations, the hepatic endoderm was able to form a pseudo-stratified epithelial liver bud that expressed hepatic genes. Moreover, as we had shown previously, the embryos lacked septum transversum mesenchyme suggesting that liver defects may be cell non-autonomous. Analyses of pancreatic development revealed a complete absence of the ventral but not the dorsal pancreas in Gata4-/- embryos. Moreover, Gata6-/- embryos displayed a similar, although less dramatic phenotype, suggesting a critical role for multiple GATA factors at the earliest stages of ventral pancreas development. CONCLUSION This study defines integral roles for GATA factors in controlling early development of the mammalian liver and pancreas.
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122
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Cirillo LA, Zaret KS. Specific interactions of the wing domains of FOXA1 transcription factor with DNA. J Mol Biol 2006; 366:720-4. [PMID: 17189638 PMCID: PMC1793999 DOI: 10.1016/j.jmb.2006.11.087] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 11/28/2006] [Accepted: 11/28/2006] [Indexed: 11/27/2022]
Abstract
FOX (forkhead box) transcription factors have diverse regulatory roles in development, signaling, and longevity, as well as being able to bind stably to target sites in silent chromatin. Crystal structure analysis showed that the FOXA DNA binding domain folds into a helix-turn-helix (HTH) motif flanked on either side by "wings" of polypeptide chain. The wings have the potential to interact with the DNA minor groove along the long axis of the DNA helix, flanking the HTH interactions with the major groove. Diverse FOX family homologs exist, and structural studies with certain DNA target sites suggest that neither of the wing regions are well ordered or provide a stable contribution to DNA target site binding. However, FOXA1 binds certain DNA target sites with high affinity, and as a monomer. To determine whether the wing domains contribute to stable DNA binding, we assessed complexes of FOXA with high and lower affinity DNA target sites by hydroxyl radical footprinting and site-directed mutagenesis. The data revealed clear protections predicted for wing interactions at the high affinity target, but less so at the lower affinity target, indicating that the wing domains stably interact with high affinity DNA sites for FOXA proteins.
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Affiliation(s)
- Lisa A Cirillo
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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123
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Bonifer C, Lefevre P, Tagoh H. The Regulation of Chromatin and DNA-Methylation Patterns in Blood Cell Development. Curr Top Microbiol Immunol 2006; 310:1-12. [PMID: 16909903 DOI: 10.1007/3-540-31181-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
All developmental processes in metazoans require the establishment of different genetic programs to generate functionally specialised cells. Differential gene expression is also the basis for the alterations in the developmental potential of differentiating cells. However, the molecular details concerning how this is achieved are still poorly understood. The haematopoietic system has for many years served as an excellent model system to studyhow developmental processes are regulated at the epigenetic level. In this article we will summarise recent results from others and from our own laboratory that have yielded profound insights into the general principles of how cell-fate decisions are regulated in the cell nucleus. We summarise (1) how the interplay of sequence-specific transcription factors and chromatin components is responsible for the cell type and cell stage-specific activation of specific genes and (2) how these findings impact on current concepts of epigenetic regulation of developmental processes.
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Affiliation(s)
- C Bonifer
- Division of Experimental Haematology, Institute for Molecular Medicine, Epidemiology and Cancer Research, University of Leeds, St James's University Hospital, UK.
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124
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Maeda J, Yamagishi H, McAnally J, Yamagisihi C, Srivastava D. Tbx1 is regulated by forkhead proteins in the secondary heart field. Dev Dyn 2006; 235:701-10. [PMID: 16444712 PMCID: PMC3316489 DOI: 10.1002/dvdy.20686] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transcriptional regulation in a tissue-specific and quantitative manner is essential for developmental events, including those involved in cardiovascular morphogenesis. Tbx1 is a T-box-containing transcription factor that is responsible for many of the defects observed in 22q11 deletion syndrome in humans. Tbx1 is expressed in the secondary heart field (SHF) and is essential for cardiac outflow tract (OFT) development. We previously reported that Tbx1 is regulated by sonic hedgehog by means of forkhead (Fox) transcription factors in the head mesenchyme and pharyngeal endoderm, but how it is regulated in the SHF is unknown. Here, we show that Tbx1 expression in the SHF is regulated by Fox proteins through a combination of two evolutionarily conserved Fox binding sites in a dose-dependent manner. Cell fate analysis using the Tbx1 enhancer suggests that SHF-derived Tbx1-expressing cells contribute extensively to the right ventricular myocardium as well as the OFT during early development and ultimately give rise to the right ventricular infundibulum, pulmonary trunk, and pulmonary valves. These results suggest that Fox proteins are involved in most, if not all, Tbx1 expression domains and that Tbx1 marks a subset of SHF-derived cells, particularly those that uniquely contribute to the right-sided outflow tract and proximal pulmonary artery.
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Affiliation(s)
- Jun Maeda
- Department of Pediatrics, Division of Pediatric Cardiology, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, TX
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Division of Pediatric Cardiology, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, TX
| | - John McAnally
- Department of Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, TX
| | - Chihiro Yamagisihi
- Department of Pediatrics, Division of Pediatric Cardiology, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, TX
| | - Deepak Srivastava
- Department of Pediatrics and Molecular Biology, University of Texas Southwestern Medical Center, TX
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125
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Kaltenbach LS, Updike DL, Mango SE. Contribution of the amino and carboxyl termini for PHA-4/FoxA function in Caenorhabditis elegans. Dev Dyn 2006; 234:346-54. [PMID: 16127716 DOI: 10.1002/dvdy.20550] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
FoxA transcription factors are central regulators of gut development in all animals that have been studied. Here we examine the sole Caenorhabditis elegans FoxA protein, which is called pha-4. We describe the molecular characterization of five pha-4 mutations and characterize their associated phenotypes. Two nonsense mutations are predicted to truncate PHA-4 after the DNA binding domain and remove the conserved carboxyl terminus. Surprisingly, animals harboring these mutations are viable, provided the mutant mRNAs are stabilized by inactivating the nonsense-mediated decay pathway. Two additional nonsense mutations reveal that the DNA binding domain is critical for activity. A missense mutation predicted to alter the PHA-4 amino terminus leads to a dramatic reduction in pha-4 activity even though the protein is expressed appropriately. We suggest that the PHA-4 amino terminus is essential for PHA-4 function in vivo, possibly as a transactivation domain, and can compensate for loss of the carboxyl terminus. We also provide evidence for autoregulation by PHA-4.
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Affiliation(s)
- Linda S Kaltenbach
- Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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126
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Abstract
Recent studies using animal models have elucidated a growing number of evolutionarily conserved genes and pathways that control liver development from the embryonic endoderm. It is increasingly clear that the genetic programs active in embryogenesis are often deregulated or reactivated in disease, cancer, and tissue repair. Understanding the molecular control of liver development should impact diagnosis and treatment of pediatric and adult liver diseases and aid in efforts to differentiate liver tissue in vitro for stem cell-based therapies.
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Affiliation(s)
- Valérie A McLin
- Baylor College of Medicine, Texas Childrens' Liver Center, 1102 Bates Street, Houston, TX 77006, USA
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127
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Yan J, Xu L, Crawford G, Wang Z, Burgess SM. The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure. Mol Cell Biol 2006; 26:155-68. [PMID: 16354687 PMCID: PMC1317626 DOI: 10.1128/mcb.26.1.155-168.2006] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Revised: 08/04/2005] [Accepted: 10/03/2005] [Indexed: 11/20/2022] Open
Abstract
All forkhead (Fox) proteins contain a highly conserved DNA binding domain whose structure is remarkably similar to the winged-helix structures of histones H1 and H5. Little is known about Fox protein binding in the context of higher-order chromatin structure in living cells. We created a stable cell line expressing FoxI1-green fluorescent protein (GFP) or FoxI1-V5 fusion proteins under control of the reverse tetracycline-controlled transactivator doxycycline inducible system and found that unlike most transcription factors, FoxI1 remains bound to the condensed chromosomes during mitosis. To isolate DNA fragments directly bound by the FoxI1 protein within living cells, we performed chromatin immunoprecipitation assays (ChIPs) with antibodies to either enhanced GFP or the V5 epitope and subcloned the FoxI1-enriched DNA fragments. Sequence analyses indicated that 88% (106/121) of ChIP sequences contain the consensus binding sites for all Fox proteins. Testing ChIP sequences with a quantitative DNase I hypersensitivity assay showed that FoxI1 created stable DNase I sensitivity changes in condensed chromosomes. The majority of ChIP targets and random targets increased in resistance to DNase I in FoxI1-expressing cells, but a small number of targets became more accessible to DNase I. Consistently, the accessibility of micrococcal nuclease to chromatin was generally inhibited. Micrococcal nuclease partial digestion generated a ladder in which all oligonucleosomes were slightly longer than those observed with the controls. On the basis of these findings, we propose that FoxI1 is capable of remodeling chromatin higher-order structure and can stably create site-specific changes in chromatin to either stably create or remove DNase I hypersensitive sites.
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Affiliation(s)
- Jizhou Yan
- National Human Genome Research Institute, Genome Technology Branch, NIH, Bldg. 50, Rm. 5537, 50 South Dr., Bethesda, MD 20892, USA
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128
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Generation of embryos directly from embryonic stem cells by tetraploid embryo complementation reveals a role for GATA factors in organogenesis. Biochem Soc Trans 2005; 33:1534-6. [PMID: 16246163 DOI: 10.1042/bst0331534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gene targeting in ES (embryonic stem) cells has been used extensively to study the role of proteins during embryonic development. In the traditional procedure, this requires the generation of chimaeric mice by introducing ES cells into blastocysts and allowing them to develop to term. Once chimaeric mice are produced, they are bred into a recipient mouse strain to establish germline transmission of the allele of interest. Although this approach has been used very successfully, the breeding cycles involved are time consuming. In addition, genes that are essential for organogenesis often have roles in the formation of extra-embryonic tissues that are essential for early stages of post-implantation development. For example, mice lacking the GATA transcription factors, GATA4 or GATA6, arrest during gastrulation due to an essential role for these factors in differentiation of extra-embryonic endoderm. This lethality has frustrated the study of these factors during the development of organs such as the liver and heart. Extraembryonic defects can, however, be circumvented by generating clonal mouse embryos directly from ES cells by tetraploid complementation. Here, we describe the usefulness and efficacy of this approach using GATA factors as an example.
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129
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Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, Skiena S, Futcher B, Leatherwood J. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol 2005; 3:e225. [PMID: 15966770 PMCID: PMC1157095 DOI: 10.1371/journal.pbio.0030225] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Accepted: 04/21/2005] [Indexed: 12/12/2022] Open
Abstract
Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 wave included many genes involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S. pombe. The G2/M wave included at least three distinctly regulated clusters of genes: one large cluster including mitosis, mitotic exit, and cell separation functions, one small cluster dedicated to DNA replication, and another small cluster dedicated to cytokinesis and division. S. pombe cell cycle genes have relatively long, complex promoters containing groups of multiple DNA sequence motifs, often of two, three, or more different kinds. Many of the genes, transcription factors, and regulatory mechanisms are conserved between S. pombe and S. cerevisiae. Finally, we found preliminary evidence for a nearly genome-wide oscillation in gene expression: 2,000 or more genes undergo slight oscillations in expression as a function of the cell cycle, although whether this is adaptive, or incidental to other events in the cell, such as chromatin condensation, we do not know. A comprehensive examination of gene expression throughout the cell cycle of fission yeast is compared with recent related studies to highlight robust transcriptional patterns.
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Affiliation(s)
- Anna Oliva
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Adam Rosebrock
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Francisco Ferrezuelo
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Saumyadipta Pyne
- 2 Department of Computer Science, Stony Brook University, Stony Brook, New York, United States of America
| | - Haiying Chen
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Steve Skiena
- 2 Department of Computer Science, Stony Brook University, Stony Brook, New York, United States of America
| | - Bruce Futcher
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Janet Leatherwood
- 1 Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
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130
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Lee CS, Friedman JR, Fulmer JT, Kaestner KH. The initiation of liver development is dependent on Foxa transcription factors. Nature 2005; 435:944-7. [PMID: 15959514 DOI: 10.1038/nature03649] [Citation(s) in RCA: 436] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 04/07/2005] [Indexed: 12/19/2022]
Abstract
The specification of the vertebrate liver is thought to occur in a two-step process, beginning with the establishment of competence within the foregut endoderm for responding to organ-specific signals, followed by the induction of liver-specific genes. On the basis of expression and in vitro studies, it has been proposed that the Foxa transcription factors establish competence by opening compacted chromatin structures within liver-specific target genes. Here we show that Foxa1 and Foxa2 (forkhead box proteins A1 and A2) are required in concert for hepatic specification in mouse. In embryos deficient for both genes in the foregut endoderm, no liver bud is evident and expression of the hepatoblast marker alpha-fetoprotein (Afp) is lost. Furthermore, Foxa1/Foxa2-deficient endoderm cultured in the presence of exogenous fibroblast growth factor 2 (FGF2) fails to initiate expression of the liver markers albumin and transthyretin. Thus, Foxa1 and Foxa2 are required for the establishment of competence within the foregut endoderm and the onset of hepatogenesis.
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Affiliation(s)
- Catherine S Lee
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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131
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Mijalski T, Harder A, Halder T, Kersten M, Horsch M, Strom TM, Liebscher HV, Lottspeich F, de Angelis MH, Beckers J. Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc Natl Acad Sci U S A 2005; 102:8621-6. [PMID: 15939889 PMCID: PMC1143582 DOI: 10.1073/pnas.0407672102] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A major advantage of the mouse model lies in the increasing information on its genome, transcriptome, and proteome, as well as in the availability of a fast growing number of targeted and induced mutant alleles. However, data from comparative transcriptome and proteome analyses in this model organism are very limited. We use DNA chip-based RNA expression profiling and 2D gel electrophoresis, combined with peptide mass fingerprinting of liver and kidney, to explore the feasibility of such comprehensive gene expression analyses. Although protein analyses mostly identify known metabolic enzymes and structural proteins, transcriptome analyses reveal the differential expression of functionally diverse and not yet described genes. The comparative analysis suggests correlation between transcriptional and translational expression for the majority of genes. Significant exceptions from this correlation confirm the complementarities of both approaches. Based on RNA expression data from the 200 most differentially expressed genes, we identify chromosomal colocalization of known, as well as not yet described, gene clusters. The determination of 29 such clusters may suggest that coexpression of colocalizing genes is probably rather common.
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Affiliation(s)
- T Mijalski
- Institute of Experimental Genetics, GSF-National Research Center GmbH, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
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132
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Abstract
In eukaryotes, chromatin is the natural form of DNA in the nucleus. For hundreds of millions of years, DNA-binding factors have evolved with chromatin. It is therefore more desirable to study the molecular mechanisms of DNA-directed processes with chromatin than with naked DNA templates. To this end, it is necessary to reconstitute DNA and histones into chromatin. Fortunately, there are a variety of methods by which a nonspecialist can prepare chromatin of high quality. Here, we describe strategies and techniques for the reconstitution of chromatin in vitro.
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Affiliation(s)
- Alexandra Lusser
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0347, USA
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133
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Affiliation(s)
- Roong Zhao
- Department of Cell Biology Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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134
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Nguyen TT, Cho K, Stratton SA, Barton MC. Transcription factor interactions and chromatin modifications associated with p53-mediated, developmental repression of the alpha-fetoprotein gene. Mol Cell Biol 2005; 25:2147-57. [PMID: 15743813 PMCID: PMC1061614 DOI: 10.1128/mcb.25.6.2147-2157.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We performed chromatin immunoprecipitation (ChIP) analyses of developmentally staged solid tissues isolated from wild-type and p53-null mice to determine specific histone N-terminal modifications, histone-modifying proteins, and transcription factor interactions at the developmental repressor region (-850) and core promoter of the hepatic tumor marker alpha-fetoprotein (AFP) gene. Both repression of AFP during liver development and silencing in the brain, where AFP is never expressed, are associated with dimethylation of histone H3 lysine 9 (DiMetH3K9) and the presence of heterochromatin protein 1 (HP1). These heterochromatic markers remain localized to AFP during developmental repression but spread to the upstream albumin gene during silencing. Developmentally regulated decreases in levels of acetylated H3 (AcH3K9) and H4 (AcH4) and of di- and trimethylated H3K4 (DiMetH3K4 and TriMetH3K4) occur at both the core promoter and distal repressor regions of AFP. Hepatic expression of AFP correlates with FoxA interaction at the repressor region and the binding of RNA polymerase II and TATA-binding protein to the core promoter. p53 acts as a developmental repressor of AFP in the liver by binding to chromatin, excluding FoxA interaction and targeting mSin3A/HDAC1 to the distal repressor region. p53-null mice exhibit developmentally delayed AFP repression, concomitant with acetylation of H3K9, methylation of H3K4, and loss of DiMetH3K9, mSin3A/HDAC1, and HP1 interactions.
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Affiliation(s)
- Thi T Nguyen
- Department of Biochemistry and Molecular Biology, Program in Genes and Development, Graduate School of Biological Sciences, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
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135
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Zhao R, Watt AJ, Li J, Luebke-Wheeler J, Morrisey EE, Duncan SA. GATA6 is essential for embryonic development of the liver but dispensable for early heart formation. Mol Cell Biol 2005; 25:2622-31. [PMID: 15767668 PMCID: PMC1061656 DOI: 10.1128/mcb.25.7.2622-2631.2005] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several lines of evidence suggest that GATA6 has an integral role in controlling development of the mammalian liver. Unfortunately, this proposal has been impossible to address directly because mouse embryos lacking GATA6 die during gastrulation. Here we show that the early embryonic deficiency associated with GATA6-knockout mice can be overcome by providing GATA6-null embryos with a wild-type extraembryonic endoderm with the use of tetraploid embryo complementation. Analysis of rescued Gata6-/- embryos revealed that, although hepatic specification occurs normally, the specified cells fail to differentiate and the liver bud does not expand. Although GATA6 is expressed in multiple tissues that impact development of the liver, including the heart, septum transversum mesenchyme, and vasculature, all are relatively unaffected by loss of GATA6, which is consistent with a cell-autonomous requirement for GATA6 during hepatogenesis. We also demonstrate that a closely related GATA factor, GATA4, is expressed transiently in the prehepatic endoderm during hepatic specification and then lost during expansion of the hepatic primordium. Our data support the proposal that GATA4 and GATA6 are functionally redundant during hepatic specification but that GATA6 alone is available for liver bud growth and commitment of the endoderm to a hepatic cell fate.
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Affiliation(s)
- Roong Zhao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, USA
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136
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Brekke KM, Garrard WT. Assembly and analysis of the mouse immunoglobulin kappa gene sequence. Immunogenetics 2004; 56:490-505. [PMID: 15378297 DOI: 10.1007/s00251-004-0659-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 02/12/2004] [Indexed: 11/30/2022]
Abstract
The mechanisms regulating V gene usage leading to the immunoglobulin (Ig) repertoire have been of interest for many years but are only partially defined. To gain insight into these processes, we have assembled the nucleotide sequence of the Mus musculus Igkappa locus using data recently made available from genome-wide sequencing efforts. We found the locus to be 3.21 Mb in length and mapped all known functional, pseudo- and relic V gene segments onto the sequence, along with known regulatory elements. We corrected errors in former gene assignments, positions and orientations and identified a novel Vkappa4 gene segment. This assembly allowed the establishment of a unified nomenclature for the V genes based on their relative positions similar to the nomenclature system adopted for the human Ig loci. The 5' boundary of the locus is defined by the presence of the tumor-associated calcium-signal transducer-2 gene located 19 kb upstream of Vkappa24-140, the most distal V gene. No non- Vkappa genes were found in the sequence of the locus. Detailed analysis of the sequences 0.5 kb upstream, within, and 0.5 kb downstream of each potentially functional V gene revealed interesting patterns of statistically significant clustering of transcription factor consensus binding sites, generally specific to a particular family. We found E boxes were clustered not only in promoter regions, but also nearby recombination signal sequences. Family members of Vkappa4/5 genes exhibit a conserved pattern of octamer sites in their downstream regions, as well as Ebf sites in their introns, and Lef-1 sites in their upstream regions. We discuss potential functional implications of these findings in the context of possible combinatorial mechanisms for targeting V genes for rearrangement. The assembled sequence and its analyses are available as a resource to the scientific community.
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Affiliation(s)
- Katherine M Brekke
- Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA
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137
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Affiliation(s)
- Lisa Cirillo
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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138
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Taganov KD, Cuesta I, Daniel R, Cirillo LA, Katz RA, Zaret KS, Skalka AM. Integrase-specific enhancement and suppression of retroviral DNA integration by compacted chromatin structure in vitro. J Virol 2004; 78:5848-55. [PMID: 15140982 PMCID: PMC415796 DOI: 10.1128/jvi.78.11.5848-5855.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Accepted: 01/23/2004] [Indexed: 01/26/2023] Open
Abstract
Integration of viral DNA into the host chromosome is an obligatory step in retroviral replication and is dependent on the activity of the viral enzyme integrase. To examine the influence of chromatin structure on retroviral DNA integration in vitro, we used a model target comprising a 13-nucleosome extended array that includes binding sites for specific transcription factors and can be compacted into a higher-ordered structure. We found that the efficiency of in vitro integration catalyzed by human immunodeficiency virus type 1 (HIV-1) integrase was decreased after compaction of this target with histone H1. In contrast, integration by avian sarcoma virus (ASV) integrase was more efficient after compaction by either histone H1 or a high salt concentration, suggesting that the compacted structure enhances this reaction. Furthermore, although site-specific binding of transcription factors HNF3 and GATA4 blocked ASV DNA integration in extended nucleosome arrays, local opening of H1-compacted chromatin by HNF3 had no detectable effect on integration, underscoring the preference of ASV for compacted chromatin. Our results indicate that chromatin structure affects integration site selection of the HIV-1 and ASV integrases in opposite ways. These distinct properties of integrases may also affect target site selection in vivo, resulting in an important bias against or in favor of integration into actively transcribed host DNA.
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Affiliation(s)
- Konstantin D Taganov
- Fox Chase Cancer Center, Institute for Cancer Research, 333 Cottman Ave., Philadelphia, PA 19111-2497, USA
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139
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Lu J, Pazin MJ, Ravid K. Properties of ets-1 binding to chromatin and its effect on platelet factor 4 gene expression. Mol Cell Biol 2004; 24:428-41. [PMID: 14673175 PMCID: PMC303331 DOI: 10.1128/mcb.24.1.428-441.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ets-1 is important for transcriptional regulation in several hematopoietic lineages, including megakaryocytes. Some transcription factors bind to naked DNA and chromatin with different affinities, while others do not. In the present study we used the megakaryocyte-specific promoters platelet factor 4 (PF4), and glycoprotein IIb (GPIIb) as model systems to explore the properties of Ets-1 binding to chromatin. Chromatin immunoprecipitation assays indicated that Ets-1 binds to proximal regions in the PF4 and GPIIb promoters in vivo. In vitro and in vivo experiments showed that Ets-1 binding to chromatin on lineage-specific promoters does not require lineage-specific factors. Moreover, this binding shows the same order of affinity as the binding to naked DNA and does not require ATP-dependent or Sarkosyl-sensitive factors. The effect of Ets-1 binding on promoter activity was examined using the PF4 promoter as a model. We identified a novel Ets-1 site (at -50), and a novel Sarkosyl-sensitive DNase I-hypersensitive site generated by Ets-1 binding to chromatin, which significantly affect PF4 promoter activity. Taken together, our results suggest a model by which Ets-1 binds to chromatin without the need for lineage-specific accessory factors, and Ets-1 binding induces changes in chromatin and affects transactivation, which are essential for PF4 promoter activation.
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Affiliation(s)
- Jun Lu
- Department of Biochemistry, Cancer Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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140
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Costa RH, Kalinichenko VV, Holterman AXL, Wang X. Transcription factors in liver development, differentiation, and regeneration. Hepatology 2003; 38:1331-47. [PMID: 14647040 DOI: 10.1016/j.hep.2003.09.034] [Citation(s) in RCA: 286] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Robert H Costa
- Department of Biochemistry and Molecular Genetics University of Illinois at Chicago, College of Medicine, Chicago, IL 60607-7170, USA.
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141
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Jeong Y, Epstein DJ. Distinct regulators of Shh transcription in the floor plate and notochord indicate separate origins for these tissues in the mouse node. Development 2003; 130:3891-902. [PMID: 12835403 DOI: 10.1242/dev.00590] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The establishment of the floor plate at the ventral midline of the CNS is dependent on an inductive signaling process mediated by the secreted protein Sonic hedgehog (Shh). To understand molecularly how floor plate induction proceeds we identified a Shh-responsive regulatory element that directs transgene reporter expression to the ventral midline of the CNS and notochord in a Shh-like manner and characterized critical cis-acting sequences regulating this element. Cross-species comparisons narrowed the activity of the Shh floor plate enhancer to an 88-bp sequence within intron 2 of Shh that included highly conserved binding sites matching the consensus for homeodomain, Tbx and Foxa transcription factors. Mutational analysis revealed that the homeodomain and Foxa binding sites are each required for activation of the Shh floor plate enhancer, whereas the Tbx site was required for repression in regions of the CNS where Shh is not normally expressed. We further show that Shh enhancer activity was detected in the mouse node from where the floor plate and notochord precursors derive. Shh reporter expression was restricted to the ventral (mesodermal) layer of the node in a pattern similar to endogenous Shh. X-gal-positive cells emerging from the node were only detected in the notochord lineage, suggesting that the floor plate and notochord arise from distinct precursors in the mouse node.
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Affiliation(s)
- Yongsu Jeong
- Department of Genetics, University of Pennsylvania School of Medicine, Clinical Research Building, Room 470, 415 Curie Blvd, Philadelphia, PA 19104, USA
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142
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Morse RH. Getting into chromatin: how do transcription factors get past the histones? Biochem Cell Biol 2003; 81:101-12. [PMID: 12897843 DOI: 10.1139/o03-039] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptional activators and the general transcription machinery must gain access to DNA that in eukaryotes may be packaged into nucleosomes. In this review, I discuss this problem from the standpoint of the types of chromatin structures that these DNA-binding proteins may encounter, and the mechanisms by which they may contend with various chromatin structures. The discussion includes consideration of experiments in which chromatin structure is manipulated in vivo to confront activators with nucleosomal binding sites, and the roles of nucleosome dynamics and activation domains in facilitating access to such sites. Finally, the role of activators in facilitating access of the general transcriptional machinery to sites in chromatin is discussed.
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Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany School of Public Health, 12201-2002, USA.
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143
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Abstract
The eukaryotic genome is organized into different domains by cis-acting elements, such as boundaries/insulators and matrix attachment regions, and is packaged with different degrees of condensation. In the M phase, the chromatin becomes further highly condensed into chromosomes. The first step for transcriptional activation of a given gene, at a particular time during development, in any locus, is the opening of its chromatin domain. This locus needs to be kept in this state in each early G(1) phase during every cell cycle. Certain distal enhance elements, including locus control regions (LCRs) and enhancers, are believed to perform this target chromatin domain opening process and several models have been proposed to explain distal enhance action. But they did not explain precisely how a given chromatin domain is opened. Based on various studies, we propose a hypothesis for the mechanism of opening chromatin on a large scale. One important mechanism may involved breaking one or two DNA strands and reducing the linking numbers within chromatin domain. The topological changes can overpass some complexes formed on DNA strands and can be transmitted from specific localized points over a broad region, until boundary elements or insulators are reached. These may initiate downstream events such as propagation of histone acetylation and the binding of transcription factors to proximal promoters and may further augment the action mediated by distal enhancer elements.
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Affiliation(s)
- Li Xin
- National Laboratory of Medical Molecular Biology, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P.R. China
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144
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Marsden MD, Fournier REK. Chromosomal elements regulate gene activity and chromatin structure of the human serpin gene cluster at 14q32.1. Mol Cell Biol 2003; 23:3516-26. [PMID: 12724410 PMCID: PMC164764 DOI: 10.1128/mcb.23.10.3516-3526.2003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human serine protease inhibitor (serpin) gene cluster at 14q32.1 contains a number of genes that are specifically expressed in hepatic cells. Cell-specific enhancers have been identified in several of these genes, but elements involved in locus-wide gene and chromatin control have yet to be defined. To identify regulatory elements in this region, we prepared a series of mutant chromosomal alleles by homologous recombination and transferred the specifically modified human chromosomes to hepatic cells for functional tests. We report that deletion of an 8-kb DNA segment upstream of the human alpha1-antitrypsin gene yields a mutant serpin allele that fails to be activated in hepatic cells. Within this region, a 2.3-kb DNA segment between kb -8.1 and -5.8 contains a previously unrecognized control region that is required not only for serpin gene activation but also for chromatin remodeling of the entire locus.
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Affiliation(s)
- Mark D Marsden
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
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145
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Katsani KR, Mahmoudi T, Verrijzer CP. Selective gene regulation by SWI/SNF-related chromatin remodeling factors. Curr Top Microbiol Immunol 2003; 274:113-41. [PMID: 12596906 DOI: 10.1007/978-3-642-55747-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chromatin is a highly dynamic structure that plays a key role in the orchestration of gene expression patterns during cellular differentiation and development. The packaging of DNA into chromatin generates a barrier to the transcription machinery. The two main strategies by which cells alleviate chromatin-mediated repression are through the action of ATP-dependent chromatin remodeling complexes and enzymes that covalently modify the histones. Various signaling pathways impinge upon the targeting and activity of these enzymes, thereby controlling gene expression in response to physiological and developmental cues. Chromatin structure also underlies many so-called epigenetic phenomena, leading to the mitotically stable propagation of differential expression of genetic information. Here, we will focus on the role of SWI/SNF-related ATP-dependent chromatin remodeling complexes in developmental gene regulation. First, we compare different models for how remodelers can act in a gene-selective manner, and either cooperate or antagonize other chromatin-modulating systems in the cell. Next, we discuss their functioning during the control of developmental gene expression programs.
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Affiliation(s)
- K R Katsani
- Department of Molecular and Cell Biology, Center for Biomedical Genetics, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden, The Netherlands
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146
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Deng Z, Chen CJ, Chamberlin M, Lu F, Blobel GA, Speicher D, Cirillo LA, Zaret KS, Lieberman PM. The CBP bromodomain and nucleosome targeting are required for Zta-directed nucleosome acetylation and transcription activation. Mol Cell Biol 2003; 23:2633-44. [PMID: 12665567 PMCID: PMC152567 DOI: 10.1128/mcb.23.8.2633-2644.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2002] [Accepted: 01/13/2003] [Indexed: 11/20/2022] Open
Abstract
The Epstein-Barr virus (EBV)-encoded lytic activator Zta is a bZIP protein that can stimulate nucleosomal histone acetyltransferase (HAT) activity of the CREB binding protein (CBP) in vitro. We now show that deletion of the CBP bromo- and C/H3 domains eliminates stimulation of nucleosomal HAT activity in vitro and transcriptional coactivation by Zta in transfected cells. In contrast, acetylation of free histones was not affected by the addition of Zta or by deletions in the bromo or C/H3 domain of CBP. Zta stimulated acetylation of oligonucleosomes assembled on supercoiled DNA and dinucleosomes assembled on linear DNA, but Zta-stimulated acetylation was significantly reduced for mononucleosomes. Western blotting and amino-terminal protein sequencing indicated that all lysine residues in the H3 and H4 amino-terminal tails were acetylated by CBP and enhanced by the addition of Zta. Histone acetylation was also dependent upon the Zta basic DNA binding domain, which could not be substituted with the homologous basic region of c-Fos, indicating specificity in the bZIP domain nucleosome binding function. Finally, we show that Zta and CBP colocalize to viral immediate-early promoters in vivo and that overexpression of Zta leads to a robust increase in H3 and H4 acetylation at various regions of the EBV genome in vivo. Furthermore, deletion of the CBP bromodomain reduced stable CBP-Zta complex formation and histone acetylation at Zta-responsive viral promoters in vivo. These results suggest that activator- and bromodomain-dependent targeting to oligonucleosomal chromatin is required for stable promoter-bound complex formation and transcription activity.
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Affiliation(s)
- Zhong Deng
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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147
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Cirillo LA, Zaret KS. Preparation of Defined Mononucleosomes, Dinucleosomes, and Nucleosome Arrays In Vitro and Analysis of Transcription Factor Binding. Methods Enzymol 2003; 375:131-58. [PMID: 14870664 DOI: 10.1016/s0076-6879(03)75009-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Lisa Ann Cirillo
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Washington, Milwaukee, Wisconsin 53149, USA
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148
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Urnov FD. A feel for the template: zinc finger protein transcription factors and chromatin. Biochem Cell Biol 2003; 80:321-33. [PMID: 12123285 DOI: 10.1139/o02-084] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transcription factors and chromatin collaborate in bringing the eukaryotic genome to life. An important, and poorly understood, aspect of this collaboration involves targeting the regulators to correct binding sites in vivo. An implicit and insufficiently tested assumption in the field has been that chromatin simply obstructs most sites and leaves only a few functionally relevant ones accessible. The major class of transcription factors in all metazoa, zinc finger proteins (ZFPs), can bind to chromatin in vitro (as clearly shown for Spl, GATA-1 and -4, and the nuclear hormone receptors, for example). Data on the accessibility of DNA within heterochromatin to nonhistone regulators (E.A. Sekinger and D.S. Gross. 2001. Mol. Cell 105: 403-414; C. Jolly et al. 2002. J. Cell. Biol. 156: 775-781) and the ability of the basal transcription machinery to reside within highly condensed chromatin (most recently, R. Christova and T. Oelgeschlaeger. 2002. Nat. Cell Biol. 4: 79-82) further weaken the argument that chromatin acts as an across-the-board deterrent to ZFP binding. These proteins, however, do not bind promiscuously in vivo, and recent data on human cells (C.E. Horak et al. 2002. Proc. Natl. Acad. Sci. U.S.A. 99: 2924-2929) confirm earlier data on budding yeast (B. Ren et al. 2000. Science (Washington, D.C.), 290: 2306-2309) that primary DNA sequence, i.e., density of binding sites per unit DNA length, is not the primary determinant of where a ZFP transcription factor will bind in vivo. This article reviews these data and uses ZFP transcription factors as a model system to compare in vitro binding to chromatin by transcription factors with their in vivo behavior in gene regulation. DNA binding domain structure, nonrandom nucleoprotein organization of chromatin at target promoters, and cooperativity of regulator action may all contribute to target site selection in vivo.
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Affiliation(s)
- Fyodor D Urnov
- Sangamo Biosciences, Pt Richmond Tech Centre, Richmond, CA 94804, USA.
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149
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Abstract
Over the last decade significant advances have been made in our understanding of the molecular mechanisms that control early aspects of mammalian liver development. Studies using tissue explant cultures and molecular biology techniques as well as the analysis of transgenic and knockout mice have identified signaling molecules and transcription factors that are necessary for the onset of hepatogenesis. This review presents an overview of these studies and discusses the role of individual factors during hepatic development.
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Affiliation(s)
- Stephen A Duncan
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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150
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Hatzis P, Talianidis I. Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol Cell 2002; 10:1467-77. [PMID: 12504020 DOI: 10.1016/s1097-2765(02)00786-4] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We analyzed the order of recruitment of factors to the HNF-4alpha regulatory regions upon the initial activation of the gene during enterocyte differentiation. An initially independent assembly of regulatory complexes at the proximal promoter and the upstream enhancer regions was followed by the tracking of the entire DNA-protein complex formed on the enhancer along the intervening DNA until it encountered the proximal promoter. This movement correlated with a unidirectional spreading of histone hyperacetylation. Transcription initiation coincided with the formation of a stable enhancer-promoter complex and remodeling of the nucleosome situated at the transcription start site. The results provide experimental evidence for the involvement of a dynamic process culminating in enhancer-promoter communication during long-distance gene activation.
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Affiliation(s)
- Pantelis Hatzis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 1527 Vassilika Vouton, 711 10 Herakleion, Crete, Greece
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