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Bag I, Chen Y, D'Orazio K, Lopez P, Wenzel S, Takagi Y, Lei EP. Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function. G3 (BETHESDA, MD.) 2022; 12:jkac152. [PMID: 35708663 PMCID: PMC9434307 DOI: 10.1093/g3journal/jkac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here, we utilized RNA-affinity pulldown coupled with mass spectrometry to identify a novel RNA-binding protein, Isha (CG4266), that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif and RNA Polymerase II C-terminal domain-interacting domain (CID). We found that Isha physically interacts with total and elongating Polymerase II and associates with chromatin at the 5' end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with the core gypsy insulator component CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor Isha that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.
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Affiliation(s)
- Indira Bag
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karole D'Orazio
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prisma Lopez
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elissa P Lei
- Corresponding author: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Casale AM, Cappucci U, Piacentini L. Unravelling HP1 functions: post-transcriptional regulation of stem cell fate. Chromosoma 2021; 130:103-111. [PMID: 34128099 PMCID: PMC8426308 DOI: 10.1007/s00412-021-00760-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Heterochromatin protein 1 (HP1) is a non-histone chromosomal protein first identified in Drosophila as a major component of constitutive heterochromatin, required for stable epigenetic gene silencing in many species including humans. Over the years, several studies have highlighted additional roles of HP1 in different cellular processes including telomere maintenance, DNA replication and repair, chromosome segregation and, surprisingly, positive regulation of gene expression. In this review, we briefly summarize past research and recent results supporting the unexpected and emerging role of HP1 in activating gene expression. In particular, we discuss the role of HP1 in post-transcriptional regulation of mRNA processing because it has proved decisive in the control of germline stem cells homeostasis in Drosophila and has certainly added a new dimension to our understanding on HP1 targeting and functions in epigenetic regulation of stem cell behaviour.
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Affiliation(s)
- Assunta Maria Casale
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
| | - Ugo Cappucci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Lucia Piacentini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
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3
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Bag I, Dale RK, Palmer C, Lei EP. The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila. J Cell Sci 2019; 132:jcs.226092. [PMID: 30718365 DOI: 10.1242/jcs.226092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/28/2019] [Indexed: 01/31/2023] Open
Abstract
Chromatin insulators are DNA-protein complexes that establish independent higher-order DNA domains to influence transcription. Insulators are functionally defined by two properties: they can block communication between an enhancer and a promoter, and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy insulator complex contains three core components; Su(Hw), CP190 and Mod(mdg4)67.2. Here, we identify a novel role for Chromatin-linked adaptor for MSL proteins (CLAMP) in promoting gypsy chromatin insulator function. When clamp is knocked down, gypsy-dependent enhancer-blocking and barrier activities are strongly reduced. CLAMP associates physically with the core gypsy insulator complex, and ChIP-seq analysis reveals extensive overlap, particularly with promoter-bound CP190 on chromatin. Depletion of CLAMP disrupts CP190 binding at a minority of shared sites, whereas depletion of CP190 results in extensive loss of CLAMP chromatin association. Finally, reduction of CLAMP disrupts CP190 localization within the nucleus. Our results support a positive functional relationship between CLAMP and CP190 to promote gypsy chromatin insulator activity.
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Affiliation(s)
- Indira Bag
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cameron Palmer
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA .,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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4
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King MR, Matzat LH, Dale RK, Lim SJ, Lei EP. The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. J Cell Sci 2014; 127:2956-66. [PMID: 24706949 DOI: 10.1242/jcs.151126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Chromatin insulators are DNA-protein complexes that are situated throughout the genome that are proposed to contribute to higher-order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here, we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, decreasing Rump levels leads to improvement of barrier activity only in tissues outside of the central nervous system (CNS). Furthermore, rump mutants restore insulator body localization in an insulator mutant background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and chromatin immunoprecipitation and sequencing analysis of Rump demonstrates extensive colocalization with a subset of insulator sites across the genome. The genome-wide binding profile and tissue specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity primarily in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity.
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Affiliation(s)
- Matthew R King
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Leah H Matzat
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Su Jun Lim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elissa P Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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5
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Matzat LH, Dale RK, Moshkovich N, Lei EP. Tissue-specific regulation of chromatin insulator function. PLoS Genet 2012; 8:e1003069. [PMID: 23209434 PMCID: PMC3510032 DOI: 10.1371/journal.pgen.1003069] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/20/2012] [Indexed: 11/18/2022] Open
Abstract
Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type–specific chromatin organization. However, factors regulating tissue-specific insulator function have not yet been discovered. Here we identify the RNA recognition motif-containing protein Shep as a direct interactor of two individual components of the gypsy insulator complex in Drosophila. Mutation of shep improves gypsy-dependent enhancer blocking, indicating a role as a negative regulator of insulator activity. Unlike ubiquitously expressed core gypsy insulator proteins, Shep is highly expressed in the central nervous system (CNS) with lower expression in other tissues. We developed a novel, quantitative tissue-specific barrier assay to demonstrate that Shep functions as a negative regulator of insulator activity in the CNS but not in muscle tissue. Additionally, mutation of shep alters insulator complex nuclear localization in the CNS but has no effect in other tissues. Consistent with negative regulatory activity, ChIP–seq analysis of Shep in a CNS-derived cell line indicates substantial genome-wide colocalization with a single gypsy insulator component but limited overlap with intact insulator complexes. Taken together, these data reveal a novel, tissue-specific mode of regulation of a chromatin insulator. Mounting evidence in human, mouse, and Drosophila demonstrates a role for the DNA–protein complexes known as chromatin insulators in orchestrating three-dimensional genome organization. Several genes that are only expressed in specific cell types display distinct chromatin configurations correlated with expression status. Recent evidence shows that chromatin insulators play a role in defining tissue-specific chromatin conformation; however, tissue-specific factors that may modulate insulator activity remain unknown. Here we identify a putative RNA–binding protein, Shep, which is expressed most highly in the CNS and interacts directly with insulator complexes. We developed a novel quantitative, tissue-specific insulator assay and found that Shep negatively regulates insulator activity in the CNS. We also find that mutation of shep alters insulator complex nuclear localization in the brain but not other tissues. Finally, we mapped Shep and gypsy insulator protein localization throughout the genome and found that Shep colocalizes with one individual insulator protein but less often than expected with an intact insulator complex. These data suggest that Shep negatively influences insulator activity in a tissue-specific manner.
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Affiliation(s)
- Leah H. Matzat
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ryan K. Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nellie Moshkovich
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Graduate Program in Molecular and Cell Biology, University of Maryland, College Park, Maryland, United States of America
| | - Elissa P. Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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6
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Abstract
A major role of the RNAi pathway in Schizosaccharomyces pombe is to nucleate heterochromatin, but it remains unclear whether this mechanism is conserved. To address this question in Drosophila, we performed genome-wide localization of Argonaute2 (AGO2) by chromatin immunoprecipitation (ChIP)-seq in two different embryonic cell lines and found that AGO2 localizes to euchromatin but not heterochromatin. This localization pattern is further supported by immunofluorescence staining of polytene chromosomes and cell lines, and these studies also indicate that a substantial fraction of AGO2 resides in the nucleus. Intriguingly, AGO2 colocalizes extensively with CTCF/CP190 chromatin insulators but not with genomic regions corresponding to endogenous siRNA production. Moreover, AGO2, but not its catalytic activity or Dicer-2, is required for CTCF/CP190-dependent Fab-8 insulator function. AGO2 interacts physically with CTCF and CP190, and depletion of either CTCF or CP190 results in genome-wide loss of AGO2 chromatin association. Finally, mutation of CTCF, CP190, or AGO2 leads to reduction of chromosomal looping interactions, thereby altering gene expression. We propose that RNAi-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome.
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7
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Onorati MC, Lazzaro S, Mallik M, Ingrassia AMR, Carreca AP, Singh AK, Chaturvedi DP, Lakhotia SC, Corona DFV. The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments. PLoS Genet 2011; 7:e1002096. [PMID: 21637796 PMCID: PMC3102753 DOI: 10.1371/journal.pgen.1002096] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/06/2011] [Indexed: 12/23/2022] Open
Abstract
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their associated ncRNAs, are emerging as important components of gene regulatory networks, although their functional connections have remained poorly defined. Here we provide multiple lines of evidence showing that the hsrω ncRNA interacts in vivo and in vitro with ISWI, regulating its ATPase activity. Remarkably, we found that the organization of nucleoplasmic omega speckles depends on ISWI function. Our findings highlight a novel role for chromatin remodelers in organization of nucleoplasmic compartments, providing the first example of interaction between an ATP-dependent chromatin remodeler and a large ncRNA. Chromatin structure and function are regulated by the concerted activity of covalent modifiers of chromatin, nucleosome remodeling factors, and several emerging classes of non-coding RNAs. ISWI is an evolutionarily conserved ATP-dependent chromatin remodeler playing essential roles in chromosome condensation, gene expression, and DNA replication. ISWI activity has been involved in a variety of nuclear functions including telomere silencing, stem cell renewal, neural morphogenesis, and epigenetic reprogramming. Using an in vivo assay to identify factors regulating ISWI activity in the model system Drosophila melanogaster, we recovered a genetic interaction between ISWI and hsrω. The hsrω gene encodes multiple non-coding RNAs (ncRNAs), of which the >10 kb nuclear hsrω-n RNA, with functional homolog in mammals, is essential for the assembly and organization of hnRNP-containing nucleoplasmic omega speckles. These special nuclear compartments play essential roles in the storage/sequestration of hnRNP family and other proteins, thus playing important roles in mRNA maturation and other regulatory processes. Here we show that the hsrω-n ncRNA interacts in vivo and in vitro with ISWI to directly regulate its ATPase activity. We also provide in vivo data showing that omega speckle nuclear organization depends on ISWI function, highlighting a novel role for chromatin remodelers in nuclear speckles organization.
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Affiliation(s)
- Maria C. Onorati
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Sandra Lazzaro
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Moushami Mallik
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Antonia M. R. Ingrassia
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anna P. Carreca
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anand K. Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Deo Prakash Chaturvedi
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Subhash C. Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Davide F. V. Corona
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
- * E-mail:
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8
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Piacentini L, Pimpinelli S. Positive regulation of euchromatic gene expression by HP1. Fly (Austin) 2010; 4:299-301. [PMID: 20855965 DOI: 10.4161/fly.4.4.13261] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
HP1 is a conserved prototype protein that plays an essential role in heterochromatin formation and epigenetic gene silencing through its interaction with histone methyltransferase enzymes (HMTases) and the histone H3 at lysine 9 (H3-MeK9). HP1 is also involved in telomere capping and, more surprisingly, in positive regulation of gene expression. Recently, a wide expression analysis, using a RIP-chip assays (RNA-immunoprecipitation on microarrays), has shown that HP1 associates with the transcripts of more than one hundred euchromatic genes and interacts with the heterogeneous nuclear ribonucleoproteins (hnRNPs) that are known to be involved in RNA processing. By these results, HP1 seems to be part of a complex that stabilizes RNA transcripts. Though previously unsuspected, it was also found that HP1-interacting hnRNPs have a functional role in heterochromatin formation. These proteins bind heterochromatin and are dominant suppressors of position effect variegation. Taken together, the results in the paper by Piacentini et al. open a window on a possible new conceptual landscape in which similar epigenetic mechanisms could have a significant role, both in the metabolism of RNA transcripts and in heterochromatin formation, producing opposite functional effects. These data seem to establish a functional link between euchromatin and heterochromatin.
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Affiliation(s)
- Lucia Piacentini
- Istituto Pasteur, Fondazione Cenci Bolognetti and Dipartimento di Genetica e Biologia molecolare, Università La Sapienza, Roma, Italy
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9
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Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila. PLoS Genet 2009; 5:e1000670. [PMID: 19798443 PMCID: PMC2743825 DOI: 10.1371/journal.pgen.1000670] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 09/02/2009] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin Protein 1 (HP1a) is a well-known conserved protein involved in heterochromatin formation and gene silencing in different species including humans. A general model has been proposed for heterochromatin formation and epigenetic gene silencing in different species that implies an essential role for HP1a. According to the model, histone methyltransferase enzymes (HMTases) methylate the histone H3 at lysine 9 (H3K9me), creating selective binding sites for itself and the chromodomain of HP1a. This complex is thought to form a higher order chromatin state that represses gene activity. It has also been found that HP1a plays a role in telomere capping. Surprisingly, recent studies have shown that HP1a is present at many euchromatic sites along polytene chromosomes of Drosophila melanogaster, including the developmental and heat-shock-induced puffs, and that this protein can be removed from these sites by in vivo RNase treatment, thus suggesting an association of HP1a with the transcripts of many active genes. To test this suggestion, we performed an extensive screening by RIP-chip assay (RNA–immunoprecipitation on microarrays), and we found that HP1a is associated with transcripts of more than one hundred euchromatic genes. An expression analysis in HP1a mutants shows that HP1a is required for positive regulation of these genes. Cytogenetic and molecular assays show that HP1a also interacts with the well known proteins DDP1, HRB87F, and PEP, which belong to different classes of heterogeneous nuclear ribonucleoproteins (hnRNPs) involved in RNA processing. Surprisingly, we found that all these hnRNP proteins also bind heterochromatin and are dominant suppressors of position effect variegation. Together, our data show novel and unexpected functions for HP1a and hnRNPs proteins. All these proteins are in fact involved both in RNA transcript processing and in heterochromatin formation. This suggests that, in general, similar epigenetic mechanisms have a significant role on both RNA and heterochromatin metabolisms. Heterochromatin Protein 1 (HP1a) is a very well known prototype protein of a general model for heterochromatin formation and epigenetic gene silencing in different species including humans. Here, we report our experiments showing that HP1a is also required for the positive regulation of more than one hundred euchromatic genes by its association with the corresponding RNA transcripts and by its interaction with heterogeneous nuclear ribonucleoproteins (hnRNPs) belonging to different classes. Importantly, we also found that all the tested hnRNP proteins bind to the heterochromatin and are dominant suppressors of position effect variegation, thus suggesting they also have a role in heterochromatin organization. Taken together, our data show novel and important functions, not only for HP1a, but also for hnRNPs, which were previously believed to participate only in RNA processing. These results shed new light on the epigenetic mechanisms of gene silencing and gene expression. They also establish a link between RNA transcript metabolism and heterochromatin formation and change several aspects of the canonical views about these apparently different processes.
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10
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Li A, Denlinger DL. Rapid cold hardening elicits changes in brain protein profiles of the flesh fly, Sarcophaga crassipalpis. INSECT MOLECULAR BIOLOGY 2008; 17:565-572. [PMID: 18828842 DOI: 10.1111/j.1365-2583.2008.00827.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rapid cold hardening (RCH) refers to the enhanced cold tolerance acquired by a brief exposure to a moderately low temperature. Although ecological aspects of this response have been well documented in insects, less is known about the physiological and biochemical mechanisms elicited by RCH. In this study we used two-dimensional electrophoresis to detect differences in brain protein abundance in pharate adults of the flesh fly Sarcophaga crassipalpis, in response to a 2 h RCH exposure at 0 degrees C. Fourteen high abundance proteins that responded to RCH were selected for mass spectrometric identification. Three proteins that increased in abundance during RCH included ATP synthase subunit alpha, a small heat shock protein (smHsp), and tropomyosin-1 isoforms 33/34. Eleven proteins that decreased in abundance or were missing following RCH included several proteins involved in energy metabolism, protein degradation, transcription, actin binding, and cytoskeleton organization. That several proteins increased in abundance during RCH underscores the dynamics of the RCH mechanism and suggests that more than one physiological response likely contribute to RCH. The increase in ATP synthase suggests an elevation of ATP during RCH, and the smHsp increase suggests that at least one of the Hsps is actually mobilized during RCH, rather than after RCH as previously assumed.
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Affiliation(s)
- A Li
- Department of Entomology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
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11
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Lei EP, Corces VG. RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 2006; 38:936-41. [PMID: 16862159 DOI: 10.1038/ng1850] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 06/20/2006] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is a conserved silencing mechanism that can act through alteration of chromatin structure. Chromatin insulators promote higher-order nuclear organization, thereby establishing DNA domains subject to distinct transcriptional controls. We present evidence for a functional relationship between RNAi and the gypsy insulator of D. melanogaster. Insulator activity is decreased when Argonaute genes required for RNAi are mutated, and insulator function is improved when the levels of the Rm62 helicase, involved in double-stranded RNA (dsRNA)-mediated silencing and heterochromatin formation, are reduced. Rm62 interacts physically with the DNA-binding insulator protein CP190 in an RNA-dependent manner. Finally, reduction of Rm62 levels results in marked nuclear reorganization of a compromised insulator. These results suggest that the RNAi machinery acts as a modulator of nuclear architecture capable of effecting global changes in gene expression.
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Affiliation(s)
- Elissa P Lei
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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12
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Kiesler E, Hase ME, Brodin D, Visa N. Hrp59, an hnRNP M protein in Chironomus and Drosophila, binds to exonic splicing enhancers and is required for expression of a subset of mRNAs. ACTA ACUST UNITED AC 2005; 168:1013-25. [PMID: 15781475 PMCID: PMC2171850 DOI: 10.1083/jcb.200407173] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we study an insect hnRNP M protein, referred to as Hrp59. Hrp59 is relatively abundant, has a modular domain organization containing three RNA-binding domains, is dynamically recruited to transcribed genes, and binds to premRNA cotranscriptionally. Using the Balbiani ring system of Chironomus, we show that Hrp59 accompanies the mRNA from the gene to the nuclear envelope, and is released from the mRNA at the nuclear pore. The association of Hrp59 with transcribed genes is not proportional to the amount of synthesized RNA, and in vivo Hrp59 binds preferentially to a subset of mRNAs, including its own mRNA. By coimmunoprecipitation of Hrp59–RNA complexes and microarray hybridization against Drosophila whole-genome arrays, we identify the preferred mRNA targets of Hrp59 in vivo and show that Hrp59 is required for the expression of these target mRNAs. We also show that Hrp59 binds preferentially to exonic splicing enhancers and our results provide new insights into the role of hnRNP M in splicing regulation.
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Affiliation(s)
- Eva Kiesler
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
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13
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Ortega A. Localization of the Drosophila protein FL(2)D in somatic cells and female gonads. Cell Tissue Res 2005; 320:361-7. [PMID: 15778853 DOI: 10.1007/s00441-004-1049-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 11/10/2004] [Indexed: 10/25/2022]
Abstract
The Drosophila gene female-lethal(2)d [fl(2)d] has been implicated in the alternative splicing regulation of genes involved in sexual determination, such as Sex-lethal and transformer, and in the alternative splicing of the gene Ultrabithorax. Here, the expression and subcellular localization of the FL(2)D protein is reported. FL(2)D is ubiquitously expressed in embryos, in imaginal discs of larvae and in ovaries. In Schneider cells, the protein is detected throughout the nucleoplasm, excluding the nucleolus, and partially co-localizes with SXL in nuclear speckles. In addition, FL(2)D associates with multiple transcriptionally active loci on salivary gland polytene chromosomes, consistent with the proposal that the protein is involved in the post-transcriptional regulation of a variety of genes. Interestingly, the localization of FL(2)D in nurse cells changes during oogenesis, from a rather diffuse early nuclear pattern in the germarium to a preferential accumulation at the nuclear periphery of nurse cells of developing cysts.
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Affiliation(s)
- A Ortega
- European Molecular Biology Laboratory, Heidelberg, Germany.
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14
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Zimowska G, Paddy MR. Structures and dynamics of Drosophila Tpr inconsistent with a static, filamentous structure. Exp Cell Res 2002; 276:223-32. [PMID: 12027452 DOI: 10.1006/excr.2002.5525] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here we report immunofluorescence localizations of the Drosophila Tpr protein which are inconsistent with a filament-forming protein statically associated with nuclear pore complex-associated intranuclear filaments. Using tissues from throughout the Drosophila life cycle, we observe that Tpr is often localized to discontinuous, likely granular or particulate structures in the deep nuclear interior. These apparent granules have no obvious connectivity to pore complexes in the nuclear periphery, and are often localized on the surfaces of chromosomes and to the perinucleolar region. Most strikingly, after 1 h of heat shock, the great majority of the Tpr in the deep nuclear interior accumulates at a single heat shock puff, while Tpr in the nuclear periphery appears unchanged. This heat shock puff, 93D, is a known repository for many components of pre-mRNA metabolism during heat shock. Although we do not observe Tpr at sites of transcription under normal conditions, the 93D heat shock result leads us to favor a role for Tpr in mRNA metabolism, such as the transport of mRNA through the nuclear interior to nuclear pore complexes. Consistent with this, we observe networks of Tpr containing granules spanning between the nucleolus and the nuclear periphery which are also decorated by an anti-SR protein antibody. Since we also observe Drosophila Tpr in reticular or fibrous structures in other nuclei, such as salivary gland polytene nuclei, these results indicate that Tpr can exist in at least two structural forms, and suggest that Tpr may relocalize or even change structural forms in response to cellular needs.
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Affiliation(s)
- Grazyna Zimowska
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610-0235, USA.
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15
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Sabri N, Farrants AKO, Hellman U, Visa N. Evidence for a posttranscriptional role of a TFIIICalpha-like protein in Chironomus tentans. Mol Biol Cell 2002; 13:1765-77. [PMID: 12006668 PMCID: PMC111142 DOI: 10.1091/mbc.01-09-0436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We have cloned and sequenced a cDNA that encodes for a nuclear protein of 238 kDa in the dipteran Chironomus tentans. This protein, that we call p2D10, is structurally similar to the alpha subunit of the general transcription factor TFIIIC. Using immunoelectron microscopy we have shown that a fraction of p2D10 is located at sites of transcription, which is consistent with a possible role of this protein in transcription initiation. We have also found that a large fraction of p2D10 is located in the nucleoplasm and in the nuclear pore complexes. Using gel filtration chromatography and coimmunoprecipitation methods, we have identified and characterized two p2D10-containing complexes that differ in molecular mass and composition. The heavy p2D10-containing complex contains at least one other component of the TFIIIC complex, TFIIIC-epsilon. Based on its molecular mass and composition, the heavy p2D10-containing complex may be the Pol III holoenzyme. The light p2D10-containing complex contains RNA together with at least two proteins that are thought to be involved in mRNA trafficking, RAE1 and hrp65. The observations reported here suggest that this new TFIIIC-alpha-like protein is involved in posttranscriptional steps of premRNA metabolism in Chironomus tentans.
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Affiliation(s)
- Nafiseh Sabri
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691, Sweden
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16
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Miralles F, Visa N. Molecular characterization of Ct-hrp65: identification of two novel isoforms originated by alternative splicing. Exp Cell Res 2001; 264:284-95. [PMID: 11262185 DOI: 10.1006/excr.2000.5127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hrp65, a protein with two conserved RNA-binding domains, has been identified in Chironomus tentans as a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. We have cloned two novel hrp65 isoforms and characterized the structure of the hrp65 gene. Comparison of the hrp65 gene to the hrp65 cDNAs revealed that the multiple hrp65 isoforms, hrp65-1, hrp65-2 and hrp65-3, are generated by alternative splicing of a single pre-mRNA. The hrp65-3 mRNA is only detected in C. tentans tissue culture cells of embryonic origin, whereas hrp65-1 and hrp65-2 mRNAs appear to be constitutively expressed. The hrp65 mRNAs are generated by differential 3' splice site selection at the last exon of the gene. Thus, the three hrp65 transcripts contain different 3' UTRs and encode proteins that vary in their C-terminal ends. Interestingly, the variant C-terminal region determines the subcellular localization of the hrp65 proteins. In transient transfection assays, hrp65-1 is efficiently targetted to the nucleus, whereas hrp65-2 and hrp65-3 localize mainly to the cytoplasm. Moreover, hrp65-3 is associated with cytoplasmic actin fibers. All together, our findings suggest that the different hrp65 isoforms serve specialized roles related to mRNA localization/transport in the different cell compartments.
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Affiliation(s)
- F Miralles
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, SE-106 91, Sweden
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17
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Sassa N, Matsushita Y, Nakamura T, Nyunoya H. The molecular characterization and in situ expression pattern of pea SCARECROW gene. PLANT & CELL PHYSIOLOGY 2001; 42:385-94. [PMID: 11333309 DOI: 10.1093/pcp/pce048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Certain mutants of shoot gravitropism were reported to be ascribed to the SCR and SHR loci in Arabidopsis thaliana. The SCR gene was known to regulate the development of endodermis cells that are responsible for sensing gravity in a shoot. With the aim of elucidating the molecular mechanism for gravitropic responses in pea seedlings, we have isolated a putative pea SCR ortholog from a shoot cDNA library. Analyses of the cDNA clones revealed the structure of a full-length ORF coding for 819 amino acid residues. A remarkable feature of pea SCR protein was the presence of asparagine stretches at the N-terminal transcriptional activation domain, which was distinct from the occurrence of glutamine or alanine stretches in the Arabidopsis or maize SCR. A Northern blot analysis revealed a single 3.2-kb pea SCR transcript in addition to a closely related 2.5-kb transcript. Our in situ hybridization data indicated that pea SCR mRNA accumulated in the shoot apical meristem, leaf primordia and a root single cell layer corresponding to the endodermis. The expression patterns were similar to those reported for A. thaliana and Zea mays, suggesting that SCR may be functionally conserved among plants and involved in the differentiation of the endodermis.
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Affiliation(s)
- N Sassa
- Laboratory of Plant Physiology, Faculty of Science, Japan Women's University, 2-8-1 Mejiro-dai, Bunkyo-ku, Tokyo, 112-8681 Japan
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18
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Reim I, Mattow J, Saumweber H. The RRM protein NonA from Drosophila forms a complex with the RRM proteins Hrb87F and S5 and the Zn finger protein PEP on hnRNA. Exp Cell Res 1999; 253:573-86. [PMID: 10585281 DOI: 10.1006/excr.1999.4647] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The RRM protein NonA, an ubiquitous nuclear protein present in puffs on polytene chromosomes, has been immunopurified as a RNA-protein complex from Drosophila Kc cells. Three other proteins present in the complex have been identified: X4/PEP (protein on ecdysone puffs), a 100-kDa zinc finger RNA-binding protein; the 70-kDa S5 protein, an as yet uncharacterized RNA-binding protein; and P11/Hrb87F, a 38-kDa RRM protein homologous to hnRNP protein A1 from mammals. Monoclonal antibodies against any of the protein components coprecipitate all four proteins although at different ratios. NonA does not coprecipitate with the hrp40 hnRNP proteins and immunolocalizes in a pattern distinct of major hnRNP proteins. Like NonA, X4/PEP, S5, and P11/Hrb87F are present on active sites on polytene chromosomes. The precipitated NonA complex is enriched for certain protein encoding RNAs, notably, histone H3 and H4 RNA.
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Affiliation(s)
- I Reim
- Institut für Biologie Abt. Zytogenetik, Humboldt Universität zu Berlin, Berlin, D-10115, Germany
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19
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Mitsui K, Matsumoto A, Ohtsuka S, Ohtsubo M, Yoshimura A. Cloning and characterization of a novel p21(Cip1/Waf1)-interacting zinc finger protein, ciz1. Biochem Biophys Res Commun 1999; 264:457-64. [PMID: 10529385 DOI: 10.1006/bbrc.1999.1516] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
p21(Cip1/Waf1) inhibits cell-cycle progression by binding to G1 cyclin/CDK complexes and proliferating cell nuclear antigen (PCNA) through its N- and C-terminal domains, respectively. Here, we report a novel p21(Cip1/Waf1)-interacting protein, Ciz1 (for Cip1 interacting zinc finger protein), which contains polyglutamine repeats and glutamine-rich region in the N-terminus as well as three zinc-finger motifs and one MH3 (matrin 3-homologous domain 3) in the C-terminal region. Ciz1 bound to the N-terminal, the CDK2-interacting part of p21(Cip1/Waf1), and the interaction was disrupted by the overexpression of CDK2. A region of about 150 amino acids containing the first zinc-finger motif in Ciz1 was the binding site for p21(Cip1/Waf1). When Ciz1 and p21(Cip1/Waf1) were individually overexpressed in U2-OS cells, they mostly localized in the nucleus. However, coexpression of Ciz1 induced cytoplasmic distribution of p21(Cip1/Waf1). These data indicate that Ciz1 is a unique nuclear protein that regulates the cellular localization of p21(Cip1/Waf1).
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Affiliation(s)
- K Mitsui
- Institute of Life Science, Kurume University, Aikawa-machi 2432-3, Kurume, 839-0861, Japan
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20
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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21
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Bhaud Y, Géraud ML, Ausseil J, Soyer-Gobillard MO, Moreau H. Cyclic expression of a nuclear protein in a dinoflagellate. J Eukaryot Microbiol 1999; 46:259-67. [PMID: 10377987 DOI: 10.1111/j.1550-7408.1999.tb05123.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclei of the dinoflagellate Crypthecodinium cohnii strain Whd were isolated and nuclear proteins were extracted in three fractions, corresponding to the increasing affinity of these proteins to genomic DNA. One fraction contained two major bands (48- and 46-kDa) and antibodies specific to this fraction revealed two major bands by Western blot on nuclear extracts, corresponding to the 46- and 48-kDa bands. The 48-kDa protein was detected in G1 phase but not in M phase cells. An expression cDNA library of C. cohnii was screened with these antibodies, and two different open reading frames were isolated. Dinoflagellate nuclear associated protein (Dinap1), one of these coding sequences, was produced in E. coli and appeared to correspond to the 48-kDa nuclear protein. No homologue of this sequence was found in the data bases, but two regions were identified, one including two putative zinc finger repeats, and one coding for two potential W/W domains. The second coding sequence showed a low similarity to non-specific sterol carrier proteins. Immunocytolocalization with specific polyclonal antibodies to recombinant Dinap1 showed that the nucleus was immunoreactive only during the G1 phase: the nucleoplasm was immunostained, while chromosome cores and nuclear envelopes were negative.
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Affiliation(s)
- Y Bhaud
- Observatoire Océanologique de Banyuls, Laboratoire Arago, UMR CNRS 7628, Banyuls-sur-Mer France
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22
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Hamann S, Strätling WH. Specific binding of Drosophila nuclear protein PEP (protein on ecdysone puffs) to hsp70 DNA and RNA. Nucleic Acids Res 1998; 26:4108-15. [PMID: 9722628 PMCID: PMC147826 DOI: 10.1093/nar/26.18.4108] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Drosophila protein PEP (protein on ecdysone puffs), a component hnRNP complexes, was previously immunocytologically localized on Drosophila giant chromosomes to puffs induced by ecdysone and to some heat shock-induced puffs (e.g. at the hsp70 locus at 87A7). Here, PEP was purified to homogeneity and characterized in its DNA and RNA binding features with specific reference to the hsp70 locus. In southwestern blotting assays, PEP was found to bind with high affinity to the hsp70 coding region, but not to a flanking region nor to the boundary elements scs and scs', and non-specifically to the intergenic hsp70 SAR. In UV cross-linking assays, PEP binds with even higher affinity to hsp70 transcripts, but not to transcripts of a flanking region or of a nearby gene, aurora . Finally, competition experiments indicate that PEP recognizes specific sequences within hsp70 mRNA; in these sequences two distinct motifs were found to be enriched. In summary, our results suggest the recognition of specific transcripts as a molecular basis for the association of the protein with specific hnRNP complexes.
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Affiliation(s)
- S Hamann
- Institut für Physiologische Chemie, Universitäts-Krankenhaus Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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23
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Sun X, Alzhanova-Ericsson AT, Visa N, Aissouni Y, Zhao J, Daneholt B. The hrp23 protein in the balbiani ring pre-mRNP particles is released just before or at the binding of the particles to the nuclear pore complex. J Cell Biol 1998; 142:1181-93. [PMID: 9732280 PMCID: PMC2149341 DOI: 10.1083/jcb.142.5.1181] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/1998] [Revised: 07/07/1998] [Indexed: 11/27/2022] Open
Abstract
Balbiani ring (BR) pre-mRNP particles reside in the nuclei of salivary glands of the dipteran Chironomus tentans and carry the message for giant-sized salivary proteins. In the present study, we identify and characterize a new protein component in the BR ribonucleoprotein (RNP) particles, designated hrp23. The protein with a molecular mass of 20 kD has a single RNA-binding domain and a glycine-arginine-serine-rich auxiliary domain. As shown by immunoelectron microscopy, the hrp23 protein is added to the BR transcript concomitant with transcription, is still present in the BR particles in the nucleoplasm, but is absent from the BR particles that are bound to the nuclear pore complex or are translocating through the central channel of the complex. Thus, hrp23 is released just before or at the binding of the particles to the nuclear pore complex. It is noted that hrp23 behaves differently from two other BR RNP proteins earlier studied: hrp36 and hrp45. These proteins both reach the nuclear pore complex, and hrp36 even accompanies the RNA into the cytoplasm. It is concluded that each BR RNA-binding protein seems to have a specific flow pattern, probably related to the particular role of the protein in gene expression.
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Affiliation(s)
- X Sun
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, S-171 77, Stockholm, Sweden
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24
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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25
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Song Q, Alnemri ES, Litwack G, Gilbert LI. An immunophilin is a component of the insect ecdysone receptor (EcR) complex. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 1997; 27:973-982. [PMID: 9501420 DOI: 10.1016/s0965-1748(97)00080-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The ecdysone receptor (EcR) complex has been identified in the prothoracic gland of Manduca sexta by specific immunoprecipitation and Western blot analyses, and includes EcR, ultraspiracle (USP) and FKBP46. The EcR complex binds ponasterone A in a dose-dependent manner with a Kd of 7.04 x 10(-9) M. Immunocytochemistry revealed that EcR, USP and FKBP46 were localized within the nucleus of the prothoracic gland cells, and suggested that the developmental expression patterns of EcR and USP changed in concert with the hemolymph ecdysteroid titer whereas that of FKBP46 did not. The composite results suggest that the hemolymph ecdysteroid titer, of which 20 hydroxyecdysone is the major component, modulates the expression of both EcR and USP in the prothoracic gland to achieve feedback regulation.
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Affiliation(s)
- Q Song
- Department of Biology, University of North Carolina, Chapel Hill 27599-3280, USA
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26
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Alexandre E, Graba Y, Fasano L, Gallet A, Perrin L, De Zulueta P, Pradel J, Kerridge S, Jacq B. The Drosophila teashirt homeotic protein is a DNA-binding protein and modulo, a HOM-C regulated modifier of variegation, is a likely candidate for being a direct target gene. Mech Dev 1996; 59:191-204. [PMID: 8951796 DOI: 10.1016/0925-4773(96)00594-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The Drosophila teashirt (tsh) gene has an homeotic function which, in combination with HOM-C genes, determines thoracic and abdominal (trunk) identities. Analysis of TSH protein distribution during embryogenesis using a specific polyclonal antibody shows that it is nuclear. The protein is present with regional modulation in several tissues within the trunk, suggesting additional tsh functions to those already studied. We identified a candidate tsh target shared with some HOM-C genes, the modifier of variegation gene modulo (mod). The TSH zinc-finger protein recognizes in vitro two specific sites within a 5' control element of the mod gene which responds in vivo to tsh activity. TSH is therefore a DNA binding protein and might directly control mod expression.
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Affiliation(s)
- E Alexandre
- Laboratoire de Génétique et Physiologie du Développement, IBDM, Marseille, France
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27
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Visa N, Alzhanova-Ericsson AT, Sun X, Kiseleva E, Björkroth B, Wurtz T, Daneholt B. A pre-mRNA-binding protein accompanies the RNA from the gene through the nuclear pores and into polysomes. Cell 1996; 84:253-64. [PMID: 8565071 DOI: 10.1016/s0092-8674(00)80980-0] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the larval salivary glands of C. tentans, it is possible to visualize by electron microscopy how Balbiani ring (BR) pre-mRNA associates with proteins to form pre-mRNP particles, how these particles move to and through the nuclear pore, and how the BR RNA is engaged in the formation of giant polysomes in the cytoplasm. Here, we study C. tentans hrp36, an abundant protein in the BR particles, and establish that it is similar to the mammalian hnRNP A1. By immuno-electron microscopy it is demonstrated that hrp36 is added to BR RNA concomitant with transcription, remains in nucleoplasmic BR particles, and is translocated through the nuclear pore still associated with BR RNA. It appears in the giant BR RNA-containing polysomes, where it remains as an abundant protein in spite of ongoing translation.
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Affiliation(s)
- N Visa
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, Stockholm, Sweden
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28
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29
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Henrich VC, Brown NE. Insect nuclear receptors: a developmental and comparative perspective. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 1995; 25:881-897. [PMID: 7550245 DOI: 10.1016/0965-1748(95)00030-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The appearance of puffs on the polytene chromosomes of insect salivary glands incubated with 20-hydroxyecdysone provided the first demonstration that steroids act directly at the gene transcriptional level to bring about subsequent cellular changes (Becker, 1959; Clever and Karlson, 1960). Despite that auspicious beginning, learning about the molecular mechanisms that underlie the hormonal regulation of insect development was impeded for many years by the difficulty associated with isolating and identifying rare regulatory factors from limited tissue sources. The advent of recombinant DNA methodology and powerful techniques such as the polymerase chain reaction (PCR) along with the recognition that many important endocrine factors are structurally conserved across a wide range of species has, however, all but eliminated the technical obstacles once facing the insect endocrinologist trying to isolate and study these regulatory molecules. This review will discuss recent progress and recall some earlier experiments concerning the molecular basis of hormonal action in insects focusing primarily on the members of the nuclear hormone receptor superfamily in Drosophila melanogaster. Two members of this family comprise the functional ecdysteroid receptor and at least a dozen other "orphans" have been identified in Drosophila for which no cognate ligand has yet been found. Many of these orphans are regulated by ecdysteroids. A discussion of juvenile hormone binding proteins that are not family members has been included because of their potential impact on nuclear receptor function. As receptor homologues have been identified in other insects, several general ideas concerning insect hormonal regulation have begun to emerge and these will be examined from a comparative point of view.
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Affiliation(s)
- V C Henrich
- Department of Biology, University of North Carolina-Greensboro 27412-5001, USA
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30
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Andrew DJ, Scott MP. Immunological methods for mapping protein distributions on polytene chromosomes. Methods Cell Biol 1994; 44:353-70. [PMID: 7707963 DOI: 10.1016/s0091-679x(08)60923-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- D J Andrew
- Department of Cell Biology and Anatomy, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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31
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A unique ribonucleoprotein complex assembles preferentially on ecdysone-responsive sites in Drosophila melanogaster. Mol Cell Biol 1993. [PMID: 8355684 DOI: 10.1128/mcb.13.9.5323] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protein on ecdysone puffs (PEP) is associated preferentially with active ecdysone-inducible puffs on Drosophila polytene chromosomes and contains sequence motifs characteristic of transcription factors and RNA-binding proteins (S. A. Amero, S. C. R. Elgin, and A. L. Beyer, Genes Dev. 5:188-200, 1991). PEP is associated with RNA in vivo, as demonstrated here by the sensitivity of PEP-specific chromosomal immunostaining in situ to RNase digestion and by the immunopurification of PEP in Drosophila cell extract with heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. As revealed by sequential immunostaining, PEP is found on a subset of chromosomal sites bound by the HRB (heterogeneous nuclear RNA-binding) proteins, which are basic Drosophila hnRNPs. These observations lead us to suggest that a unique, PEP-containing hnRNP complex assembles preferentially on the transcripts of ecdysone-regulated genes in Drosophila melanogaster presumably to expedite the transcription and/or processing of these transcripts.
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32
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Amero SA, Matunis MJ, Matunis EL, Hockensmith JW, Raychaudhuri G, Beyer AL. A unique ribonucleoprotein complex assembles preferentially on ecdysone-responsive sites in Drosophila melanogaster. Mol Cell Biol 1993; 13:5323-30. [PMID: 8355684 PMCID: PMC360230 DOI: 10.1128/mcb.13.9.5323-5330.1993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The protein on ecdysone puffs (PEP) is associated preferentially with active ecdysone-inducible puffs on Drosophila polytene chromosomes and contains sequence motifs characteristic of transcription factors and RNA-binding proteins (S. A. Amero, S. C. R. Elgin, and A. L. Beyer, Genes Dev. 5:188-200, 1991). PEP is associated with RNA in vivo, as demonstrated here by the sensitivity of PEP-specific chromosomal immunostaining in situ to RNase digestion and by the immunopurification of PEP in Drosophila cell extract with heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. As revealed by sequential immunostaining, PEP is found on a subset of chromosomal sites bound by the HRB (heterogeneous nuclear RNA-binding) proteins, which are basic Drosophila hnRNPs. These observations lead us to suggest that a unique, PEP-containing hnRNP complex assembles preferentially on the transcripts of ecdysone-regulated genes in Drosophila melanogaster presumably to expedite the transcription and/or processing of these transcripts.
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Affiliation(s)
- S A Amero
- Department of Molecular and Cellular Biochemistry, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153
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33
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Amero SA, Raychaudhuri G, Cass CL, van Venrooij WJ, Habets WJ, Krainer AR, Beyer AL. Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription. Proc Natl Acad Sci U S A 1992; 89:8409-13. [PMID: 1388268 PMCID: PMC49929 DOI: 10.1073/pnas.89.18.8409] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The major nuclear ribonucleoproteins (RNPs) involved in pre-mRNA processing are classified in broad terms either as small nuclear RNPs (snRNPs), which are major participants in the splicing reaction, or heterogeneous nuclear RNPs (hnRNPs), which traditionally have been thought to function in general pre-mRNA packaging. We obtained antibodies that recognize these two classes of RNP in Drosophila melanogaster. Using a sequential immunostaining technique to compare directly the distribution of these RNPs on Drosophila polytene chromosomes, we found that the two patterns were very similar qualitatively but not quantitatively, arguing for the independent deposition of the two RNP types and supporting a role for hnRNP proteins, but not snRNPs, in general transcript packaging.
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Affiliation(s)
- S A Amero
- Department of Microbiology, University of Virginia School of Medicine, Charlottesville 22908
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34
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1992; 20:147-68. [PMID: 1738598 PMCID: PMC310346 DOI: 10.1093/nar/20.1.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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