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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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2
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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3
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Li D, Wang Y, Zhang K, Jiao Z, Zhu X, Skogerboe G, Guo X, Chinnusamy V, Bi L, Huang Y, Dong S, Chen R, Kan Y. Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori. Nucleic Acids Res 2011; 39:3792-805. [PMID: 21227919 PMCID: PMC3089462 DOI: 10.1093/nar/gkq1317] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidences show that small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. The silkworm is an important model for studies on insect genetics and control of lepidopterous pests. Here, we have performed the first systematic identification and analysis of intermediate size ncRNAs (50–500 nt) in the silkworm. We identified 189 novel ncRNAs, including 141 snoRNAs, six snRNAs, three tRNAs, one SRP and 38 unclassified ncRNAs. Forty ncRNAs showed significantly altered expression during silkworm development or across specific stage transitions. Genomic comparisons revealed that 123 of these ncRNAs are potentially silkworm-specific. Analysis of the genomic organization of the ncRNA loci showed that 32.62% of the novel snoRNA loci are intergenic, and that all the intronic snoRNAs follow the pattern of one-snoRNA-per-intron. Target site analysis predicted a total of 95 2′-O-methylation and pseudouridylation modification sites of rRNAs, snRNAs and tRNAs. Together, these findings provide new clues for future functional study of ncRNA during insect development and evolution.
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Affiliation(s)
- Dandan Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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4
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Gladstein N, McKeon MN, Horabin JI. Requirement of male-specific dosage compensation in Drosophila females--implications of early X chromosome gene expression. PLoS Genet 2010; 6:e1001041. [PMID: 20686653 PMCID: PMC2912388 DOI: 10.1371/journal.pgen.1001041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/24/2010] [Indexed: 11/18/2022] Open
Abstract
Dosage compensation equates between the sexes the gene dose of sex chromosomes that carry substantially different gene content. In Drosophila, the single male X chromosome is hypertranscribed by approximately two-fold to effect this correction. The key genes are male lethal and appear not to be required in females, or affect their viability. Here, we show these male lethals do in fact have a role in females, and they participate in the very process which will eventually shut down their function—female determination. We find the male dosage compensation complex is required for upregulating transcription of the sex determination master switch, Sex-lethal, an X-linked gene which is specifically activated in females in response to their two X chromosomes. The levels of some X-linked genes are also affected, and some of these genes are used in the process of counting the number of X chromosomes early in development. Our data suggest that before the female state is set, the ground state is male and female X chromosome expression is elevated. Females thus utilize the male dosage compensation process to amplify the signal which determines their fate. When substantially different, sex chromosomes present the challenge of not only gene dose inequity between the sexes, in the heterogametic sex where one chromosome (frequently the Y) carries few genes, but also an inequity relative to the autosomes which are diploid. Dosage compensation refers to the process which equates gene dose between the sexes. Recent results, however, indicate that the mammalian X chromosome avoids monosomy and has a level of expression that is two-fold relative to the autosomes. Hyperactive X chromosome expression in Caenorhabditis elegans has also been suggested, and dosage compensation in the hermaphrodite appears to lower expression of the X chromosomes to match autosome levels. We find that, before the female state is set in Drosophila, the X chromosomes may also express their genes at the two-fold male level and that this level of expression is used to female advantage to consolidate their sex determination. Together, the results suggest that elevated X chromosome expression may be the norm, and that the various dosage compensation processes different organisms utilize reflect a mechanism to counteract an initial hyperactive X chromosome state.
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Affiliation(s)
- Natalie Gladstein
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
| | - Meghan N. McKeon
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
| | - Jamila I. Horabin
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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5
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Brosnan CA, Voinnet O. The long and the short of noncoding RNAs. Curr Opin Cell Biol 2009; 21:416-25. [PMID: 19447594 DOI: 10.1016/j.ceb.2009.04.001] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 04/06/2009] [Indexed: 12/27/2022]
Abstract
Controlling protein-coding gene expression can no longer be attributed purely to proteins involved in transcription, RNA processing, and translation. The role that noncoding RNAs (ncRNAs) play as potent and specific regulators of gene expression is now widely recognized in almost all species studied to date. Long ncRNAs can both upregulate and downregulate gene expression in both eukaryotes and prokaryotes and are essential in processes such as dosage compensation, genomic imprinting, developmental patterning and differentiation, and stress response. Small ncRNAs also play essential roles in diverse organisms, although are limited to eukaryotes. Different small RNA classes regulate diverse processes such as transposon and virus suppression, as well as many key developmental processes.
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Affiliation(s)
- Christopher A Brosnan
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357-Université de Strasbourg, Strasbourg, France
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6
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7
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Dmitriev RI, Shakhparonov MI, Pestov NB. Structure and function of MYST1 histone acetyltransferase in the interactome of animal cells. BIOCHEMISTRY (MOSCOW) 2008; 73:839-52. [PMID: 18774930 DOI: 10.1134/s0006297908080014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The major function of protein MYST1 is acetylation of histone H4 at the K16 residue. This modification is essential for chromatin remodeling and is used for regulation of gene expression in eukaryotes. MYST1 is a part of multiprotein complexes that accomplish functions of male X-chromosome activation and thereby functions of dosage compensation in drosophila and, in mammals, global acetylation of histone H4 K16. Recently, novel functional links between MYST1 and proteins ATM and p53 have been observed, and it is recognized that MYST1 plays a role in tumor suppression mechanisms. In the present review, we examine novel data about functional composition and mechanisms of MYST1-containing complexes. Interplay between MYST1 and other components of the animal cell interactome is also discussed.
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Affiliation(s)
- R I Dmitriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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8
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Khil PP, Camerini-Otero RD. Molecular Features and Functional Constraints in the Evolution of the Mammalian X Chromosome. Crit Rev Biochem Mol Biol 2008; 40:313-30. [PMID: 16338684 DOI: 10.1080/10409230500356703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recent advances in genomic sequencing of multiple organisms have fostered significant advances in our understanding of the evolution of the sex chromosomes. The integration of this newly available sequence information with functional data has facilitated a considerable refinement of our conceptual framework of the forces driving this evolution. Here we address multiple functional constraints that were encountered in the evolution of the X chromosome and the impact that this evolutionary history has had on its modern behavior.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Incorporation of the noncoding roX RNAs alters the chromatin-binding specificity of the Drosophila MSL1/MSL2 complex. Mol Cell Biol 2007; 28:1252-64. [PMID: 18086881 DOI: 10.1128/mcb.00910-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The male-specific lethal (MSL) protein-RNA complex is required for X chromosome dosage compensation in Drosophila melanogaster. The MSL2 and MSL1 proteins form a complex and are essential for X chromosome binding. In addition, the MSL complex must integrate at least one of the noncoding roX RNAs for normal X chromosome binding. Here we find the amino-terminal RING finger domain of MSL2 binds as a complex with MSL1 to the heterochromatic chromocenter and a few sites on the chromosome arms. This binding required the same amino-terminal basic motif of MSL1 previously shown to be essential for binding to high-affinity sites on the X chromosome. While the RING finger domain of MSL2 is sufficient to increase the expression of roX1 in females, activation of roX2 requires motifs in the carboxyl-terminal domain. Binding to hundreds of sites on the X chromosome and efficient incorporation of the roX RNAs into the MSL complex require proline-rich and basic motifs in the carboxyl-terminal domain of MSL2. We suggest that incorporation of the roX RNAs into the MSL complex alters the binding specificity of the chromatin-binding module formed by the amino-terminal domains of MSL1 and MSL2.
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10
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Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 2007; 120:2498-506. [PMID: 17623775 DOI: 10.1242/jcs.009357] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Recent transcriptome analyses have revealed that a large body of noncoding regions of mammalian genomes are actually transcribed into RNAs. Our understanding of the molecular features of these noncoding RNAs is far from complete. We have identified a novel mRNA-like noncoding gene, named Gomafu, which is expressed in a distinct set of neurons in the mouse nervous system. Interestingly, spliced mature Gomafu RNA is localized to the nucleus despite its mRNA-like characteristics, which usually act as potent export signals to the cytoplasm. Within the nucleus, Gomafu RNA is detected as numerous spots that do not colocalize with known nuclear domain markers. Gomafu RNA is extremely insoluble and remains intact after nuclear matrix preparation. Furthermore, heterokaryon assays revealed that Gomafu RNA does not shuttle between the nucleus and cytoplasm, but is retained in the nucleus after its transcription. We propose that Gomafu RNA represents a novel family of mRNA-like noncoding RNA that constitutes a cell-type-specific component of the nuclear matrix.
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Affiliation(s)
- Masamitsu Sone
- Nakagawa Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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11
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Funaguma S, Hashimoto SI, Suzuki Y, Omuro N, Sugano S, Mita K, Katsuma S, Shimada T. SAGE analysis of early oogenesis in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2007; 37:147-54. [PMID: 17244543 DOI: 10.1016/j.ibmb.2006.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 11/05/2006] [Accepted: 11/06/2006] [Indexed: 05/13/2023]
Abstract
To identify genes involved in the differentiation of Bombyx cystoblast, we constructed two 3' long serial analysis of gene expression (Long SAGE) libraries from stage 1-3 or stage 2-3 egg chambers and compared their gene expression profiles. In both libraries, the most frequent tags were derived from the same novel transcript. The transcript does not have any open reading frame capable of encoding a protein with over 100 amino acids in length. RNA blot analysis revealed that this transcript is specifically and abundantly expressed in the Bombyx ovary, mainly the germ line cells in the ovarioles. These results suggest that Bombyx oogenesis may be regulated by a previously unidentified non-coding RNA. Comparison of the gene expression profiles between the stage 1-3 and stage 2-3 egg chamber libraries revealed that 272 tags were significantly more abundant in stage 1-3 egg chambers (p<0.05 and at least two-fold change) than in library 2. Among the differentially expressed transcripts were the sequences that correspond to ATP synthase subunit d (3.1-fold enriched) and ATP synthase coupling factor 6 (9.1-fold enriched), suggesting that they are involved in regulation of cell cycle of cystocytes.
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Affiliation(s)
- Shunsuke Funaguma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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12
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Prasanth KV, Spector DL. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 2007; 21:11-42. [PMID: 17210785 DOI: 10.1101/gad.1484207] [Citation(s) in RCA: 301] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A large portion of the eukaryotic genome is transcribed as noncoding RNAs (ncRNAs). While once thought of primarily as "junk," recent studies indicate that a large number of these RNAs play central roles in regulating gene expression at multiple levels. The increasing diversity of ncRNAs identified in the eukaryotic genome suggests a critical nexus between the regulatory potential of ncRNAs and the complexity of genome organization. We provide an overview of recent advances in the identification and function of eukaryotic ncRNAs and the roles played by these RNAs in chromatin organization, gene expression, and disease etiology.
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13
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Schulze SR, Wallrath LL. Gene regulation by chromatin structure: paradigms established in Drosophila melanogaster. ANNUAL REVIEW OF ENTOMOLOGY 2007; 52:171-92. [PMID: 16881818 DOI: 10.1146/annurev.ento.51.110104.151007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Studies in Drosophila melanogaster have revealed paradigms for regulating gene expression through chromatin structure, including mechanisms of gene activation and silencing. Regulation occurs at the level of individual genes, chromosomal domains, and entire chromosomes. The chromatin state is dynamic, allowing for changes in gene expression in response to cellular signals and/or environmental cues. Changes in chromatin result from the action of ATP-dependent chromatin-remodeling complexes, reversible epigenetic histone modifications, and the incorporation of histone variants. Many of the chromatin-based transcriptional regulatory mechanisms discovered in D. melanogaster are evolutionarily conserved and therefore serve as a foundation for studies in other organisms.
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Affiliation(s)
- Sandra R Schulze
- Department of Biology, Western Washington University, Bellingham, Washington 98225, USA.
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14
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Storchová R, Divina P. Nonrandom representation of sex-biased genes on chicken Z chromosome. J Mol Evol 2006; 63:676-81. [PMID: 17031459 DOI: 10.1007/s00239-006-0022-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 07/25/2006] [Indexed: 10/24/2022]
Abstract
Several lines of evidence suggest that the X chromosome of various animal species has an unusual complement of genes with sex-biased or sex-specific expression. However, the study of the X chromosome gene content in different organisms provided conflicting results. The most striking contrast concerns the male-biased genes, which were reported to be almost depleted from the X chromosome in Drosophila but overrepresented on the X chromosome in mammals. To elucidate the reason for these discrepancies, we analysed the gene content of the Z chromosome in chicken. Our analysis of the publicly available expressed sequence tags (EST) data and genome draft sequence revealed a significant underrepresentation of ovary-specific genes on the chicken Z chromosome. For the brain-expressed genes, we found a significant enrichment of male-biased genes but an indication of underrepresentation of female-biased genes on the Z chromosome. This is the first report on the nonrandom gene content in a homogametic sex chromosome of a species with heterogametic female individuals. Further comparison of gene contents of the independently evolved X and Z sex chromosomes may offer new insight into the evolutionary processes leading to the nonrandom genomic distribution of sex-biased and sex-specific genes.
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Affiliation(s)
- R Storchová
- Institute of Molecular Genetics, Academy of Sciences of Czech Republic and Center for Applied Genomics, Vídenská 1083, CZ-142 20, Prague 4, Czech Republic.
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15
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Deng X, Meller VH. Non-coding RNA in fly dosage compensation. Trends Biochem Sci 2006; 31:526-32. [PMID: 16890440 DOI: 10.1016/j.tibs.2006.07.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/15/2006] [Accepted: 07/20/2006] [Indexed: 01/27/2023]
Abstract
Dosage compensation modulates global expression of an X chromosome and is necessary to restore the balance between X-chromosome and autosome expression in both sexes. A central question in the field is how this regulation is directed. Large non-coding RNAs, such as Xist in mammals and roX in flies, have pivotal roles in targeting chromosome-wide modification for dosage compensation. Several recent studies in Drosophila provide new insight into the principles of X-chromosome recognition and the function of non-coding RNA in this process.
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Affiliation(s)
- Xinxian Deng
- Department of Biological Science, Wayne State University, Detroit, MI 48201, USA
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16
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Abstract
Regulation of gene expression involves a number of different levels of organization in the cell nucleus. The main agents of transcriptional control are the cis-acting sequences in the immediate vicinity of a gene, which combine to form the functional unit or domain. Contacts between these sequences through the formation of chromatin loops forms the most basic level of organization. The activity of functional domains is also influenced by higher order chromatin structures that impede or permit access of factors to the genes. Epigenetic modifications can maintain and propagate these active or repressive chromatin structures across large genomic regions or even entire chromosomes. There is also evidence that transcription is organized into structures called 'factories' and that this can lead to inter-chromosomal contacts between genes that have the potential to influence their regulation.
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Affiliation(s)
- Niall Dillon
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, Du Cane Road, London W12 ONN, UK.
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17
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Inagaki S, Numata K, Kondo T, Tomita M, Yasuda K, Kanai A, Kageyama Y. Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells 2006; 10:1163-73. [PMID: 16324153 DOI: 10.1111/j.1365-2443.2005.00910.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
One of the most surprising results to emerge from mammalian cDNA sequencing projects is that thousands of mRNA-like non-coding RNAs (ncRNAs) are expressed and constitute at least 10% of poly(A)(+) RNAs. In most cases, however, the functions of these RNA molecules remain unclear. To clarify the biological significance of mRNA-like ncRNAs, we computationally screened 11,691 Drosophila melanogaster full-length cDNAs. After eliminating presumable protein-coding transcripts, 136 were identified as strong candidates for mRNA-like ncRNAs. Although most of these putative ncRNAs are found throughout the Drosophila genus, predicted amino acid sequences are not conserved even in related species, suggesting that these transcripts are actually non-coding RNAs. In situ hybridization analyses revealed that 35 of the transcripts are expressed during embryogenesis, of which 27 were detected only in specific tissues including the tracheal system, midgut primordial cells, visceral mesoderm, germ cells and the central and peripheral nervous system. These highly regulated expression patterns suggest that many mRNA-like ncRNAs play important roles in multiple steps of organogenesis and cell differentiation in Drosophila. This is the first report that the majority of mRNA-like ncRNAs in a model organism are expressed in specific tissues and cell types.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Differentiation/genetics
- Conserved Sequence
- DNA, Complementary/analysis
- DNA, Complementary/genetics
- Drosophila/embryology
- Drosophila/genetics
- Embryonic Development/genetics
- Evolution, Molecular
- Gene Expression Regulation, Developmental
- Models, Genetic
- Open Reading Frames/genetics
- Organogenesis/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Sachi Inagaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Japan
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18
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Regha K, Latos PA, Spahn L. The imprinted mouse Igf2r/Air cluster – a model maternal imprinting system. Cytogenet Genome Res 2006; 113:165-77. [PMID: 16575177 DOI: 10.1159/000090829] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2005] [Accepted: 09/01/2005] [Indexed: 12/30/2022] Open
Abstract
Every diploid organism inherits a complete chromosome set from its father and mother in addition to the sex chromosomes, so that all autosomal genes are available in two copies. For most genes, both copies are expressed without preference. Imprinted genes, however, are expressed depending on their parental origin, being active on the paternal or maternal allele only. To date 73 imprinted genes are known in mouse (www.mgu.har.mrc.ac.uk/research/imprinting), 37 show paternal expression while 36 show maternal expression, indicating no bias for imprinting to occur in one sex or the other. Therefore, two different parental-specific imprinting systems may have evolved in mammals, acting specifically in the paternal or maternal gamete. Similarities and differences between the two imprinting systems will be reviewed, with specific reference to the role of non-coding RNAs and chromatin modifications. The mouse Igf2r/Air cluster is presented as a model of the maternal imprinting system.
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Affiliation(s)
- K Regha
- CeMM-Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
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19
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Krawitz DC, Forrest W, Moreno GT, Kittleson J, Champion KM. Proteomic studies support the use of multi-product immunoassays to monitor host cell protein impurities. Proteomics 2006; 6:94-110. [PMID: 16302279 DOI: 10.1002/pmic.200500225] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the biopharmaceutical industry, recombinant protein drugs are commonly produced in Chinese hamster ovary (CHO) cells. During the development process, removal of CHO cell-derived proteins from the biopharmaceutical product is monitored using multi-product immunoassays. Such immunoassays are developed by raising antibodies to a single CHO cell protein preparation. However, these assays are utilized to monitor CHO cell protein impurities during the recovery of products from different CHO cell lines. To address whether underlying differences between CHO cell lines result in sufficient protein expression changes to exclude the suitability of multi-product immunoassays, a comparative proteomics study of three independently generated CHO cell lines was performed. Statistical analysis of over 1000 proteins resolved by 2-D PAGE demonstrated that the protein expression profiles of three different CHO cell lines exhibit very few differences in protein expression. Only 11 qualitative changes in protein expression and 26 quantitative changes greater than two-fold were observed. Identification of protein spots by mass spectrometry revealed that many of the observed changes were due to post-translational modifications rather than expression of novel proteins in each cell line. These results suggest that multi-product immunoassays are suitable for monitoring host cell proteins in biopharmaceuticals produced in different CHO cell lines.
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Affiliation(s)
- Denise C Krawitz
- Department of Early-Stage Analytical Development, Genentech Inc., MS #62, 1 DNA Way, South San Francisco, CA 94080, USA.
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Dahlsveen IK, Gilfillan GD, Shelest VI, Lamm R, Becker PB. Targeting determinants of dosage compensation in Drosophila. PLoS Genet 2006; 2:e5. [PMID: 16462942 PMCID: PMC1359073 DOI: 10.1371/journal.pgen.0020005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 12/05/2005] [Indexed: 11/19/2022] Open
Abstract
The dosage compensation complex (DCC) in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females. Visualization of the DCC, a large ribonucleoprotein complex, on male larval polytene chromosomes reveals that the complex binds selectively to many interbands on the X chromosome. The targeting of the DCC is thought to be in part determined by DNA sequences that are enriched on the X. So far, lack of knowledge about DCC binding sites has prevented the identification of sequence determinants. Only three binding sites have been identified to date, but analysis of their DNA sequence did not allow the prediction of further binding sites. We have used chromatin immunoprecipitation to identify a number of new DCC binding fragments and characterized them in vivo by visualizing DCC binding to autosomal insertions of these fragments, and we have demonstrated that they possess a wide range of potential to recruit the DCC. By varying the in vivo concentration of the DCC, we provide evidence that this range of recruitment potential is due to differences in affinity of the complex to these sites. We were also able to establish that DCC binding to ectopic high-affinity sites can allow nearby low-affinity sites to recruit the complex. Using the sequences of the newly identified and previously characterized binding fragments, we have uncovered a number of short sequence motifs, which in combination may contribute to DCC recruitment. Our findings suggest that the DCC is recruited to the X via a number of binding sites of decreasing affinities, and that the presence of high- and moderate-affinity sites on the X may ensure that lower-affinity sites are occupied in a context-dependent manner. Our bioinformatics analysis suggests that DCC binding sites may be composed of variable combinations of degenerate motifs.
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Affiliation(s)
- Ina K Dahlsveen
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | - Gregor D Gilfillan
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Rosemarie Lamm
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | - Peter B Becker
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
- * To whom correspondence should be addressed. E-mail:
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21
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Abstract
In many multicellular organisms, males have one X chromosome and females have two. Dosage compensation refers to a regulatory mechanism that insures the equalization of X-linked gene products in males and females. The mechanism has been studied at the molecular level in model organisms belonging to three distantly related taxa; in these organisms, equalization is achieved by shutting down one of the two X chromosomes in the somatic cells of females, by decreasing the level of transcription of the two doses of X-linked genes in females relative to males, or by increasing the level of transcription of the single dose of X-linked genes in males. The study of dosage compensation in these different forms has revealed the existence of an amazing number of interacting chromatin remodeling mechanisms that affect the function of entire chromosomes.
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Affiliation(s)
- John C Lucchesi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA.
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22
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Smith ER, Cayrou C, Huang R, Lane WS, Côté J, Lucchesi JC. A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16. Mol Cell Biol 2005; 25:9175-88. [PMID: 16227571 PMCID: PMC1265810 DOI: 10.1128/mcb.25.21.9175-9188.2005] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2005] [Revised: 05/20/2005] [Accepted: 07/26/2005] [Indexed: 02/06/2023] Open
Abstract
We describe a stable, multisubunit human histone acetyltransferase complex (hMSL) that contains homologs of the Drosophila dosage compensation proteins MOF, MSL1, MSL2, and MSL3. This complex shows strong specificity for histone H4 lysine 16 in chromatin in vitro, and RNA interference-mediated knockdown experiments reveal that it is responsible for the majority of H4 acetylation at lysine 16 in the cell. We also find that hMOF is a component of additional complexes, forming associations with host cell factor 1 and a protein distantly related to MSL1 (hMSL1v1). We find two versions of hMSL3 in the hMSL complex that differ by the presence of the chromodomain. Lastly, we find that reduction in the levels of hMSLs and acetylation of H4 at lysine 16 are correlated with reduced transcription of some genes and with a G(2)/M cell cycle arrest. This is of particular interest given the recent correlation of global loss of acetylation of lysine 16 in histone H4 with tumorigenesis.
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Affiliation(s)
- Edwin R Smith
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
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Spierer A, Seum C, Delattre M, Spierer P. Loss of the modifiers of variegation Su(var)3-7 or HP1 impacts male X polytene chromosome morphology and dosage compensation. J Cell Sci 2005; 118:5047-57. [PMID: 16234327 DOI: 10.1242/jcs.02623] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Loss of Su(var)3-7 or HP1 suppresses the genomic silencing of position-effect variegation, whereas over-expression enhances it. In addition, loss of Su(var)3-7 results in preferential male lethality. In polytene chromosomes deprived of Su(var)3-7, we observe a specific bloating of the male X chromosome, leading to shortening of the chromosome and to blurring of its banding pattern. In addition, the chromocenter, where heterochromatin from all polytene chromosomes fuses, appears decondensed. The same chromosomal phenotypes are observed as a result of loss of HP1. Mutations of Su(var)3-7 or of Su(var)2-5, the gene encoding HP1, also cause developmental defects, including a spectacular increase in size of the prothoracic gland and its polytene chromosomes. Thus, although structurally very different, the two proteins cooperate closely in chromosome organization and development. Finally, bloating of the male X chromosome in the Su(var)3-7 mutant depends on the presence of a functional dosage compensation complex on this chromosome. This observation reveals a new and intriguing genetic interaction between epigenetic silencing and compensation of dose.
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Affiliation(s)
- Anne Spierer
- Department of Zoology and Animal Biology, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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24
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Abstract
Flies, worms and mammals employ dosage compensation complexes that alter chromatin or chromosome structure to equalize X-linked gene expression between the sexes. Recent work has improved our understanding of how dosage compensation complexes achieve X chromosome-wide association and has provided significant insight into the epigenetic modifications directed by these complexes to modulate gene expression. In flies, the prevailing view that dosage compensation complexes assemble on the X chromosome at approximately 35 chromatin-entry sites and then spread in cis to cover the chromosome has been re-evaluated in light of the evidence that these chromatin-entry sites are not required for localization of the complex. By contrast, identification of discrete recruitment elements indicates that nucleation at and spread from a limited number of sites directs dosage compensation complex localization on the worm X-chromosome. Studies in flies and mammals have extended our understanding of how ribonucleoprotein complexes are used to modify X chromatin, for either activation or repression of transcription. Finally, evidence from mammals suggests that the chromatin modifications that mediate dosage compensation are very dynamic, because they are established, reversed and re-established early in development.
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Affiliation(s)
- Dmitri A Nusinow
- Department of Biochemistry and Biophysics, Genentech Hall, S374, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2200, USA
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25
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Abstract
A small but growing number of loci that exhibit covalent histone modifications, such as hyperacetylation, over broad regions of 10 kb or more have been characterized. These hyperacetylated domains occur exclusively at loci containing highly expressed, tissue-specific genes, and the available evidence suggests that they are involved in the activation of these genes. Although to date little is known concerning the formation or function of these domains, rather more is known concerning repressive, heterochromatic domains, and the example provided by heterochromatin may be instructive in considering mechanisms of active domain formation.
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Affiliation(s)
- Michael Bulger
- Center for Pediatric Biomedical Research and Department of Biochemistry and Biophysics, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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Tupy JL, Bailey AM, Dailey G, Evans-Holm M, Siebel CW, Misra S, Celniker SE, Rubin GM. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci U S A 2005; 102:5495-500. [PMID: 15809421 PMCID: PMC555963 DOI: 10.1073/pnas.0501422102] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of EST and cDNA collections from a number of metazoan species has identified genes encoding long polyadenylated transcripts that do not contain ORFs of lengths typical for protein-encoding mRNAs. Noncoding functions of such polyadenylated transcripts have been elucidated in only a few examples. The corresponding genes neither contain hallmark sequence motifs nor appear to have been conserved across phyla. Thus, it is impossible to systematically identify new members of this class of gene by using sequence homology and traditional gene-finding algorithms that depend on protein-coding potential. Consequently, even their approximate number has not been established for any metazoan genome. We curated polyadenylated transcripts with limited protein-coding capacity from intergenic regions of the Drosophila melanogaster genome. We used RT-PCR assays, hybridization to RNA blots and whole-mount embryos, and computational analyses to characterize candidate transcripts. We verify the structures and expression of 17 distinct, likely non-protein-coding polyadenylated transcripts. We show that the expression of many of these transcripts is conserved in other Drosophila species, indicating that they have important biological functions.
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Affiliation(s)
- Jonathan L Tupy
- Berkeley Drosophila Genome Project and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA
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Straub T, Dahlsveen IK, Becker PB. Dosage compensation in flies: Mechanism, models, mystery. FEBS Lett 2005; 579:3258-63. [PMID: 15943970 DOI: 10.1016/j.febslet.2005.03.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2005] [Indexed: 11/20/2022]
Abstract
Dosage compensation involves fine-tuning of gene expression at the level of entire chromosomes. The principles that assure selective targeting of the male X chromosome in Drosophila and the mechanism by which transcription levels are adjusted in a twofold range are still mysterious. We discuss the prevalent models in the context of recent experimental observations.
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Affiliation(s)
- Tobias Straub
- Adolf-Butenandt-Institut, Molekularbiologie, Schillerstrasse 44, 80336 München, Germany
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