201
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Lopes AM, Arnold-Croop SE, Amorim A, Carrel L. Clustered transcripts that escape X inactivation at mouse XqD. Mamm Genome 2011; 22:572-82. [PMID: 21769671 DOI: 10.1007/s00335-011-9350-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/08/2011] [Indexed: 12/19/2022]
Abstract
X Chromosome inactivation (XCI) silences one copy of most X-linked genes in female mammals. Notably, human and mouse differ strikingly in the number and organization of the genes that escape XCI. While on the human X Chromosome (Chr) escape genes are organized in domains, the few known genes that escape inactivation in the mouse appear to be isolated. Here we characterize the gene Cxorf26 and adjacent noncoding transcripts that map to XqD. We assess allelic expression in a nonrandomly X-inactivated cell line and directly demonstrate that 2610029G23Rik (Cxorf26) and its head-to-head neighbor (5530601H04Rik) escape X inactivation, creating a small escape domain. Both genes are robustly expressed from the inactive X Chr at approximately 50 and 30% of the expression levels of the active X, respectively. Additionally, consistent with XCI escape, the first exon of Cxorf26 is embedded within an unmethylated CpG island. To extend these results, we assayed ncRNAs adjacent to three other escape genes, Eif2s3x, Kdm5c, and Ddx3x. By allelic expression, three ncRNAs (D330035k16Rik, D930009k15Rik, and Gm16481) also escape X inactivation in the mouse, consistent with previous studies that reported female-biased expression. Altogether, these results establish that mouse escapees, like their human counterparts, can be clustered. Moreover, the fact that these ncRNAs are not found on the human X raises intriguing questions about potential regulatory roles of rapidly evolving ncRNAs in controlling escape gene expression.
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Affiliation(s)
- Alexandra M Lopes
- Institute of Molecular Pathology and Immunology of the University of Porto, R. Dr. Roberto Frias, S/N, 4200-465 Porto, Portugal.
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202
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Muñoz-Lopez M, Macia A, Garcia-Cañadas M, Badge RM, Garcia-Perez JL. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans. Mob Genet Elements 2011; 1:122-127. [PMID: 22016860 DOI: 10.4161/mge.1.2.16730] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 05/27/2011] [Indexed: 01/14/2023] Open
Abstract
The ongoing activity of the human retrotransposon Long Interspersed Element 1 (LINE-1 or L1) continues to impact the human genome in various ways. Throughout evolution, mammalian and primate genomes have been under selection to generate strategies to reduce the activity of selfish DNA like L1. Similarly, selfish DNA has evolved to elude these containment systems. This intragenomic conflict has left many inactive versions of LINEs and other Transposable Elements (TEs) littering the human genome, which together account for roughly half of our DNA. Here, we survey the distinct mechanisms operating in the human genome that seem to reduce the mobility of L1s. In addition, we discuss recent findings that strongly suggest epigenetic mechanisms specifically regulate L1 activity in pluripotent human cells.
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Affiliation(s)
- Martin Muñoz-Lopez
- Department of Human DNA Variability; GENYO (Centre Pfizer-University of Granada-Junta de Andalucía of Genomics and Oncology); Granada, Spain
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203
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Hedges DJ, Belancio VP. Restless genomes humans as a model organism for understanding host-retrotransposable element dynamics. ADVANCES IN GENETICS 2011; 73:219-62. [PMID: 21310298 DOI: 10.1016/b978-0-12-380860-8.00006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since their initial discovery in maize, there have been various attempts to categorize the relationship between transposable elements (TEs) and their host organisms. These have ranged from TEs being selfish parasites to their role as essential, functional components of organismal biology. Research over the past several decades has, in many respects, only served to complicate the issue even further. On the one hand, investigators have amassed substantial evidence concerning the negative effects that TE-mutagenic activity can have on host genomes and organismal fitness. On the other hand, we find an increasing number of examples, across several taxa, of TEs being incorporated into functional biological roles for their host organism. Some 45% of our own genomes are comprised of TE copies. While many of these copies are dormant, having lost their ability to mobilize, several lineages continue to actively proliferate in modern human populations. With its complement of ancestral and active TEs, the human genome exhibits key aspects of the host-TE dynamic that has played out since early on in organismal evolution. In this review, we examine what insights the particularly well-characterized human system can provide regarding the nature of the host-TE interaction.
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Affiliation(s)
- Dale J Hedges
- Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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204
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Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 2011; 21:813-20. [PMID: 21632748 PMCID: PMC3106314 DOI: 10.1101/gr.110528.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
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Affiliation(s)
- David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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205
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Kitkumthorn N, Mutirangura A. Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clin Epigenetics 2011; 2:315-30. [PMID: 22704344 PMCID: PMC3365388 DOI: 10.1007/s13148-011-0032-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/20/2011] [Indexed: 12/31/2022] Open
Abstract
Epigenetic changes in long interspersed nuclear element-1s (LINE-1s or L1s) occur early during the process of carcinogenesis. A lower methylation level (hypomethylation) of LINE-1 is common in most cancers, and the methylation level is further decreased in more advanced cancers. Consequently, several previous studies have suggested the use of LINE-1 hypomethylation levels in cancer screening, risk assessment, tumor staging, and prognostic prediction. Epigenomic changes are complex, and global hypomethylation influences LINE-1s in a generalized fashion. However, the methylation levels of some loci are dependent on their locations. The consequences of LINE-1 hypomethylation are genomic instability and alteration of gene expression. There are several mechanisms that promote both of these consequences in cis. Therefore, the methylation levels of different sets of LINE-1s may represent certain phenotypes. Furthermore, the methylation levels of specific sets of LINE-1s may indicate carcinogenesis-dependent hypomethylation. LINE-1 methylation pattern analysis can classify LINE-1s into one of three classes based on the number of methylated CpG dinucleotides. These classes include hypermethylation, partial methylation, and hypomethylation. The number of partial and hypermethylated loci, but not hypomethylated LINE-1s, is different among normal cell types. Consequently, the number of hypomethylated loci is a more promising marker than methylation level in the detection of cancer DNA. Further genome-wide studies to measure the methylation level of each LINE-1 locus may improve PCR-based methylation analysis to allow for a more specific and sensitive detection of cancer DNA or for an analysis of certain cancer phenotypes.
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206
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Aporntewan C, Phokaew C, Piriyapongsa J, Ngamphiw C, Ittiwut C, Tongsima S, Mutirangura A. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PLoS One 2011; 6:e17934. [PMID: 21423624 PMCID: PMC3057998 DOI: 10.1371/journal.pone.0017934] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/18/2011] [Indexed: 01/23/2023] Open
Abstract
In human cancers, the methylation of long interspersed nuclear element -1 (LINE-1
or L1) retrotransposons is reduced. This occurs within the context of genome
wide hypomethylation, and although it is common, its role is poorly understood.
L1s are widely distributed both inside and outside of genes, intragenic and
intergenic, respectively. Interestingly, the insertion of active full-length L1
sequences into host gene introns disrupts gene expression. Here, we evaluated if
intragenic L1 hypomethylation influences their host gene expression in cancer.
First, we extracted data from L1base (http://l1base.molgen.mpg.de), a database containing putatively
active L1 insertions, and compared intragenic and intergenic L1 characters. We
found that intragenic L1 sequences have been conserved across evolutionary time
with respect to transcriptional activity and CpG dinucleotide sites for
mammalian DNA methylation. Then, we compared regulated mRNA levels of cells from
two different experiments available from Gene Expression Omnibus (GEO), a
database repository of high throughput gene expression data, (http://www.ncbi.nlm.nih.gov/geo) by chi-square. The odds ratio
of down-regulated genes between demethylated normal bronchial epithelium and
lung cancer was high (p<1E−27;
OR = 3.14; 95%
CI = 2.54–3.88), suggesting cancer genome wide
hypomethylation down-regulating gene expression. Comprehensive analysis between
L1 locations and gene expression showed that expression of genes containing L1s
had a significantly higher likelihood to be repressed in cancer and
hypomethylated normal cells. In contrast, many mRNAs derived from genes
containing L1s are elevated in Argonaute 2 (AGO2 or EIF2C2)-depleted cells.
Hypomethylated L1s increase L1 mRNA levels. Finally, we found that AGO2 targets
intronic L1 pre-mRNA complexes and represses cancer genes. These findings
represent one of the mechanisms of cancer genome wide hypomethylation altering
gene expression. Hypomethylated intragenic L1s are a nuclear siRNA mediated
cis-regulatory element that can repress genes. This
epigenetic regulation of retrotransposons likely influences many aspects of
genomic biology.
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Affiliation(s)
- Chatchawit Aporntewan
- Department of Mathematics, Faculty of Science,
Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Inter-Department Program of BioMedical
Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok,
Thailand
| | - Jittima Piriyapongsa
- National Center for Genetic Engineering and
Biotechnology, Genome Institute, Thailand Science Park, Pathumtani,
Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and
Biotechnology, Genome Institute, Thailand Science Park, Pathumtani,
Thailand
| | - Chupong Ittiwut
- Department of Anatomy, Faculty of Medicine,
Center of Excellence in Molecular Genetics of Cancer and Human Diseases,
Chulalongkorn University, Bangkok, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and
Biotechnology, Genome Institute, Thailand Science Park, Pathumtani,
Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine,
Center of Excellence in Molecular Genetics of Cancer and Human Diseases,
Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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207
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Ogino S, Chan AT, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field. Gut 2011; 60:397-411. [PMID: 21036793 PMCID: PMC3040598 DOI: 10.1136/gut.2010.217182] [Citation(s) in RCA: 436] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is a complex disease resulting from somatic genetic and epigenetic alterations, including locus-specific CpG island methylation and global DNA or LINE-1 hypomethylation. Global molecular characteristics such as microsatellite instability (MSI), CpG island methylator phenotype (CIMP), global DNA hypomethylation, and chromosomal instability cause alterations of gene function on a genome-wide scale. Activation of oncogenes including KRAS, BRAF and PIK3CA affects intracellular signalling pathways and has been associated with CIMP and MSI. Traditional epidemiology research has investigated various factors in relation to an overall risk of colon and/or rectal cancer. However, colorectal cancers comprise a heterogeneous group of diseases with different sets of genetic and epigenetic alterations. To better understand how a particular exposure influences the carcinogenic and pathologic process, somatic molecular changes and tumour biomarkers have been studied in relation to the exposure of interest. Moreover, an investigation of interactive effects of tumour molecular changes and the exposures of interest on tumour behaviour (prognosis or clinical outcome) can lead to a better understanding of tumour molecular changes, which may be prognostic or predictive tissue biomarkers. These new research efforts represent 'molecular pathologic epidemiology', which is a multidisciplinary field of investigations of the inter-relationship between exogenous and endogenous (eg, genetic) factors, tumoural molecular signatures and tumour progression. Furthermore, integrating genome-wide association studies (GWAS) with molecular pathological investigation is a promising area (GWAS-MPE approach). Examining the relationship between susceptibility alleles identified by GWAS and specific molecular alterations can help elucidate the function of these alleles and provide insights into whether susceptibility alleles are truly causal. Although there are challenges, molecular pathological epidemiology has unique strengths, and can provide insights into the pathogenic process and help optimise personalised prevention and therapy. In this review, we overview this relatively new field of research and discuss measures to overcome challenges and move this field forward.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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208
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Singh V, Mishra RK. RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes. BMC Bioinformatics 2010; 11:609. [PMID: 21184688 PMCID: PMC3024322 DOI: 10.1186/1471-2105-11-609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 12/26/2010] [Indexed: 01/19/2023] Open
Abstract
Background - The availability of multiple whole genome sequences has facilitated in silico identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and forensic analysis, fixed species-specific transposon insertions, when compared to orthologous loci in other closely related species, may give insights into their evolutionary significance. Besides, TE insertions are not isolated events and are frequently associated with subtle sequence changes concurrent with insertion or post insertion. These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied independently, no automated platform to identify differential transposon insertions and the associated array of sequence changes in genomes of the same or closely related species is available till date. To this end, we have designed RISCI - 'Repeat Induced Sequence Changes Identifier' - a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify differential transposon insertions and associated sequence changes using specific alignment signatures, which may then be examined for their downstream effects. Results - We showcase the utility of RISCI by comparing full length and truncated L1HS and AluYa5 retrotransposons in the reference human genome with the chimpanzee genome and the alternate human assemblies (Celera and HuRef). Comparison of the reference human genome with alternate human assemblies using RISCI predicts 14 novel polymorphisms in full length L1HS, 24 in truncated L1HS and 140 novel polymorphisms in AluYa5 insertions, besides several insertion and post insertion changes. We present comparison with two previous studies to show that RISCI predictions are broadly in agreement with earlier reports. We also demonstrate its versatility by comparing various strains of Mycobacterium tuberculosis for IS 6100 insertion polymorphism. Conclusions - RISCI combines comparative genomics with subtractive hybridization, inferring changes only when exclusive to one of the two genomes being compared. The pipeline is generic and may be applied to most transposons and to any two or more genomes sharing high sequence similarity. Such comparisons, when performed on a larger scale, may pull out a few critical events, which may have seeded the divergence between the two species under comparison.
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Affiliation(s)
- Vipin Singh
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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209
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Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol 2010; 31:300-16. [PMID: 21041477 DOI: 10.1128/mcb.00561-10] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Long interspersed element 1s (LINE-1s or L1s) are a family of non-long-terminal-repeat retrotransposons that predominate in the human genome. Active LINE-1 elements encode proteins required for their mobilization. L1-encoded proteins also act in trans to mobilize short interspersed elements (SINEs), such as Alu elements. L1 and Alu insertions have been implicated in many human diseases, and their retrotransposition provides an ongoing source of human genetic diversity. L1/Alu elements are expected to ensure their transmission to subsequent generations by retrotransposing in germ cells or during early embryonic development. Here, we determined that several subfamilies of Alu elements are expressed in undifferentiated human embryonic stem cells (hESCs) and that most expressed Alu elements are active elements. We also exploited expression from the L1 antisense promoter to map expressed elements in hESCs. Remarkably, we found that expressed Alu elements are enriched in the youngest subfamily, Y, and that expressed L1s are mostly located within genes, suggesting an epigenetic control of retrotransposon expression in hESCs. Together, these data suggest that distinct subsets of active L1/Alu elements are expressed in hESCs and that the degree of somatic mosaicism attributable to L1 insertions during early development may be higher than previously anticipated.
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210
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Kim DS, Hahn Y. Identification of human-specific transcript variants induced by DNA insertions in the human genome. ACTA ACUST UNITED AC 2010; 27:14-21. [PMID: 21037245 DOI: 10.1093/bioinformatics/btq612] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MOTIVATION Many genes in the human genome produce a wide variety of transcript variants resulting from alternative exon splicing, differential promoter usage, or altered polyadenylation site utilization that may function differently in human cells. Here, we present a bioinformatics method for the systematic identification of human-specific novel transcript variants that might have arisen after the human-chimpanzee divergence. RESULTS The procedure involved collecting genomic insertions that are unique to the human genome when compared with orthologous chimpanzee and rhesus macaque genomic regions, and that are expressed in the transcriptome as exons evidenced by mRNAs and/or expressed sequence tags (ESTs). Using this procedure, we identified 112 transcript variants that are specific to humans; 74 were associated with known genes and the remaining transcripts were located in unannotated genomic loci. The original source of inserts was mostly transposable elements including L1, Alu, SVA, and human endogenous retroviruses (HERVs). Interestingly, some non-repetitive genomic segments were also involved in the generation of novel transcript variants. Insert contributions to the transcripts included promoters, terminal exons and insertions in exons, splice donors and acceptors and complete exon cassettes. Comparison of personal genomes revealed that at least seven loci were polymorphic in humans. The exaptation of human-specific genomic inserts as novel transcript variants may have increased human gene versatility or affected gene regulation.
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Affiliation(s)
- Dong Seon Kim
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, Korea
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211
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Rouchka E, Montoya-Durango DE, Stribinskis V, Ramos K, Kalbfleisch T. Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. BMC Bioinformatics 2010; 11 Suppl 9:S12. [PMID: 21044359 PMCID: PMC2967742 DOI: 10.1186/1471-2105-11-s9-s12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site. Results In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother/father/daughter trio. Conclusions It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.
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Affiliation(s)
- Eric Rouchka
- Computer Engineering and Computer Science Department, Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA.
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212
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Lizardi PM. As we bring demethylating drugs to the clinic, we better know the DICE being cast. Oncogene 2010; 29:5772-4. [DOI: 10.1038/onc.2010.372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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213
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Mobile interspersed repeats are major structural variants in the human genome. Cell 2010; 141:1171-82. [PMID: 20602999 DOI: 10.1016/j.cell.2010.05.026] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 03/29/2010] [Accepted: 05/13/2010] [Indexed: 01/22/2023]
Abstract
Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further.
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214
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Belancio VP, Roy-Engel AM, Deininger PL. All y'all need to know 'bout retroelements in cancer. Semin Cancer Biol 2010; 20:200-10. [PMID: 20600922 DOI: 10.1016/j.semcancer.2010.06.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/14/2010] [Accepted: 06/17/2010] [Indexed: 01/08/2023]
Abstract
Genetic instability is one of the principal hallmarks and causative factors in cancer. Human transposable elements (TE) have been reported to cause human diseases, including several types of cancer through insertional mutagenesis of genes critical for preventing or driving malignant transformation. In addition to retrotransposition-associated mutagenesis, TEs have been found to contribute even more genomic rearrangements through non-allelic homologous recombination. TEs also have the potential to generate a wide range of mutations derivation of which is difficult to directly trace to mobile elements, including double strand breaks that may trigger mutagenic genomic rearrangements. Genome-wide hypomethylation of TE promoters and significantly elevated TE expression in almost all human cancers often accompanied by the loss of critical DNA sensing and repair pathways suggests that the negative impact of mobile elements on genome stability should increase as human tumors evolve. The biological consequences of elevated retroelement expression, such as the rate of their amplification, in human cancers remain obscure, particularly, how this increase translates into disease-relevant mutations. This review is focused on the cellular mechanisms that control human TE-associated mutagenesis in cancer and summarizes the current understanding of TE contribution to genetic instability in human malignancies.
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Affiliation(s)
- Victoria P Belancio
- Tulane University, Department of Structural and Cellular Biology, School of Medicine, Tulane Cancer Center and Tulane Center for Aging, New Orleans, LA 70112, USA
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215
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Weber B, Kimhi S, Howard G, Eden A, Lyko F. Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription. Oncogene 2010; 29:5775-84. [DOI: 10.1038/onc.2010.227] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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216
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Abstract
Retrotransposons like L1 are silenced in somatic cells by a
variety of mechanisms acting at different levels. Protective
mechanisms include DNA methylation and packaging into inactive
chromatin to suppress transcription and prevent recombination,
potentially supported by cytidine deaminase editing of RNA.
Furthermore, DNA strand breaks arising during attempted
retrotranspositions ought to activate cellular checkpoints, and L1
activation outside immunoprivileged sites may elicit immune
responses. A number of observations indicate that L1 sequences
nevertheless become reactivated in human cancer. Prominently,
methylation of L1 sequences is diminished in many cancer types and
full-length L1 RNAs become detectable, although strong expression
is restricted to germ cell cancers. L1 elements have been found to
be enriched at sites of illegitimate recombination in many
cancers. In theory, lack of L1 repression in cancer might cause
transcriptional deregulation, insertional mutations, DNA breaks,
and an increased frequency of recombinations, contributing to
genome disorganization, expression changes, and chromosomal
instability. There is however little evidence that such effects
occur at a gross scale in human cancers. Rather, as a rule, L1
repression is only partly alleviated. Unfortunately, many
techniques commonly used to investigate genetic and epigenetic
alterations in cancer cells are not well suited to detect subtle
effects elicited by partial reactivation of retroelements like L1
which are present as abundant, but heterogeneous copies.
Therefore, effects of L1 sequences exerted on the local chromatin
structure, on the transcriptional regulation of individual genes,
and on chromosome fragility need to be more closely investigated
in normal and cancer cells.
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Affiliation(s)
- Wolfgang A. Schulz
- Department of Urology, Heinrich Heine University, Mooreustrasse 5, 40225 Düsseldorf, Germany
- *Wolfgang A. Schulz:
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217
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Abstract
Long interspersed elements (LINE-1 or L1) are the most active
transposable elements in the human genome. Due to their high copy
number and ability to sponsor retrotransposition of nonautonomous
RNA sequences, unchecked L1 activity can negatively impact the
genome by a number of means. Substantial evidence in lower
eukaryotes demonstrates that the RNA interference (RNAi) machinery
plays a major role in containing transposon activity. Despite
extensive analysis in other eukaryotes, no experimental evidence
has been presented that L1-derived siRNAs exist, or that the RNAi
plays a significant role in restricting L1 activity in the human
genome. This review will present evidence showing a direct role
for RNAi in suppressing the movement of transposable elements in
other eukaryotes, as well as speculate on the role RNAi might play
in protecting the human genome from LINE-1 activity.
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Affiliation(s)
- Harris S. Soifer
- Beckman Research Institute of the City of Hope, Fox North 2002, 1450 East Duarte Road, Duarte, CA 91010-3011, USA
- *Harris S. Soifer:
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218
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Mätlik K, Redik K, Speek M. L1 antisense promoter drives tissue-specific transcription of human genes. J Biomed Biotechnol 2010; 2006:71753. [PMID: 16877819 PMCID: PMC1559930 DOI: 10.1155/jbb/2006/71753] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription of transposable elements interspersed in the genome
is controlled by complex interactions between their regulatory
elements and host factors. However, the same regulatory elements
may be occasionally used for the transcription of host genes. One
such example is the human L1 retrotransposon, which contains an
antisense promoter (ASP) driving transcription into adjacent genes
yielding chimeric transcripts. We have characterized 49 chimeric
mRNAs corresponding to sense and antisense strands of human genes.
Here we show that L1 ASP is capable of functioning as an
alternative promoter, giving rise to a chimeric transcript whose
coding region is identical to the ORF of mRNA of the following
genes: KIAA1797, CLCN5, and SLCO1A2.
Furthermore, in these cases the activity of L1 ASP is
tissue-specific and may expand the expression pattern of the
respective gene. The activity of L1 ASP is tissue-specific also in
cases where L1 ASP produces antisense RNAs complementary to
COL11A1 and BOLL mRNAs. Simultaneous assessment
of the activity of L1 ASPs in multiple loci revealed the presence
of L1 ASP-derived transcripts in all human tissues examined. We
also demonstrate that L1 ASP can act as a promoter in vivo and
predict that it has a heterogeneous transcription initiation site.
Our data suggest that L1 ASP-driven transcription may increase the
transcriptional flexibility of several human genes.
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Affiliation(s)
- Kert Mätlik
- Department of Gene Technology, Tallinn University of
Technology, Akadeemia tee 15, Tallinn 19086, Estonia
| | - Kaja Redik
- Department of Gene Technology, Tallinn University of
Technology, Akadeemia tee 15, Tallinn 19086, Estonia
| | - Mart Speek
- Department of Gene Technology, Tallinn University of
Technology, Akadeemia tee 15, Tallinn 19086, Estonia
- *Mart Speek:
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Horman SR, Svoboda P, Luning Prak ET. The potential regulation of L1 mobility by RNA interference. J Biomed Biotechnol 2010; 2006:32713. [PMID: 16877813 PMCID: PMC1559915 DOI: 10.1155/jbb/2006/32713] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The hypothesis that RNA interference constrains L1 mobility seems
inherently reasonable: L1 mobility can be dangerous and L1 RNA,
the presumed target of RNAi, serves as a critical
retrotransposition intermediate. Despite its plausibility, proof
for this hypothesis has been difficult to obtain. Studies
attempting to link the L1 retrotransposition frequency to
alterations in RNAi activity have been hampered by the long times
required to measure retrotransposition frequency, the pleiotropic
and toxic effects of altering RNAi over similar time periods, and
the possibility that other cellular machinery may contribute to
the regulation of L1s. Another problem is that the commonly used
L1 reporter cassette may serve as a substrate for RNAi. Here we
review the L1-RNAi hypothesis and describe a genetic assay with a
modified reporter cassette that detects approximately 4 times more
L1 insertions than the conventional retrotransposition assay.
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Affiliation(s)
- Shane R. Horman
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia,
PA 19104-6055, USA
| | - Petr Svoboda
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia,
PA 19104-6055, USA
- *Eline T. Luning Prak:
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220
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Baba Y, Huttenhower C, Nosho K, Tanaka N, Shima K, Hazra A, Schernhammer ES, Hunter DJ, Giovannucci EL, Fuchs CS, Ogino S. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Mol Cancer 2010; 9:125. [PMID: 20507599 PMCID: PMC2892454 DOI: 10.1186/1476-4598-9-125] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 05/27/2010] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon) constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features. DESIGN Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing). Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP), microsatellite instability, expression of TP53 (p53), CDKN1A (p21), CTNNB1 (beta-catenin), PTGS2 (cyclooxygenase-2), and FASN, and mutations in KRAS, BRAF, and PIK3CA. RESULTS Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6), and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation < 40; N = 22 (2.5%), which were far more than what could be expected by normal distribution]. LINE-1 extreme hypomethylators were significantly associated with younger patients (p = 0.0058). Residual plot by multivariate linear regression showed that LINE-1 extreme hypomethylators clustered as one distinct group, separate from the main tumor group. The multivariate linear regression model could explain 8.4% of the total variability of LINE-1 methylation (R-square = 0.084). Multivariate logistic regression models for binary LINE-1 hypomethylation outcomes (cutoffs of 40, 50 and 60) showed at most fair predictive ability (area under receiver operator characteristics curve < 0.63). CONCLUSIONS LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.
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Affiliation(s)
- Yoshifumi Baba
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
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221
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Huh JW, Kim YH, Lee SR, Kim DS, Park SJ, Kim H, Kim JS, Song BS, Kim HS, Chang KT. Four different ways of alternative transcripts generation mechanism in ADRA1A gene. Genes Genet Syst 2010; 85:65-73. [PMID: 20410666 DOI: 10.1266/ggs.85.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The ADRA1A (Alpha-1-adrenergic receptor) gene is one of the members of G protein-coupled receptor superfamily. Alternative splicing of this gene was known to generate four transcript variants which code four isoforms with various C-terminal regions. In this study, we conducted expression analysis and evolutionary characterization of alternative transcripts of the ADRA1A gene. In total, 10 alternative transcripts were identified using experimental approaches and in silico analysis. Among them, 6 alternative transcripts (T1, T2, T3, T4, T4-1, and T8) were validated by RT-PCR approaches and sequencing procedures. From the alternative splicing analysis, it could be assumed that there were three different alternative transcripts generation mechanisms and unknown mechanism. First one is the integration event of three different TEs (AluSc, L1MC5, and MIR3) as seen on the last exons of T3, T4, T4-1, T5, T6, and T7 transcripts. The second mechanism is a differential promoter usage on T8. The third one is a substitution event of the 3' splicing site during the primate evolution on T3. The last one is an unknown mechanism which was identified in the T4-1 transcript. Therefore, alternative transcripts of human ADRA1A gene occurred by four different ways, such as integration of TEs, differential promoter usage, substitution of splicing sites, and unknown mechanism.
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Affiliation(s)
- Jae-Won Huh
- National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-833, Republic of Korea
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222
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Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet 2010; 6:e1000917. [PMID: 20421991 PMCID: PMC2858672 DOI: 10.1371/journal.pgen.1000917] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 03/19/2010] [Indexed: 12/31/2022] Open
Abstract
It was recently shown that a large portion of the human transcriptome can originate from within repetitive elements, leading to ectopic expression of protein-coding genes. However the mechanism of transcriptional activation of repetitive elements has not been definitively elucidated. For the first time, we directly demonstrate that hypomethylation of retrotransposons can cause altered gene expression in humans. We also reveal that active LINE-1s switch from a tetranucleosome to dinucleosome structure, acquiring H2A.Z- and nucleosome-free regions upstream of TSSs, previously shown only at active single-copy genes. Hypomethylation of a specific LINE-1 promoter was also found to induce an alternate transcript of the MET oncogene in bladder tumors and across the entire urothelium of tumor-bearing bladders. These data show that, in addition to contributing to chromosomal instability, hypomethylation of LINE-1s can alter the functional transcriptome and plays a role not only in human disease but also in disease predisposition. A surprisingly large portion of our transcriptome originates within repetitive elements, most commonly LINE-1s. However, the mechanism of activation has not been definitively shown. We directly demonstrate for the first time the causal relationship between DNA hypomethylation and transcriptional activation of LINE-1 promoters. Hypomethylation of specific LINE-1 promoters can alter the transcriptome, including activating an alternate transcript of the MET oncogene, not only in primary bladder tumors but also in premalignant urothelium across entire bladders with tumors. Our study has important implications for tumor biology, cancer detection, and treatment, and it also answers the long-standing question of whether hypomethylation of retrotransposons induces ectopic gene expression and influences disease susceptibility in humans, a phenomenon first described in agouti mice.
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Affiliation(s)
- Erika M. Wolff
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Hyang-Min Byun
- Department of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Han F. Han
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Pharmacology and Pharmaceutical Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Shikhar Sharma
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peter W. Nichols
- Department of Pathology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Allen S. Yang
- Department of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peter A. Jones
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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223
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Konkel MK, Batzer MA. A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. Semin Cancer Biol 2010; 20:211-21. [PMID: 20307669 DOI: 10.1016/j.semcancer.2010.03.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 03/04/2010] [Accepted: 03/16/2010] [Indexed: 02/06/2023]
Abstract
It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families - long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements - mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development.
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
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224
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Mourier T, Willerslev E. Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons. BMC Genomics 2010; 11:167. [PMID: 20226011 PMCID: PMC2848245 DOI: 10.1186/1471-2164-11-167] [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] [Received: 10/20/2009] [Accepted: 03/12/2010] [Indexed: 12/02/2022] Open
Abstract
Background Retrotransposons are transposable elements that proliferate within eukaryotic genomes through a process involving reverse transcription. The numbers of retrotransposons within genomes and differences between closely related species may yield insight into the evolutionary history of the elements. Less is known about the ongoing dynamics of retrotransposons, as analysis of genome sequences will only reveal insertions of retrotransposons that are fixed - or near fixation - in the population or strain from which genetic material has been extracted for sequencing. One pre-requisite for retrotransposition is transcription of the elements. Given their intrinsic sequence redundancy, transcriptome-level analyses of transposable elements are scarce. We have used recently published transcriptome data from the fission yeast Schizosaccharomyces pombe to assess the ability to detect and describe transcriptional activity from Long Terminal Repeat (LTR) retrotransposons. LTR retrotransposons are normally flanked by two LTR sequences. However, the majority of LTR sequences in S. pombe exist as solitary LTRs, i.e. as single terminal repeat sequences not flanking a retrotransposon. Transcriptional activity was analysed for both full-length LTR retrotransposons and solitary LTRs. Results Two independent sets of transcriptome data reveal the presence of full-length, polyadenylated transcripts from LTR retrotransposons in S. pombe during growth phase in rich medium. The redundancy of retrotransposon sequences makes it difficult to assess which elements are transcriptionally active, but data strongly indicates that only a subset of the LTR retrotransposons contribute significantly to the detected transcription. A considerable level of reverse strand transcription is also detected. Equal levels of transcriptional activity are observed from both strands of solitary LTR sequences. Transcriptome data collected during meiosis suggests that transcription of solitary LTRs is correlated with the transcription of nearby protein-coding genes. Conclusions Presumably, the host organism negatively regulates proliferation of LTR retrotransposons. The finding of considerable transcriptional activity of retrotransposons suggests that part of this regulation is likely to take place at a post-transcriptional level. Alternatively, the transcriptional activity may signify a hitherto unrecognized activity level of retrotransposon proliferation. Our findings underline the usefulness of transcriptome data in elucidating dynamics in retrotransposon transcription.
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Affiliation(s)
- Tobias Mourier
- Ancient DNA and Evolution Group, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark.
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225
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Belancio VP, Deininger PL, Roy-Engel AM. LINE dancing in the human genome: transposable elements and disease. Genome Med 2009; 1:97. [PMID: 19863772 PMCID: PMC2784310 DOI: 10.1186/gm97] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transposable elements (TEs) have been consistently underestimated in their contribution to genetic instability and human disease. TEs can cause human disease by creating insertional mutations in genes, and also contributing to genetic instability through non-allelic homologous recombination and introduction of sequences that evolve into various cis-acting signals that alter gene expression. Other outcomes of TE activity, such as their potential to cause DNA double-strand breaks or to modulate the epigenetic state of chromosomes, are less fully characterized. The currently active human transposable elements are members of the non-LTR retroelement families, LINE-1, Alu (SINE), and SVA. The impact of germline insertional mutagenesis by TEs is well established, whereas the rate of post-insertional TE-mediated germline mutations and all forms of somatic mutations remain less well quantified. The number of human diseases discovered to be associated with non-allelic homologous recombination between TEs, and particularly between Alu elements, is growing at an unprecedented rate. Improvement in the technology for detection of such events, as well as the mounting interest in the research and medical communities in resolving the underlying causes of the human diseases with unknown etiology, explain this increase. Here, we focus on the most recent advances in understanding of the impact of the active human TEs on the stability of the human genome and its relevance to human disease.
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Affiliation(s)
- Victoria P Belancio
- Department of Structural and Cellular Biology, School of Medicine, Tulane Cancer Center and Tulane Center for Aging, Tulane University, SL-49 1430 Tulane Ave, New Orleans, LA 70112, USA.
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226
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Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009; 10:691-703. [PMID: 19763152 DOI: 10.1038/nrg2640] [Citation(s) in RCA: 1104] [Impact Index Per Article: 73.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons--including LINE-1, Alu and SVA elements--have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage.
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Affiliation(s)
- Richard Cordaux
- CNRS UMR 6556 Ecologie, Evolution, Symbiose, Université de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France
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227
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Rangwala SH, Zhang L, Kazazian HH. Many LINE1 elements contribute to the transcriptome of human somatic cells. Genome Biol 2009; 10:R100. [PMID: 19772661 PMCID: PMC2768975 DOI: 10.1186/gb-2009-10-9-r100] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/21/2009] [Accepted: 09/22/2009] [Indexed: 11/29/2022] Open
Abstract
Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome. Background While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to the transcriptome of human somatic cells? We have cloned out expressed sequence tags corresponding to the 5' and 3' flanks of L1 elements in order to characterize the population of elements that are being actively transcribed. We also examined expression of a select number of elements in different individuals. Results We isolated expressed sequence tags from human lymphoblastoid cell lines corresponding to 692 distinct L1 element sites, including 410 full-length elements. Four of the expression tagged sites corresponding to full-length elements from the human specific L1Hs subfamily were examined in European-American individuals and found to be differentially expressed in different family members. Conclusions A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
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Affiliation(s)
- Sanjida H Rangwala
- Department of Genetics, University of Pennsylvania School of Medicine, Hamilton Walk, Philadelphia, Pennsylvania 19104, USA.
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228
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Mourier T, Willerslev E. Retrotransposons and non-protein coding RNAs. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:493-501. [PMID: 19729447 DOI: 10.1093/bfgp/elp036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Retrotransposons constitute a significant fraction of mammalian genomes. Considering the finding of widespread transcriptional activity across entire genomes, it is not surprising that retrotransposons contribute to the collective RNA pool. However, the transcriptional output from retrotransposons does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review the emerging understanding of how retrotransposons themselves are regulated by small RNAs.
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Affiliation(s)
- Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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229
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Huh JW, Kim YH, Lee SR, Kim H, Kim DS, Kim HS, Kang HS, Chang KT. Gain of new exons and promoters by lineage-specific transposable elements-integration and conservation event on CHRM3 gene. Mol Cells 2009; 28:111-7. [PMID: 19669628 DOI: 10.1007/s10059-009-0106-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 06/09/2009] [Accepted: 06/23/2009] [Indexed: 10/20/2022] Open
Abstract
The CHRM3 gene is a member of the muscarinic acetylcholine receptor family that plays important roles in the regulation of fundamental physiological functions. The evolutionary mechanism of exon-acquisition and alternative splicing of the CHRM3 gene in relation to transposable elements (TEs) were analyzed using experimental approaches and in silico analysis. Five different transcript variants (T1, T2, T3, T3-1, and T4) derived from three distinct promoter regions (T1: L1HS, T2, T4: original, T3, T3-1: THE1C) were identified. A placenta (T1) and testis (T3 and T3-1)-dominated expression pattern appeared to be controlled by different TEs (L1HS and THE1C) that were integrated into the common ancestor genome during primate evolution. Remarkably, the T1 transcript was formed by the integration event of the human specific L1HS element. Among the 12 different brain regions, the brain stem, olfactory region, and cerebellum showed decreased expression patterns. Evolutionary analysis of splicing sites and alternative splicing suggested that the exon-acquisition event was determined by a selection and conservation mechanism. Furthermore, continuous integration events of transposable elements could produce lineage specific alternative transcripts by providing novel promoters and splicing sites. Taken together, exon-acquisition and alternative splicing events of CHRM3 genes were shown to have occurred through the continuous integration of transposable elements following conservation.
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Affiliation(s)
- Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, 363-883, Korea
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230
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Cruickshanks HA, Tufarelli C. Isolation of cancer-specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter. Genomics 2009; 94:397-406. [PMID: 19720139 DOI: 10.1016/j.ygeno.2009.08.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 08/10/2009] [Accepted: 08/22/2009] [Indexed: 11/19/2022]
Abstract
The antisense promoter of human LINE-1 (L1) retroelements can direct transcription of adjacent unique genomic sequences generating chimeric RNAs, which can perturb transcription of neighbouring genes. As L1 elements constitute 17% of the human genome, chimeric transcription is potentially widespread, but the extent to which this occurs is largely unknown. Using a genome-wide screen we have isolated novel chimeric transcripts that are unique to breast cancer cell lines, primary tumours and colon cancer cells. Expression of the cancer-specific chimeric transcripts can be induced in non-malignant breast epithelial cells by the demethylating drug 5-azacytidine. These findings indicate that loss of L1 methylation in cancer cells is linked to the expression of L1-chimeric transcripts which may therefore constitute a useful set of markers of malignancy.
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MESH Headings
- Azacitidine/pharmacology
- Breast/cytology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cell Line, Tumor/drug effects
- Cell Line, Tumor/metabolism
- Cells, Cultured/drug effects
- Cells, Cultured/metabolism
- Colonic Neoplasms/genetics
- Colonic Neoplasms/pathology
- DNA Methylation/drug effects
- Female
- Humans
- Long Interspersed Nucleotide Elements/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/isolation & purification
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription, Genetic/drug effects
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Affiliation(s)
- Hazel A Cruickshanks
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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231
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Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene 2009; 448:151-67. [PMID: 19699787 DOI: 10.1016/j.gene.2009.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/19/2009] [Accepted: 08/06/2009] [Indexed: 12/18/2022]
Abstract
Close to 50% of the human genome harbors repetitive sequences originally derived from mobile DNA elements, and in normal cells, this sequence compartment is tightly regulated by epigenetic silencing mechanisms involving chromatin-mediated repression. In cancer cells, repetitive DNA elements suffer abnormal demethylation, with potential loss of silencing. We used a genome-wide microarray approach to measure DNA methylation changes in cancers of the head and neck and to compare these changes to alterations found in adjacent non-tumor tissues. We observed specific alterations at thousands of small clusters of CpG dinucleotides associated with DNA repeats. Among the 257,599 repetitive elements probed, 5% to 8% showed disease-related DNA methylation alterations. In dysplasia, a large number of local events of loss of methylation appear in apparently stochastic fashion. Loss of DNA methylation is most pronounced for certain members of the SVA, HERV, LINE-1P, AluY, and MaLR families. The methylation levels of retrotransposons are discretely stratified, with younger elements being highly methylated in healthy tissues, while in tumors, these young elements suffer the most dramatic loss of methylation. Wilcoxon test statistics reveals that a subset of primate LINE-1 elements is demethylated preferentially in tumors, as compared to non-tumoral adjacent tissue. Sequence analysis of these strongly demethylated elements reveals genomic loci harboring full length, as opposed to truncated elements, while possible enrichment for functional LINE-1 ORFs is weaker. Our analysis suggests that, in non-tumor adjacent tissues, there is generalized and highly variable disruption of epigenetic control across the repetitive DNA compartment, while in tumor cells, a specific subset of LINE-1 retrotransposons that arose during primate evolution suffers the most dramatic DNA methylation alterations.
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Affiliation(s)
- Sebastian Szpakowski
- Interdepartmental Program in Computational, Biology and Bioinformatics, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA
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The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 2009; 41:563-71. [PMID: 19377475 DOI: 10.1038/ng.368] [Citation(s) in RCA: 592] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 03/05/2009] [Indexed: 12/14/2022]
Abstract
Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5' of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3' UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.
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234
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Beauregard A, Curcio MJ, Belfort M. The take and give between retrotransposable elements and their hosts. Annu Rev Genet 2009; 42:587-617. [PMID: 18680436 DOI: 10.1146/annurev.genet.42.110807.091549] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths. For this review, we have selected for our focus elements from among target-primed (TP) retrotransposons, also called non-LTR retrotransposons, and extrachromosomally-primed (EP) retrotransposons, also called LTR retrotransposons. The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elements considered are the Ty and Tf retrotransposons, with a brief comparison to retroviruses. Recurring themes for these elements, in hosts ranging from bacteria to humans, are tie-ins of the retrotransposons to RNA metabolism, DNA replication and repair, and cellular stress. Likewise, there are parallels among host-cell defenses to combat rampant retrotransposon spread. The interactions between the retrotransposon and the host, and their coevolution to balance the tension between retrotransposon proliferation and host survival, form the basis of this review.
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Affiliation(s)
- Arthur Beauregard
- New York State Department of Health, Center for Medical Sciences, Albany, New York 12208, 12201-2002, USA.
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235
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Chueh AC, Northrop EL, Brettingham-Moore KH, Choo KHA, Wong LH. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin. PLoS Genet 2009; 5:e1000354. [PMID: 19180186 PMCID: PMC2625447 DOI: 10.1371/journal.pgen.1000354] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 12/23/2008] [Indexed: 11/23/2022] Open
Abstract
We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10) containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A–binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A–binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s) across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A–binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A–associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation. The centromere is an essential chromosomal structure for the correct segregation of chromosomes during cell division. Normal human centromeres comprise a 171-bp α-satellite DNA arranged into tandem and higher-order arrays. Neocentromeres are fully functional centromeres that form epigenetically on noncentromeric regions of the chromosomes, with recent evidence indicating an important role they play in centromere repositioning, karyotype evolution, and speciation. Neocentromeres contain fully definable DNA sequences and provide a tractable system for the molecular analysis of the centromere chromatin. Here, the authors investigate the role of epigenetic determinants in the regulation of neocentromere structure and function. They identify that a retrotransposable DNA element found within the neocentromere domain is actively transcribed and that the transcribed RNA is essential for the structural and functional integrity of the neocentromere. This study defines a previously undescribed epigenetic determinant that regulates the neocentromeric chromatin and provides insight into the mechanism of neocentromere formation and centromere repositioning.
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Affiliation(s)
- Anderly C. Chueh
- Chromosome and Chromatin Research Laboratory, Murdoch Children's Research Institute, Melbourne University Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Emma L. Northrop
- Chromosome and Chromatin Research Laboratory, Murdoch Children's Research Institute, Melbourne University Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kate H. Brettingham-Moore
- Chromosome and Chromatin Research Laboratory, Murdoch Children's Research Institute, Melbourne University Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - K. H. Andy Choo
- Chromosome and Chromatin Research Laboratory, Murdoch Children's Research Institute, Melbourne University Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
- * E-mail: (KHAC); (LHW)
| | - Lee H. Wong
- Chromosome and Chromatin Research Laboratory, Murdoch Children's Research Institute, Melbourne University Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
- * E-mail: (KHAC); (LHW)
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Shpiz S, Kwon D, Rozovsky Y, Kalmykova A. rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus. Nucleic Acids Res 2008; 37:268-78. [PMID: 19036789 PMCID: PMC2615633 DOI: 10.1093/nar/gkn960] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Telomeres in Drosophila are maintained by the specialized telomeric retrotransposons HeT-A, TART and TAHRE. Sense transcripts of telomeric retroelements were shown to be the targets of a specialized RNA-interference mechanism, a repeat-associated short interfering (rasi)RNA-mediated system. Antisense rasiRNAs play a key role in this mechanism, highlighting the importance of antisense expression in retrotransposon silencing. Previously, bidirectional transcription was reported for the telomeric element TART. Here, we show that HeT-A is also bidirectionally transcribed, and HeT-A antisense transcription in ovaries is regulated by a promoter localized within its 3' untranslated region. A remarkable feature of noncoding HeT-A antisense transcripts is the presence of multiple introns. We demonstrate that sense and antisense HeT-A-specific rasiRNAs are present in the same tissue, indicating that transcripts of both directions may be considered as natural targets of the rasiRNA pathway. We found that the expression of antisense transcripts of telomeric elements is regulated by the RNA silencing machinery, suggesting rasiRNA-mediated interplay between sense and antisense transcripts in the cell. Finally, this regulation occurs in the nucleus since disruption of the rasiRNA pathway leads to an accumulation of TART and HeT-A transcripts in germ cell nuclei.
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Affiliation(s)
- Sergey Shpiz
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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237
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Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes? PLoS One 2008; 3:e3760. [PMID: 19018283 PMCID: PMC2582637 DOI: 10.1371/journal.pone.0003760] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 10/31/2008] [Indexed: 11/29/2022] Open
Abstract
Background Eukaryotic genomes are scattered with retroelements that proliferate through retrotransposition. Although retroelements make up around 40 percent of the human genome, large regions are found to be completely devoid of retroelements. This has been hypothesised to be a result of genomic regions being intolerant to insertions of retroelements. The inadvertent transcriptional activity of retroelements may affect neighbouring genes, which in turn could be detrimental to an organism. We speculate that such retroelement transcription, or transcriptional interference, is a contributing factor in generating and maintaining retroelement-free regions in the human genome. Methodology/Principal Findings Based on the known transcriptional properties of retroelements, we expect long interspersed elements (LINEs) to be able to display a high degree of transcriptional interference. In contrast, we expect short interspersed elements (SINEs) to display very low levels of transcriptional interference. We find that genomic regions devoid of long interspersed elements (LINEs) are enriched for protein-coding genes, but that this is not the case for regions devoid of short interspersed elements (SINEs). This is expected if genes are subject to selection against transcriptional interference. We do not find microRNAs to be associated with genomic regions devoid of either SINEs or LINEs. We further observe an increased relative activity of genes overlapping LINE-free regions during early embryogenesis, where activity of LINEs has been identified previously. Conclusions/Significance Our observations are consistent with the notion that selection against transcriptional interference has contributed to the maintenance and/or generation of retroelement-free regions in the human genome.
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238
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Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 2008; 18:869-80. [PMID: 18381897 DOI: 10.1101/gr.075770.107] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Numerous inbred mouse strains comprise models for human diseases and diversity, but the molecular differences between them are mostly unknown. Several mammalian genomes have been assembled, providing a framework for identifying structural variations. To identify variants between inbred mouse strains at a single nucleotide resolution, we aligned 26 million individual sequence traces from four laboratory mouse strains to the C57BL/6J reference genome. We discovered and analyzed over 10,000 intermediate-length genomic variants (from 100 nucleotides to 10 kilobases), distinguishing these strains from the C57BL/6J reference. Approximately 85% of such variants are due to recent mobilization of endogenous retrotransposons, predominantly L1 elements, greatly exceeding that reported in humans. Many genes' structures and expression are altered directly by polymorphic L1 retrotransposons, including Drosha (also called Rnasen), Parp8, Scn1a, Arhgap15, and others, including novel genes. L1 polymorphisms are distributed nonrandomly across the genome, as they are excluded significantly from the X chromosome and from genes associated with the cell cycle, but are enriched in receptor genes. Thus, recent endogenous L1 retrotransposition has diversified genomic structures and transcripts extensively, distinguishing mouse lineages and driving a major portion of natural genetic variation.
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Affiliation(s)
- Keiko Akagi
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
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239
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Ichiyanagi K, Okada N. Mobility pathways for vertebrate L1, L2, CR1, and RTE clade retrotransposons. Mol Biol Evol 2008; 25:1148-57. [PMID: 18343891 DOI: 10.1093/molbev/msn061] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Autonomous non-long terminal repeat retrotransposons (NLRs) are ubiquitous mobile genetic elements that insert their DNA copies at new locations by retrotransposition. In vertebrates, there are 4 NLR clades, L1, L2, CR1, and RTE, which diverged in the Precambrian era. It has been demonstrated that retrotransposition of L1 and L2 members proceeds via coordinated reactions of targeted DNA cleavage and reverse transcription catalyzed by the NLR-encoded proteins, which are followed by the joining of the 5' (upstream) junction. However, the study on the mobility pathways for vertebrate NLRs is so far limited to L1 and L2. In this report, using target analysis of nested transposons for genomic copies, we studied retrotransposition pathways for a variety of vertebrate NLRs, including those of the L1, L2, CR1, and RTE clades in the human, cow, opossum, chicken, and zebrafish genomes. Thus, this study constitutes the first comprehensive analysis of NLR retrotransposition products in vertebrates. Our data revealed that these elements share similar mechanisms for the cleavages of the 2 target DNA strands and for the initiation of reverse transcription. Possible endonuclease-independent insertions were also identified. Overall, our results suggest the existence of multiple retrotransposition pathways that are conserved among the diverse NLR clades in various vertebrate hosts.
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Affiliation(s)
- Kenji Ichiyanagi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
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240
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Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 2008; 18:136-48. [PMID: 18282709 DOI: 10.1016/j.tcb.2008.01.004] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/03/2008] [Accepted: 01/11/2008] [Indexed: 11/23/2022]
Abstract
Eukaryotes are engaged in a constant struggle against transposable elements, which have invaded and profoundly shaped their genomes. Over the past decade, a growing body of evidence has pointed to a role for small RNAs in transposon defense. Although the strategies used in different organisms vary in their details, they have strikingly similar general properties. Basically, all mechanisms consist of three components. First, transposon detection prompts the production of small RNAs, which are Piwi-interacting RNAs in some organisms and small interfering RNAs in others. Second, the population of small RNAs targeting active transposons is amplified through an RNA-dependent RNA polymerase-based or Slicer-based mechanism. Third, small RNAs are incorporated into Argonaute- or Piwi-containing effector complexes, which target transposon transcripts for post-transcriptional silencing and/or target transposon DNA for repressive chromatin modification and DNA methylation. These properties produce robust systems that limit the catastrophic consequences of transposon mobilization, which can result in the accumulation of deleterious mutations, changes in gene expression patterns, and conditions such as gonadal hypotrophy and sterility.
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241
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Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 2008; 18:343-58. [PMID: 18256243 DOI: 10.1101/gr.5558208] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from the activity of type I retrotransposons, which amplify in a "copy-and-paste" fashion through an RNA intermediate. For better or worse, the sequences of these retrotransposons are now wedded to the genomes of their mammalian hosts. Although there are several reported instances of the positive contribution of mobile elements to their host genomes, these discoveries have occurred alongside growing evidence of the role of TEs in human disease and genetic instability. Here we examine, with a particular emphasis on human retrotransposon activity, several newly discovered aspects of mammalian retrotransposon biology. We consider their potential impact on host biology as well as their ultimate implications for the nature of the TE-host relationship.
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Affiliation(s)
- Victoria P Belancio
- Tulane Cancer Center and Department of Epidemiology, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA
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242
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Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M. Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics 2007; 8:392. [PMID: 17963496 PMCID: PMC2176070 DOI: 10.1186/1471-2164-8-392] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 10/26/2007] [Indexed: 12/02/2022] Open
Abstract
Background Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results Here, we show that members of the three active mouse L1 subfamilies (A, GF and TF) contain, in addition to those on their sense strands, conserved functional splice sites on their antisense strands, which trigger multiple exonization events. The latter is particularly intriguing in the light of the strong antisense orientation bias of intronic L1s, implying that the toleration of antisense insertions results in an increased potential for exonization. Conclusion In a genome-wide analysis, we have uncovered evidence suggesting that the mobility of the large number of retrotransposition-competent mouse L1s (~2400 potentially active L1s in NCBIm35) has significant potential to shape the mouse transcriptome by continuously generating insertions into transcriptional units.
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Affiliation(s)
- Tomasz Zemojtel
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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243
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Olovnikov IA, Adyanova ZV, Galimov ER, Andreev DE, Terenin IM, Ivanov DS, Prassolov VS, Dmitriev SE. Key role of the internal 5′-UTR segment in the transcription activity of the human L1 retrotransposon. Mol Biol 2007. [DOI: 10.1134/s0026893307030119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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244
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Abstract
Long interspersed nucleotide element (LINE)-1 retrotransposon (L1) has emerged as the largest contributor to mammalian genome mass, responsible for over 35% of the human genome. Differences in the number and activity levels of L1s contribute to interindividual variation in humans, both by affecting an individual's likelihood of acquiring new L1-mediated mutations, as well as by differentially modifying gene expression. Here, we report on recent progress in understanding L1 biology, with a focus on mechanisms of L1-mediated disease. We discuss known details of L1 life cycle, including L1 structure, transcriptional regulation, and the mechanisms of translation and retrotransposition. Current views on cell type specificity, timing, and control of retrotransposition are put forth. Finally, we discuss the role of L1 as a mutagen, using the latest findings in L1 biology to illuminate molecular mechanisms of L1-mediated gene disruption.
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Affiliation(s)
- Daria V Babushok
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA
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245
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Horie K, Saito ES, Keng VW, Ikeda R, Ishihara H, Takeda J. Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits. Genetics 2007; 176:815-27. [PMID: 17435252 PMCID: PMC1894610 DOI: 10.1534/genetics.107.071647] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Massive accumulation of retrotransposons, comprising >40% of human and mouse genomes, is one of the major events in the evolution of the genome. However, most retrotransposons have lost retrotransposition competency, which makes studying their role in genome evolution elusive. Intracisternal A-particle (IAP) elements are long terminal repeat (LTR)-type mouse retrotransposons consisting of full-length and internally deleted types. Some are retrotransposition competent and their upregulated activity has been reported in mutant mice deficient in genome defense systems, suggesting that IAP elements provide a unique platform for studying the interaction between retrotransposons and mammalian genomes. Using the IAP element as a model case, here we show that mobilization of retrotransposons alters the mouse transcriptome. Retrotransposition assay in cultured cells demonstrated that a subset of internally deleted IAP elements, called IDelta1 type, retrotranspose efficiently when supplied with functional IAP proteins. Furthermore, the IDelta1 type IAP element exhibited substantial transcription-inducing activity in the flanking region. Genomewide transcript analysis of embryonic stem (ES) cells identified IAP-induced transcripts, including fusion transcripts between IAP sequence and endogenous genes. Unexpectedly, nearly half of these IAP elements obtained from ES cells derived from 129 mouse strain were absent in the C57BL/6 genome, suggesting that IAP-driven transcription contributes to the unique trait of the individual mouse strain. On the basis of these data, we propose that retrotransposons are one of the drivers that shape the mammalian transcriptome.
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Affiliation(s)
- Kyoji Horie
- Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, Inage-ku, Chiba 263-8555, Japan.
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Copeland CS, Mann VH, Brindley PJ. Both sense and antisense strands of the LTR of the Schistosoma mansoni Pao-like retrotransposon Sinbad drive luciferase expression. Mol Genet Genomics 2006; 277:161-70. [PMID: 17131159 DOI: 10.1007/s00438-006-0181-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2006] [Accepted: 10/04/2006] [Indexed: 11/25/2022]
Abstract
Long terminal repeat (LTR) retrotransposons, mobile genetic elements comprising substantial proportions of many eukaryotic genomes, are so named for the presence of LTRs, direct repeats about 250-600 bp in length flanking the open reading frames that encode the retrotransposon enzymes and structural proteins. LTRs include promotor functions as well as other roles in retrotransposition. LTR retrotransposons, including the Gypsy-like Boudicca and the Pao/BEL-like Sinbad elements, comprise a substantial proportion of the genome of the human blood fluke, Schistosoma mansoni. In order to deduce the capability of specific copies of Boudicca and Sinbad LTRs to function as promotors, these LTRs were investigated analytically and experimentally. Sequence analysis revealed the presence of TATA boxes, canonical polyadenylation signals, and direct inverted repeats within the LTRs of both the Boudicca and Sinbad retrotransposons. Inserted in the reporter plasmid pGL3, the LTR of Sinbad drove firefly luciferase activity in HeLa cells in its forward and inverted orientation. In contrast, the LTR of Boudicca did not drive luciferase activity in HeLa cells. The ability of the Sinbad LTR to transcribe in both its forward and inverted orientation represents one of few documented examples of bidirectional promotor function.
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Affiliation(s)
- Claudia S Copeland
- Department of Tropical Medicine, and Interdisciplinary Program in Molecular and Cellular Biology, Tulane University Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
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248
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Cropley JE, Suter CM, Beckman KB, Martin DIK. Germ-line epigenetic modification of the murine A vy allele by nutritional supplementation. Proc Natl Acad Sci U S A 2006; 103:17308-12. [PMID: 17101998 PMCID: PMC1838538 DOI: 10.1073/pnas.0607090103] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Environmental effects on phenotype can be mediated by epigenetic modifications. The epigenetic state of the murine A vy allele is highly variable, and determines phenotypic effects that vary in a mosaic spectrum that can be shifted by in utero exposure to methyl donor supplementation. We have asked if methyl donor supplementation affects the germ-line epigenetic state of the A vy allele. We find that the somatic epigenetic state of A vy is affected by in utero methyl donor supplementation only when the allele is paternally contributed. Exposure to methyl donor supplementation during midgestation shifts A vy phenotypes not only in the mice exposed as fetuses, but in their offspring. This finding indicates that methyl donors can change the epigenetic state of the A vy allele in the germ line, and that the altered state is retained through the epigenetic resetting that takes place in gametogenesis and embryogenesis. Thus a mother's diet may have an enduring influence on succeeding generations, independent of later changes in diet. Although other reports have suggested such heritable epigenetic changes, this study demonstrates that a specific mammalian gene can be subjected to germ-line epigenetic change.
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Affiliation(s)
- Jennifer E. Cropley
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
| | - Catherine M. Suter
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Anzac Parade, Kensington 2033, Sydney, Australia; and
| | - Kenneth B. Beckman
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
| | - David I. K. Martin
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences and
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
- To whom correspondence should be addressed. E-mail:
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249
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Eller CD, Regelson M, Merriman B, Nelson S, Horvath S, Marahrens Y. Repetitive sequence environment distinguishes housekeeping genes. Gene 2006; 390:153-65. [PMID: 17141428 PMCID: PMC1857324 DOI: 10.1016/j.gene.2006.09.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 09/18/2006] [Accepted: 09/24/2006] [Indexed: 12/14/2022]
Abstract
Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes by their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element-1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, was used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.
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Affiliation(s)
- C. Daniel Eller
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
| | - Moira Regelson
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
| | - Barry Merriman
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
| | - Stan Nelson
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
| | - Steve Horvath
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
- UCLA Department of Biostatistics, School of Public Health, Box 951772, Los Angeles, California 90095-1772, USA
| | - York Marahrens
- UCLA Department of Human Genetics David Geffen School of Medicine, Gonda Center, 695 E. Young Drive South, Los Angeles, California 90095-7088, USA
- * to whom correspondence should be addressed: York Marahrens, UCLA Department of Human Genetics, Gonda Center, Room 4554b, 695 Charles E. Young Drive, Los Angeles, CA 90095, USA, Phone: (310) 267-2466, Fax: (310) 794-5446, E-mail:
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250
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Soifer HS, Rossi JJ. Small interfering RNAs to the rescue: blocking L1 retrotransposition. Nat Struct Mol Biol 2006; 13:758-9. [PMID: 16955095 DOI: 10.1038/nsmb0906-758] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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