301
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Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 2007; 17:556-65. [PMID: 17387145 PMCID: PMC1855172 DOI: 10.1101/gr.6036807] [Citation(s) in RCA: 529] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby leaving an impression that, instead, they represent "transcriptional noise." Here, we describe an analysis of 3122 long and full-length, noncoding RNAs ("macroRNAs") from the mouse, and compare their sequences and their promoters with orthologous sequence from human and from rat. We considered three independent signatures of purifying selection related to substitutions, sequence insertions and deletions, and splicing. We find that the evolution of the set of noncoding RNAs is not consistent with neutralist explanations. Rather, our results indicate that purifying selection has acted on the macroRNAs' promoters, primary sequence, and consensus splice site motifs. Promoters have experienced the greatest elimination of nucleotide substitutions, insertions, and deletions. The proportion of conserved sequence (4.1%-5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs' functions.
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Affiliation(s)
- Jasmina Ponjavic
- MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
| | - Chris P. Ponting
- MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
- Corresponding authors.E-mail ; fax 44-1865-282651.E-mail ; fax 44-1865-282651
| | - Gerton Lunter
- MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
- Corresponding authors.E-mail ; fax 44-1865-282651.E-mail ; fax 44-1865-282651
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302
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Shevchenko AI, Zakharova IS, Elisaphenko EA, Kolesnikov NN, Whitehead S, Bird C, Ross M, Weidman JR, Jirtle RL, Karamysheva TV, Rubtsov NB, VandeBerg JL, Mazurok NA, Nesterova TB, Brockdorff N, Zakian SM. Genes flanking Xist in mouse and human are separated on the X chromosome in American marsupials. Chromosome Res 2007; 15:127-36. [PMID: 17333537 PMCID: PMC2797855 DOI: 10.1007/s10577-006-1115-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 12/13/2006] [Accepted: 12/13/2006] [Indexed: 11/26/2022]
Abstract
X inactivation, the transcriptional silencing of one of the two X chromosomes in female mammals, achieves dosage compensation of X-linked genes relative to XY males. In eutherian mammals X inactivation is regulated by the X-inactive specific transcript (Xist), a cis-acting non-coding RNA that triggers silencing of the chromosome from which it is transcribed. Marsupial mammals also undergo X inactivation but the mechanism is relatively poorly understood. We set out to analyse the X chromosome in Monodelphis domestica and Didelphis virginiana, focusing on characterizing the interval defined by the Chic1 and Slc16a2 genes that in eutherians flank the Xist locus. The synteny of this region is retained on chicken chromosome 4 where other loci belonging to the evolutionarily ancient stratum of the human X chromosome, the so-called X conserved region (XCR), are also located. We show that in both M. domestica and D. virginiana an evolutionary breakpoint has separated the Chic1 and Slc16a2 loci. Detailed analysis of opossum genomic sequences revealed linkage of Chic1 with the Lnx3 gene, recently proposed to be the evolutionary precursor of Xist, and Fip1, the evolutionary precursor of Tsx, a gene located immediately downstream of Xist in eutherians. We discuss these findings in relation to the evolution of Xist and X inactivation in mammals.
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Affiliation(s)
- Alexander I. Shevchenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Irina S. Zakharova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Eugeny A. Elisaphenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Nicolay N. Kolesnikov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Siobhan Whitehead
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Christine Bird
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Mark Ross
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Jennifer R. Weidman
- Departments of Radiation Oncology and Pathology, Duke University Medical Center, Durham, NC 27710 USA
| | - Randy L. Jirtle
- Departments of Radiation Oncology and Pathology, Duke University Medical Center, Durham, NC 27710 USA
| | - Tatiana V. Karamysheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Nicolay B. Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - John L. VandeBerg
- Department of Genetics and Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX 78245-0549 USA
| | - Nina A. Mazurok
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
| | - Tatyana B. Nesterova
- Developmental Epigenetics Group, MRC Clinical Sciences Centre ICFM, Hammersmith Hospital, London, UK
| | - Neil Brockdorff
- Developmental Epigenetics Group, MRC Clinical Sciences Centre ICFM, Hammersmith Hospital, London, UK
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
- Institute of Cytology and Genetics, ac.Lavrentiev avenue, 10, Novosibirsk, 630090 Russia
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303
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Hore TA, Koina E, Wakefield MJ, Marshall Graves JA. The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. Chromosome Res 2007; 15:147-61. [PMID: 17333539 DOI: 10.1007/s10577-007-1119-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/29/2006] [Accepted: 12/29/2006] [Indexed: 10/23/2022]
Abstract
Marsupial, as well as eutherian, mammals are subject to X chromosome inactivation in the somatic cells of females, although the phenotype and the molecular mechanism differ in important respects. Monotreme mammals appear to subscribe at least to a form of dosage compensation of X-borne genes. An important question is whether inactivation in these non-eutherian mammals involves co-ordination by a control locus homologous to the XIST gene and neighbouring genes, which play a key regulatory role in human and mouse X inactivation. We mapped BACs containing several orthologues of protein-coding genes that flank human and mouse XIST and genes that lie in the homologous region in chicken and frog. We found that these genes map to two distant locations on the opossum X, and also to different locations on a platypus autosome. We failed to find any trace of an XIST orthologue in any marsupial or monotreme or on any flanking BAC, confirming the conclusion from recent work that non-eutherian mammals lack XIST. We propose the region homologous to the human and mouse X-inactivation centre expanded in early mammals, and this unstable region was disrupted independently in marsupial and monotreme lineages. In the eutherian lineage, inserted and existing sequences provided the starting material for the non-translated RNAs of the X-inactivation centre, including XIST.
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Affiliation(s)
- Timothy A Hore
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia.
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304
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Davidow LS, Breen M, Duke SE, Samollow PB, McCarrey JR, Lee JT. The search for a marsupial XIC reveals a break with vertebrate synteny. Chromosome Res 2007; 15:137-46. [PMID: 17333538 DOI: 10.1007/s10577-007-1121-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 01/19/2007] [Accepted: 01/19/2007] [Indexed: 01/09/2023]
Abstract
X-chromosome inactivation (XCI) evolved in mammals to deal with X-chromosome dosage imbalance between the XX female and the XY male. In eutherian mammals, random XCI of the soma requires a master regulatory locus known as the 'X-inactivation center' (XIC/Xic), wherein lies the noncoding XIST/Xist silencer RNA and its regulatory antisense Tsix gene. By contrast, marsupial XCI is imprinted to occur on the paternal X chromosome. To determine whether marsupials and eutherians share the XIC-driven mechanism, we search for the sequence equivalents in the genome of the South American opossum, Monodelphis domestica. Positional cloning and bioinformatic analysis reveal several interesting findings. First, protein-coding genes that flank the eutherian XIC are well-conserved in M. domestica, as well as in chicken, frog, and pufferfish. However, in M. domestica we fail to identify any recognizable XIST or TSIX equivalents. Moreover, cytogenetic mapping shows a surprising break in synteny with eutherian mammals and other vertebrates. Therefore, during the evolution of the marsupial X chromosome, one or more rearrangements broke up an otherwise evolutionarily conserved block of vertebrate genes. The failure to find XIST/TSIX in M. domestica may suggest that the ancestral XIC is too divergent to allow for detection by current methods. Alternatively, the XIC may have arisen relatively late in mammalian evolution, possibly in eutherians with the emergence of random XCI. The latter argues that marsupial XCI does not require XIST and opens the search for alternative mechanisms of dosage compensation.
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Affiliation(s)
- Lance S Davidow
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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305
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Male non-coding RNA genes identified by comparative genomic analysis of the Drosophila genomes. CHINESE SCIENCE BULLETIN-CHINESE 2007. [DOI: 10.1007/s11434-007-0144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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306
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Abstract
X chromosome inactivation is most commonly studied in the context of female mammalian development, where it performs an essential role in dosage compensation. However, another form of X-inactivation takes place in the male, during spermatogenesis, as germ cells enter meiosis. This second form of X-inactivation, called meiotic sex chromosome inactivation (MSCI) has emerged as a novel paradigm for studying the epigenetic regulation of gene expression. New studies have revealed that MSCI is a special example of a more general mechanism called meiotic silencing of unsynapsed chromatin (MSUC), which silences chromosomes that fail to pair with their homologous partners and, in doing so, may protect against aneuploidy in subsequent generations. Furthermore, failure in MSCI is emerging as an important etiological factor in meiotic sterility.
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Affiliation(s)
- James M A Turner
- Division of Stem Cell Biology and Developmental Genetics, MRC NIMR, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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307
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Waters PD, Wallis MC, Marshall Graves JA. Mammalian sex--Origin and evolution of the Y chromosome and SRY. Semin Cell Dev Biol 2007; 18:389-400. [PMID: 17400006 DOI: 10.1016/j.semcdb.2007.02.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 01/16/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
Sex determination in vertebrates is accomplished through a highly conserved genetic pathway. But surprisingly, the downstream events may be activated by a variety of triggers, including sex determining genes and environmental cues. Amongst species with genetic sex determination, the sex determining gene is anything but conserved, and the chromosomes that bear this master switch subscribe to special rules of evolution and function. In mammals, with a few notable exceptions, female are homogametic (XX) and males have a single X and a small, heterochromatic and gene poor Y that bears a male dominant sex determining gene SRY. The bird sex chromosome system is the converse in that females are the heterogametic sex (ZW) and males the homogametic sex (ZZ). There is no SRY in birds, and the dosage-sensitive Z-borne DMRT1 gene is a credible candidate sex determining gene. Different sex determining switches seem therefore to have evolved independently in different lineages, although the complex sex chromosomes of the platypus offer us tantalizing clues that the mammal XY system may have evolved directly from an ancient reptile ZW system. In this review we will discuss the organization and evolution of the sex chromosomes across a broad range of mammals, and speculate on how the Y chromosome, and SRY, evolved.
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Affiliation(s)
- Paul D Waters
- Comparative Genomics Group, Research School of Biological Sciences, The Australian National University, GPO Box 475, ACT 2601, Canberra, Australia.
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308
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Cohen DE, Davidow LS, Erwin JA, Xu N, Warshawsky D, Lee JT. The DXPas34 repeat regulates random and imprinted X inactivation. Dev Cell 2007; 12:57-71. [PMID: 17199041 DOI: 10.1016/j.devcel.2006.11.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 10/19/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
X chromosome inactivation (XCI) is initiated by expression of the noncoding Xist RNA in the female embryo. Tsix, the antisense noncoding partner of Xist, serves as its regulator during both imprinted and random XCI. Here, we show that Tsix in part acts through a 34mer repeat, DXPas34. DXPas34 contains bidirectional promoter activity, producing overlapping forward and reverse transcripts. We generate three new Tsix alleles in mouse embryonic stem cells and show that, while the Tsix promoter is unexpectedly dispensable, DXPas34 plays dual positive-negative functions. At the onset of XCI, DXPas34 stimulates Tsix expression through its enhancer activity. Once XCI is established, DXPas34 becomes repressive and stably silences Tsix. Germline transmission of the DXPas34 mutation demonstrates its necessity for both random and imprinted XCI in mice. Intriguingly, sequence analysis suggests that DXPas34 could potentially have descended from an ancient retrotransposon. We hypothesize that DXPas34 was acquired by Tsix to regulate antisense function.
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MESH Headings
- Animals
- Base Sequence
- Consensus Sequence
- Down-Regulation
- Embryo, Mammalian/cytology
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryonic Stem Cells/metabolism
- Female
- Gene Expression Regulation, Developmental
- Gene Targeting
- Genomic Imprinting
- In Situ Hybridization, Fluorescence
- Mice
- Models, Genetic
- Molecular Sequence Data
- Phylogeny
- Promoter Regions, Genetic/genetics
- RNA, Long Noncoding
- RNA, Untranslated/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Deletion
- Up-Regulation
- X Chromosome/genetics
- X Chromosome Inactivation/genetics
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Affiliation(s)
- Dena E Cohen
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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309
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Prasanth KV, Spector DL. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 2007; 21:11-42. [PMID: 17210785 DOI: 10.1101/gad.1484207] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A large portion of the eukaryotic genome is transcribed as noncoding RNAs (ncRNAs). While once thought of primarily as "junk," recent studies indicate that a large number of these RNAs play central roles in regulating gene expression at multiple levels. The increasing diversity of ncRNAs identified in the eukaryotic genome suggests a critical nexus between the regulatory potential of ncRNAs and the complexity of genome organization. We provide an overview of recent advances in the identification and function of eukaryotic ncRNAs and the roles played by these RNAs in chromatin organization, gene expression, and disease etiology.
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310
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Hornecker JL, Samollow PB, Robinson ES, VandeBerg JL, McCarrey JR. Meiotic sex chromosome inactivation in the marsupialMonodelphis domestica. Genesis 2007; 45:696-708. [DOI: 10.1002/dvg.20345] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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311
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Abstract
New cytological techniques combined with genome-wide expression studies and ChIP-on-chip have revealed that random X-inactivation is not a simple one-step process that occurs uniformly across the entire chromosome, but a complex series of events with clear links to both the epigenetic silencing of autosomal genes and the imprinted X-inactivation that occurs in male meiosis. It appears to be less bizarre, as the French love to say, and as such an even better model of epigenetic gene silencing, than previously thought.
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Affiliation(s)
- Emma Whitelaw
- Queensland Institute of Medical Research, Brisbane, Australia.
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312
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Heard E, Disteche CM. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 2006; 20:1848-67. [PMID: 16847345 DOI: 10.1101/gad.1422906] [Citation(s) in RCA: 377] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mammalian females have two X chromosomes and males have only one. This has led to the evolution of special mechanisms of dosage compensation. The inactivation of one X chromosome in females equalizes gene expression between the sexes. This process of X-chromosome inactivation (XCI) is a remarkable example of long-range, monoallelic gene silencing and facultative heterochromatin formation, and the questions surrounding it have fascinated biologists for decades. How does the inactivation of more than a thousand genes on one X chromosome take place while the other X chromosome, present in the same nucleus, remains genetically active? What are the underlying mechanisms that trigger the initial differential treatment of the two X chromosomes? How is this differential treatment maintained once it has been established, and how are some genes able to escape the process? Does the mechanism of X inactivation vary between species and even between lineages? In this review, X inactivation is considered in evolutionary terms, and we discuss recent insights into the epigenetic changes and developmental timing of this process. We also review the discovery and possible implications of a second form of dosage compensation in mammals that deals with the unique, potentially haploinsufficient, status of the X chromosome with respect to autosomal gene expression.
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Affiliation(s)
- Edith Heard
- CNRS UMR218, Curie Institute, Paris, France.
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