Megabase deletions of gene deserts result in viable mice

DOE Joint Genome Institute Walnut Creek, California 94598, USA.
Nature (Impact Factor: 41.46). 11/2004; 431(7011):988-93. DOI: 10.1038/nature03022
Source: PubMed


The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.

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Available from: Yiwen Zhu, Apr 14, 2014
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    • "Thus, indifferent DNA should show no evidence of selection for or against point mutations, but deletions and insertions should be under selection. For example, Nó brega et al. (2004) deleted 2,356 kb from the mouse genome, yet mice homozygous for the deletions were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity, and a variety of parameters assaying general homeostasis. Thus, these sequences should be considered junk DNA rather than indifferent DNA. "
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    ABSTRACT: The pronouncements of the ENCODE Project Consortium regarding "junk DNA" exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into "functional DNA," i.e., DNA sequences that have a selected-effect function, and "rubbish DNA," i.e., sequences that do not. Functional DNA is further subdivided into "literal DNA" and "indifferent DNA." In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into "junk DNA" and "garbage DNA." Junk DNA neither contributes nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be (1) transcribed and translated, (2) transcribed but not translated, or (3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on, however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided in to pseudogenes, Lazarus DNA, zombie DNA, and Hyde DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Preview · Article · Jan 2015 · Genome Biology and Evolution
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    • "As in the first set of experiments, in-gel PCR was performed on soluble material with primers and molecular beacons targeting Pβmaj, Pβmin and LCR HS5. Also, we included in the analysis the HS−62 enhancer that had been reported to participate in the assembly of β-globin ACH (17) and two ‘negative controls’: −42 region and a region from a gene desert on another chromosome (Chr3) (41) (see Figure 2A and Table 1). With the doubly cross-linked material, a notable variation in number of colonies produced from different test regions was observed. "
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    ABSTRACT: Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.
    Full-text · Article · Mar 2014 · Nucleic Acids Research
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    • "Many non-exonic UCEs in vertebrates associate with genes involved in regulation of development and transcription [7] and are often embedded within large conserved regions [14], [27]. We analyzed the distribution of Sophophora UCEs in the 22 largest conserved syntenic regions, or homologous collinear blocks, HCBs [52]. "
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    ABSTRACT: Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
    Full-text · Article · Dec 2013 · PLoS ONE
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