Comparative Sequence Analysis of the Mouse and Human Lgn1/SMA Interval

Endrizzi, Matthew G.; Huang, Sidong; Scharf, Jeremiah M.; Kelter, Arndt-René; Wirth, Brunhilde; Kunkel, Louis M.; Miller, Webb; Dietrich, William F.

doi:10.1006/geno.1999.5910

Cited by 39 publications

(44 citation statements)

References 57 publications

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“…In contrast, the imprinted domain between H19 and Mash2 showed approximately twice the degree of alignment (35.8%), which indicates either that it contains a larger fraction of functional DNA or that neutral mutations are being fixed at a lower rate. Although variable, these numbers are in the range (6.4%-78.1%) observed using the same technique in nine other genomic regions (see Endrizzi et al 1999, Table 3). …”

Section: Global Comparison Of the Mouse And Human Orthologous Imprintmentioning

confidence: 77%

“…For example, mouse Igf2 consists of eight exons whereas the human gene contains one additional exon, and the single-exon encoded ribosomal proteins L26 and L13 were only present in the human and mouse, respectively (Table 4). To assess the level of background sequence similarity between human and mouse, we determined the fraction of noncoding, nonrepetitive mouse sequence that can be aligned to the human sequence using the protocol of Endrizzi et al (1999) and Zhang et al (1999). The imprinted domain between Trpc51 and Tssc3 and the nonimprinted domain from Tssc6 to Tssc4 showed a similar fraction of aligned positions (19.6% and 18.8%, respectively).…”

Section: Global Comparison Of the Mouse And Human Orthologous Imprintmentioning

confidence: 99%

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Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

et al. 2000

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A major barrier to conceptual advances in understanding the mechanisms and regulation of imprinting of a genomic region is our relatively poor understanding of the overall organization of genes and of the potentially important cis-acting regulatory sequences that lie in the nonexonic segments that make up 97% of the genome. Interspecies sequence comparison offers an effective approach to identify sequence from conserved functional elements. In this article we describe the successful use of this approach in comparing a ∼1-Mb imprinted genomic domain on mouse chromosome 7 to its orthologous region on human 11p15.5. Within the region, we identified 112 exons of known genes as well as a novel gene identified uniquely in the mouse region, termed Msuit, that was found to be imprinted. In addition to these coding elements, we identified 33 CpG islands and 49 orthologous nonexonic, nonisland sequences that met our criteria as being conserved, and making up 4.1% of the total sequence. These conserved noncoding sequence elements were generally clustered near imprinted genes and the majority were between Igf2 and H19 or within Kvlqt1.

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Section: Global Comparison Of the Mouse And Human Orthologous Imprintmentioning

confidence: 77%

Section: Global Comparison Of the Mouse And Human Orthologous Imprintmentioning

confidence: 99%

Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

et al. 2000

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“…Alignments of these sequences showed that some loci have extensive matches outside the coding region (Koop and Hood 1994;Epp et al 1995;Oeltjen et al 1997;Ellsworth et al 2000), whereas in others the matches are largely limited to the coding regions (Lamerdin et al 1996;Endrizzi et al 1999), and still others have an intermediate level of noncoding sequence matches (Margot et al 1989;Shehee et al 1989;Lamerdin et al 1995;Ansari-Lari et al 1998). Quantitative analysis showed that the fraction of noncoding, nonrepetitive genomic sequence that aligns in comparisons between mammalian orders varies over a 10-fold range at different loci (Endrizzi et al 1999;DeSilva et al 2002). Thus, analysis both of substitutions at apparently neutral sites in coding regions and the extent of aligning DNA in noncoding regions reveals substantial regional differences in the amount of divergence between mammalian genomic DNA sequences.…”

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confidence: 99%

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Hardison¹,

et al. 2003

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Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements active only before the human–mouse speciation, and (3) the nonaligning fraction of human DNA that is nonrepetitive or in ancestral repeats; and three derived from human genome data alone, consisting of (4) SNP density, (5) frequency of insertion of transposable elements, and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of “neutral” sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary significantly in megabase-sized regions genome-wide, and many vary together. This indicates that some regions of a genome change slowly by all processes that alter DNA, and others change faster. Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse. [Supplemental material is available online at www.genome.org and http://www.soe.ucsc.edu/research/compbio/covariation/.

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“…Linkage studies have indicated that a single autosomal, recessive gene, designated Lgn1 (11), determines macrophage permissiveness to intracellular replication of L. pneumophila. Lgn1 maps to the distal mouse chromosome 13 (13)(14)(15)(16)(17), within a genetic interval of 0.32 centiMorgan (95% confidence interval), defined distally by the genetic marker D13Die3 and proximally by D13Die6/D13Die26. Physical mapping studies and assembly of a cloned contig of BAC and YAC clones for the region suggest a minimal physical interval for Lgn1 of ϳ350 kb (15)(16)(17)(18).…”

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confidence: 99%

The Neuronal Apoptosis Inhibitory Protein (Naip) Is Expressed in Macrophages and Is Modulated After Phagocytosis and During Intracellular Infection withLegionella pneumophila

Diez

Yaraghi

MacKenzie

et al. 2000

The Journal of Immunology

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Legionella pneumophila is an intracellular pathogen that causes Legionnaires’ disease in humans. Inbred mouse strains are uniformly resistant to L. pneumophila infection with the notable exception of A/J, where the chromosome 13 locus Lgn1 renders A/J macrophages permissive to L. pneumophila replication. The mouse Lgn1 region is syntenic with the spinal muscular atrophy (SMA) locus on human chromosome 5 and includes several copies of the neuronal apoptosis inhibitory protein (Naip) gene. We have analyzed a possible link among Lgn1, Naip, and macrophage function. RNA expression studies show that Naip (mostly copy 2) mRNA transcripts are expressed in macrophage-rich tissues, such as spleen, lung, and liver and are abundant in primary macrophages. Immunoblotting and immunoprecipitation analyses identify Naip protein expression in mouse macrophages and in macrophage cell lines RAW 264.7 and J774A. Interestingly, macrophages from permissive A/J mice express significantly less Naip protein than their nonpermissive C57BL/6J counterpart. Naip protein expression is increased after phagocytic events. Naip protein levels during infection with either virulent or avirulent strains of L. pneumophila increase during the first 6 h postinfection and remain elevated during the 48-h observation period. This enhanced expression is also observed in macrophages infected with Salmonella typhimurium. Likewise, an increase in Naip protein levels in macrophages is observed 24 h after phagocytosis of Latex beads. The cosegregation of Lgn1 and Naip together with the detected Naip protein expression in host macrophages as well as its modulation after phagocytic events and during intracellular infection make it an attractive candidate for the Lgn1 locus.

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Comparative Sequence Analysis of the Mouse and Human Lgn1/SMA Interval

Cited by 39 publications

References 57 publications

Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

The Neuronal Apoptosis Inhibitory Protein (Naip) Is Expressed in Macrophages and Is Modulated After Phagocytosis and During Intracellular Infection withLegionella pneumophila

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