Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by activation of the type I interferon (IFN) pathway. Here we convincingly replicate association of the IFN regulatory factor 5 (IRF5) rs2004640 T allele with SLE in four independent case-control cohorts (P = 4.4 x 10(-16)) and by family-based transmission disequilibrium test analysis (P = 0.0006). The rs2004640 T allele creates a 5' donor splice site in an alternate exon 1 of IRF5, allowing expression of several unique IRF5 isoforms. We also identify an independent cis-acting variant associated with elevated expression of IRF5 and linked to the exon 1B splice site. Haplotypes carrying the variant associated with elevated expression and lacking the exon 1B donor site do not confer risk of SLE. Thus, a common IRF5 haplotype driving elevated expression of multiple unique isoforms of IRF5 is an important genetic risk factor for SLE, establishing a causal role for type I IFN pathway genes in human autoimmunity.

Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific functional variants responsible for the disease. The challenges of identifying causal variants include the need for complete ascertainment of genetic variants and the need to consider the possibility of multiple causal alleles. We recently reported that risk of systemic lupus erythematosus (SLE) is strongly associated with a common SNP in IFN regulatory factor 5 (IRF5), and that this variant altered spicing in a way that might provide a functional explanation for the reproducible association to SLE risk. Here, by resequencing and genotyping in patients with SLE, we find evidence for three functional alleles of IRF5: the previously described exon 1B splice site variant, a 30-bp in-frame insertion/deletion variant of exon 6 that alters a proline-, glutamic acid-, serine-and threonine-rich domain region, and a variant in a conserved polyA؉ signal sequence that alters the length of the 3 UTR and stability of IRF5 mRNAs. Haplotypes of these three variants define at least three distinct levels of risk to SLE. Understanding how combinations of variants influence IRF5 function may offer etiological and therapeutic insights in SLE; more generally, IRF5 and SLE illustrates how multiple common variants of the same gene can together influence risk of common disease.interferon pathway ͉ systemic lupus erythematosus

Smith-Magenis syndrome (SMS), caused by del(17)p11.2, represents one of the most frequently observed human microdeletion syndromes. We have identified three copies of a low-copy-number repeat (SMS-REPs) located within and flanking the SMS common deletion region and show that SMS-REP represents a repeated gene cluster. We have isolated a corresponding cDNA clone that identifies a novel junction fragment from 29 unrelated SMS patients and a different-sized junction fragment from a patient with dup(17)p11.2. Our results suggest that homologous recombination of a flanking repeat gene cluster is a mechanism for this common microdeletion syndrome.

Objective. Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by unpredictable flares of disease activity and irreversible damage to multiple organ systems. An earlier study showed that SLE patients carrying an interferon (IFN) gene expression signature in blood have elevated serum levels of IFN-regulated chemokines. These chemokines were associated with more-severe and active disease and showed promise as SLE disease activity biomarkers. This study was designed to validate IFN-regulated chemokines as biomarkers of SLE disease activity in 267 SLE patients followed up longitudinally.Methods. To validate the potential utility of serum chemokine levels as biomarkers of disease activity, we measured serum levels of CXCL10 (IFN␥-inducible 10-kd protein), CCL2 (monocyte chemotactic protein 1), and CCL19 (macrophage inflammatory protein 3␤) in an independent cohort of 267 SLE patients followed up longitudinally over 1 year (1,166 total clinic visits).Results. Serum chemokine levels correlated with lupus activity at the current visit (P ‫؍‬ 2 ؋ 10 ؊10 ), rising at the time of SLE flare (P ‫؍‬ 2 ؋ 10 ؊3 ) and decreasing as disease remitted (P ‫؍‬ 1 ؋ 10 ؊3 ); they also performed better than the currently available laboratory tests. Chemokine levels measured at a single baseline visit in patients with a Systemic Lupus Erythematosus Disease Activity Index of <4 were predictive of lupus flare over the ensuing year (P ‫؍‬ 1 ؋ 10 ؊4 ).Conclusion. Monitoring serum chemokine levels in SLE may improve the assessment of current disease activity, the prediction of future disease flares, and the overall clinical decision-making.Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease defined by autoantibodies to nuclear components, immune complex deposition, and systemic vasculitis (1). Many organ systems are targeted, including the skin, joints, blood cells, kidneys, and nervous system. The disease affects 0.1% of the US population, with a striking 9:1 preponderance in women. The factors that contribute to the onset and progression of SLE are not well understood; however, genetic, environmental, and hormonal factors are likely to be important. SLE disease activity can be difficult to monitor, and flares are unpredictable, both in frequency and in severity. Certain clinical laboratory tests, including antidouble-stranded DNA (anti-dsDNA) antibody titers, complement factor levels, and the erythrocyte sedimen-

7.8 kb, due to the presence of an NsiI site located outside of the hotspot region in both CMT1A-REPs which changes the size of this fragment. The sizes of the CMT1A duplication junction fragments and the region of exchange in both duplication and deletion patients are unaffected by this size discrepancy. Figure: This Southern blot contains EcoRI + SacI digested (E/S) or EcoRI + SacI+NsiI digested (E/S/N) DNA from YACs spanning the proximal and distal CMT1A-REPs (yc49H7 and yc225A3), genomic DNA from HNPP deletion patients (BAB944 and BAB957), genomic DNA from CMT1A duplication patients (BAB603 and BAB681) and genomic DNA from an unaffected control individual. The blot was hybridized with the 6.0-kb insert from plasmid pLR6.0 which originates from the distal CMT1A-REP and spans the recombination hotspot previously described. Arrows indicate the locations of HNPP deletion and CMT1A duplication junction fragments. Note that the 7.8-kb HNPP deletion junction fragments change to 7.3 kb in the triple digest while the sizes for the CMT1A duplication fragments remain as previously reported (3.2 kb for E/S and 1.7 kb for E/S/N).

These results suggest that serum IL-6 production and the type I IFN gene signature are candidate biomarkers for disease activity in adult and juvenile DM. Coregulation of the expression of IFN-driven chemokines and IL-6 suggests a novel pathogenic linkage in DM.

Evolutionary conservation of an interspersed repetitive DNA sequence, BOX, from Streptococcus pneumoniae was investigated to explore the mosaic nature of these elements. BOX elements consist of various combinations of three subunits, boxA, boxB, and boxC. Eight oligonucleotide probes were designed based on consensus DNA sequences of boxA, boxB, and boxC subunits. DNA hybridization studies and PCR using these probes/primers demonstrate that oligonucleotide sequences within the boxA subunit appear to be conserved among diverse bacterial species. 1A). (7) For example, the boxB subunit was present alone as a single copy or as a variable n u m b e r of direct tandem repeats flanked by boxA and boxC. (7~ The DNA sequences of the BOX elements are entirely different from the prokaryotic interspersed repetitive DNA sequences REP and ERIC, although there are similarities to REP and ERIC with respect to size, copy number, and potential to form stable stem-loop structures. ~2-7~ Although the exact functions of interspersed repetitive DNA elements are unknown, the presence of these repetitive DNA sequences can be utilized for rapid physical mapping procedures (8~ and for DNA fingerprinting of prokaryotic genomes. (4'9-2a~ REP and ERIC sequences were used to design primers for PCR, in a technique known as repetitive sequence-based PCR (rep-PCR), to obtain DNA fingerprints from various microorganisms. Interspersed repetitive sequences can serve as primer binding sites that are separated by various distances in the bacterial chromosome. PCR of unique sequence located between interspersed repeats results in differently sized DNA amplification products. PCR products of different sizes constitute polymorphic DNA markers and yield DNA fingerprints that m a y be specific for individual bacterial strains or isolates. The apparent evolutionary conservation of these repetitive elements enables the use of a limited primer repertoire for DNA fingerprinting of a wide array of bacteria.