Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures.

Urethral and endocervical swabs and self-collected vaginal swabs (SCVSs) and urine specimens are all used as samples for diagnosis of urogenital infection with Chlamydia trachomatis. We have now determined chlamydial organism load in matched specimens from different anatomic sites and examined its relation to clinical signs and symptoms in men and women. Organism load was measured with assays based on the ligase chain reaction or real-time PCR analysis. The mean organism loads in 58 infected men were 1,200 and 821 elementary bodies (EBs) per 100 l of sample for first-void urine (FVU) and urethral swabs, respectively (P > 0.05). Organism load in FVU samples or urethral swabs was positively associated with symptoms (P < 0.01) and clinical signs (P < 0.01) in men. The mean organism loads in 73 infected women were 2,231, 773, 162, and 47 EBs/100 l for endocervical swabs, SCVSs, urethral swabs, and FVU samples, respectively (P < 0.001 for each comparison). Only the presence of multiple symptoms or clinical signs was associated with organism load in women. These results show that FVU is a suitable noninvasive sample type for men, given the fact that its chlamydial load did not differ significantly from that of urethral swabs. Given their higher organism load compared with FVU, SCVSs are the preferred noninvasive sample type for women.Urogenital infection with Chlamydia trachomatis is the most commonly reported bacterial sexually transmitted infection (STI) and continues to be a major public health problem worldwide (4, 35). Given that most chlamydial infections are asymptomatic in both men and women, they often remain undiagnosed and untreated and therefore provide a reservoir for the disease (33). Infection of the upper genital tract may lead to complications, such as epididymitis in men and pelvic inflammatory disease in women. The inflammation and subsequent tissue scarring associated with the latter can lead to more serious sequelae (4).Effective control of chlamydial infection within a population requires early diagnosis and prompt treatment of asymptomatic individuals (28). Targeted and regular screening is also recommended for people in high-risk groups or with a past history of genital chlamydial infection (14). The most common sites of infection in women are the cervix and urethra. Infected cells are shed from the endocervix into the vagina and are present in vaginal secretions. Infected epithelial cells from the urethra and the associated C. trachomatis elementary bodies (EBs) can also be detected in first-void urine (FVU) (3, 16). Potentially suitable clinical specimens for detection of chlamydial infection in women thus include urethral, vaginal, and endocervical swabs, self-inserted tampons, and FVU samples (3, 12). For screening programs, noninvasive specimens, such as vaginal swabs, tampons, and FVU, are preferable to invasive urethral and endocervical swabs because they overcome several barriers associated with the traditional diagnostic pathway (5, 11). Sensitivity of C. trachomatis detection with vag...

The parasegment-specific expression of the three Drosophila Bithorax complex homeotic genes is orchestrated by nine functionally autonomous regulatory domains. Functional autonomy depends upon special elements called boundaries or insulators that are located between each domain. The boundaries ensure the independent activity of each domain by blocking adventitious interactions with initiators, enhancers and silencers in the neighboring domains. However, this blocking activity poses a regulatory paradox--the Bithorax boundaries are also able to insulate promoters from regulatory interactions with enhancers and silencers and six of the nine Bithorax regulatory domains are separated from their target genes by at least one boundary element. Here we consider several mechanisms that have been suggested for how the Bithorax regulatory domains are able to bypass intervening boundary elements and direct the appropriate parasegment-specific temporal and spatial expression of their target gene.

It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

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