Expression was examined at four phases of embryonic stage 5. The striped pattern becomes visible in phase 1, (0-5'), all stripes except stripe 7 are expressed during phase 2 (5-17'), and their spacing and expression levels become largely uniform by phase 3 (17-30'). The stripes initially appear less clearly separated and more graded.

run is expressed in anterior midline glia but not in posterior midline glia in stage 12 embryos. After its early pair rule and segment polarity expression patterns in early embryos, run expression becomes more expansive. At stage 10, run expression along with en expression divides the midline into four regions, anterior (runt[+], en[-]), middle (runt[-], en[-]), posterior (runt[-], en[+]), and extreme posterior (runt[-], en[-]). At stage 10, run is expressed in 4-5 midline cells. At stage 11, expression is initiated in 2-3 additional cells flanking the runt[+] en[-] region, thus generating about six run[+] anterior midline glia in the anterior of each segment. By the end of stage 11, run is expressed in all anterior midline glia.

run transcription is repressed by ectopic eve protein in eve^hs.PS embryos. Timing suggests that eve is a direct regulator of run. run is activated by ectopic eve if the heat shock (and resulting pulse of eve protein) occurs earlier.

run transcripts are most abundant between 2 and 4 hours of embryonic development on northern blots. They are detected in younger and older embryos at much lower levels. Low levels of transcript are also detected in larvae and adult females. run transcripts are detected by in situ hybridization at embryonic cycle 13 in a broad domain extending from 10% to 70% egg length. Early in stage 14, a pair rule pattern of seven stripes becomes apparent with the stripes of expression appearing to be wider than the intervening gaps of expression. Just prior to the completion of cellularization, the pattern changes to a pattern of expression in every segment. This pattern persists throughout germ band extension. At this time, expression is also observed in the head region from 75-85% egg length and in the proctodeal primordium. The boundaries of the run expression stripes were compared to those of other segmentation genes. The run stripes are as wide or wider than the ftz stripes. The run stripes partially overlap the eve stripes and partilly overlap the ftz stripes but appear to be in direct opposition to the h stripes. A difference was observed in the localization of run and Kr transcripts within the cortical cytoplasm.

run protein is expressed in the differentiated neurons of the middle domain of the medulla anlage from third instar larvae and in pupa until 12h APF. Its domain is located in between the concentric domains of vvl distally and hth proximally. Thereafter and in adults, run protein is found in layers 8 to 10 of the medulla.

Expression assayed at stages 9, 11, 13, and 17. Expression may be continuous between assayed stages in some tissues.

Expression in procephalic neuroblasts stage 9-11: deuterocerebrum - d1-3, d5, v2, v5-7; protocerebrum - ad3, ad11, cd8-12, cd15-20, pd3, pd9, pd12, pd13, pd17, pd18, pv1

run protein is localized to row 2/3 in wild type embryos but expands posteriorly into row 4 in wg^- embryos.

run is expressed extensively in the developing nervous system. Neural expression is first observed in delaminating neuroblasts at 4.5 hours of development (about 5 per hemisegment). Expression is also observed in daughter ganglion mother cells and becomes increasingly complex as development proceeds. Double staining with antibodies against eve protein show that one site of run protein expression is in all of the neurons and GMCs of the EL neuron lineage. Another site of run protein expression is in some of the U neurons (CQ neurons).

run protein is expressed in a pair rule pattern of 7 stripes in the blastoderm embryo. The position of run protein stripes was compared to that of other segmentation genes. The h protein stripes are anterior to and complementary to the run protein stripes. The eve protein stripes lie anterior to the run protein stripes but overlap them partially. Two rows of eve expression are anterior to a two-row region of overlap with run followed by two rows of run expression and then two rows of non-expression before the next eve stripe. Similarly, run and ftz double staining shows that the run stripes are anterior to the ftz stripes but are partially overlapping. In early germ band extension the run pattern changes from a pair rule pattern to a segmental pattern and in addition, expression is observed in the head. Two groups of cells are stained in the head, a dorso-lateral group of 10 cells and a ventral group of 7 less intensely staining cells. The pattern becomes more complex at full germ band extension. At this stage in the segmented part of the embryo, the staining is strongest just off the midline and fades laterally. The stained cells along the midline probably correspond to neuroblasts. During germ band retraction, staining becomes evident in both the CNS and the PNS. Roughly 50 cells per hemi-segment are stained in the CNS at the completion of germ band retraction. PNS staining is also evident.