The ubiquitous tandem kinase JIL-1 is essential for Drosophila development. Its 
role in defining decondensed domains of larval polytene chromosomes is well 
established, but its involvement in transcription regulation has remained 
controversial. For a first comprehensive molecular characterisation of JIL-1, we 
generated a high-resolution, chromosome-wide interaction profile of the kinase 
in Drosophila cells and determined its role in transcription. JIL-1 binds active 
genes along their entire length. The presence of the kinase is not proportional 
to average transcription levels or polymerase density. Comparison of JIL-1 
association with elongating RNA polymerase and a variety of histone 
modifications suggests two distinct targeting principles. A basal level of JIL-1 
binding can be defined that correlates best with the methylation of histone H3 
at lysine 36, a mark that is placed co-transcriptionally. The additional 
acetylation of H4K16 defines a second state characterised by approximately 
twofold elevated JIL-1 levels, which is particularly prominent on the 
dosage-compensated male X chromosome. Phosphorylation of the histone H3 
N-terminus by JIL-1 in vitro is compatible with other tail modifications. In 
vivo, phosphorylation of H3 at serine 10, together with acetylation at lysine 
14, creates a composite histone mark that is enriched at JIL-1 binding regions. 
Its depletion by RNA interference leads to a modest, but significant, decrease 
of transcription from the male X chromosome. Collectively, the results suggest 
that JIL-1 participates in a complex histone modification network that 
characterises active, decondensed chromatin. We hypothesise that one specific 
role of JIL-1 may be to reinforce, rather than to establish, the status of 
active chromatin through the phosphorylation of histone H3 at serine 10.