Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved 
patterns of histone modification. Whereas histone modifications have established 
roles in transcription initiation, their functions during elongation are not 
understood. Mono-ubiquitylation of histone H2B (H2Bub1) plays a key role in 
coordinating co-transcriptional histone modification by promoting site-specific 
methylation of histone H3. H2Bub1 also regulates gene expression through an 
unidentified, methylation-independent mechanism. Here we reveal bidirectional 
communication between H2Bub1 and Cdk9, the ortholog of metazoan positive 
transcription elongation factor b (P-TEFb), in the fission yeast 
Schizosaccharomyces pombe. Chemical and classical genetic analyses indicate that 
lowering Cdk9 activity or preventing phosphorylation of its substrate, the 
transcription processivity factor Spt5, reduces H2Bub1 in vivo. Conversely, 
mutations in the H2Bub1 pathway impair Cdk9 recruitment to chromatin and 
decrease Spt5 phosphorylation. Moreover, an Spt5 phosphorylation-site mutation, 
combined with deletion of the histone H3 Lys4 methyltransferase Set1, 
phenocopies morphologic and growth defects due to H2Bub1 loss, suggesting 
independent, partially redundant roles for Cdk9 and Set1 downstream of H2Bub1. 
Surprisingly, mutation of the histone H2B ubiquitin-acceptor residue relaxes the 
Cdk9 activity requirement in vivo, and cdk9 mutations suppress cell-morphology 
defects in H2Bub1-deficient strains. Genome-wide analyses by chromatin 
immunoprecipitation also demonstrate opposing effects of Cdk9 and H2Bub1 on 
distribution of transcribing RNAPII. Therefore, whereas mutual dependence of 
H2Bub1 and Spt5 phosphorylation indicates positive feedback, mutual suppression 
by cdk9 and H2Bub1-pathway mutations suggests antagonistic functions that must 
be kept in balance to regulate elongation. Loss of H2Bub1 disrupts that balance 
and leads to deranged gene expression and aberrant cell morphologies, revealing 
a novel function of a conserved, co-transcriptional histone modification.