YY1-dependent chromatin structure stabilization of B lineage commitment

During B cell lineage commitment, a dynamic shift of genes between transcriptionally restricted and
transcriptionally permissive compartments at the pre-pro-B to pro-B cell transition results in activation of
the B lineage program and repression of alternative lineage programs. While B lineage commitment is
generally believed to be driven by lineage-specific transcription factors, we have made the surprising
discovery that conditional knock-out of the ubiquitous transcription factor YY1 results in loss of B lineage
commitment, allowing subsequent development into the T cell lineage both in vitro and in vivo. Pioneer
transcription factors such as Ebf1 promote transcription of B lineages genes and repress expression of
alternative lineage genes to initiate B lineage commitment, but stable commitment requires changes in
chromatin structures at the pro-B cell stage. As YY1 is a key factor controlling lineage-specific gene
regulatory long-range chromatin interactions (LRCIs), we hypothesize that YY1 knock-out in pro-B cells
results in loss of chromatin LRCIs that stably maintain B lineage-specific gene expression. Consistent
with this, we found reduction of B lineage transcripts after YY1 knock-out. YY1 can also mediate
Polycomb Group (PcG) repression, and we found that YY1 knock-out resulted in increased expression
of alternative lineage genes, suggesting that YY1 loss abrogates repressive chromatin structures
needed to prevent expression of these genes. Thus, we hypothesize that YY1 knock-out in pro-B cells
results in lost chromatin structures that stably maintain lineage-specific gene expression, as well as loss
of repressive chromatin structures needed to prevent alternative lineage gene expression, thus leading
to lost B lineage commitment. To test this, we will determine chromatin folding patterns, nuclear
localization of key genes, chromatin accessibility, and epigenetic structures in wild-type and YY1-null
pro-B cells to define the genomic structures regulated by YY1 during B lineage commitment. To
determine if analogous effects of YY1 are operative in the T lineage, we will determine if YY1 loss
promotes lineage plasticity of YY1-null DN3 cells. YY1 is also necessary in pro-B cells for Igk locus
contraction required for rearrangement of distal Vk genes. It has been suggested that YY1 plays a
structural role in regulating chromatin structures, but it is unclear if this requires the YY1 transcriptional
activation, PcG, or self-association functions. We will utilize an established panel of YY1 mutants that
are compromised in these functions to assess in parallel, the mechanisms of YY1 regulation of
chromatin structures needed for B lineage commitment, and those needed for Igk locus contraction and
Jk-Vk rearrangement. As YY1 is involved in embryogenesis and development of multiple tissue types,
determining how YY1 controls genomic structures to specify B lineage commitment will provide a new
paradigm for the function of a ubiquitous factor in lineage-specific development.

Grant Number: 5R01AI155540-05
NIH Institute/Center: NIH
Principal Investigator: Michael Atchison