We have shown that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin, modulate gene expression and have epistatic interactions with transcription factors. We also found that, similar to the lack of penetrance for biallelic SMARCAL1 mutations in humans, deficiency of the orthologs in fruit flies and mice is insufficient to cause disease in these organisms and that penetrance is associated with environmental or genetic insults that further modify gene expression. From these observations, we hypothesize that the annealing helicase function of SMARCAL1, Marcal1 or Smarcal1 maintains DNA topology to buffer variability in gene expression and thereby mitigates penetrance of pathologic traits arising from environmental and genetic insults (Fig. ).
Figure 7. Model depicting the contribution of thresholded variations in gene expression to the penetrance of SIOD. (A) SMARCAL1 orthologs buffer random fluctuations in gene expression by modulating DNA helicity within the promoter and across transcribed regions. (more ...)
As an annealing helicase, SMARCAL1 resolves ss-to-ds DNA transitions (26
). Such transitions occur during DNA replication, repair, recombination and transcription, and recent studies have shown that SMARCAL1 participates in the DNA stress response both at stalled replication forks and at double-strand DNA breaks repaired by recombination or end joining (28
). However, since defects of DNA repair, replication and recombination have not been detected clinically in SIOD patients (53
), we reasoned that, like many DNA repair enzymes (33
), SMARCAL1 contributes to transcription and that its deficiency results in gene expression changes contributing to the pathophysiology of SIOD.
There are at least three non-exclusive models by which SMARCAL1 deficiency can alter gene expression. First, unrepaired DNA damage impedes RpII progression and impairs transcription (55
). Second, like ERCC6, SMARCAL1 could be part of the transcriptional complex and thus its deficiency directly affects RpII transcription (34
). Third, the DNA structure maintained by SMARCAL1 modulates gene expression. Evidence against the first is the findings that (i) SIOD patients do not have ultraviolet light hypersensitivity (53
), (ii) SMARCAL1
-deficient fibroblasts do not have delayed recovery of mRNA synthesis following exposure to ultraviolet light or illudin S (C.F.B., unpublished data), and (iii) the proliferation rate of SMARCAL1-deficient cells is not detectably perturbed relative to control cells even though the transition from G2 to M phase is slightly delayed (28
). Evidence against the second proposed mechanism includes (i) failure of SMARCAL1 homologues to co-purify or co-immunoprecipitate with RpII and transcription complexes studied (56
) and (ii) failure of RpII to co-purify or co-immunoprecipitate with SMARCAL1 or Marcal1. We hypothesize, therefore, that the SMARCAL1
orthologs influence gene expression through the maintenance of DNA structure.
SMARCAL1 could modulate RpII transcription through the maintenance of the topology and helicity of duplex DNA. In prokaryotes, changes in DNA helicity cause gene expression to be enhanced, repressed or unchanged (59
), and the equilibrium between duplex DNA and strand opening modulates transcription factor binding and production of full-length RNA (60
). Similarly, in eukaryotes, in vitro
and in vivo
studies of MYC
expression show that transcription-induced supercoiling melts MYC
far upstream element (FUSE) to enable binding by structure-sensitive regulatory proteins such as FUSE-binding protein (FBP) and FBP-interacting repressor (FIR) (62
). Binding of FBP and FIR to FUSE modifies the rate of MYC
promoter firing (62
). Since negative supercoiling and positive supercoiling are generated upstream and downstream of the transcription bubbles (64
), respectively, SMARCAL1, Marcal1 or Smarcal1 might contribute to the maintenance of DNA topology within and adjacent to transcribed regions. Deficiency of these orthologs would then alter gene expression as a consequence of the changes in DNA helicity or topology.
This model could also explain why, in contrast to transcription factors that bind conserved promoter elements, SMARCAL1
deficiencies do not consistently affect expression of homologous genes. Homologous genes in human, flies and mice frequently reside in different genomic neighborhoods or chromatin regions (66
); therefore, the need for the SMARCAL1, Marcal1 and Smarcal1 to maintain duplex DNA around homologous genes might vary among species and thereby have differing effects on expression of homologous genes.
In summary, SMARCAL1 deficiency is insufficient to cause SIOD, but the addition of environmental and genetic insults affecting transcription does cause penetrance and partial recapitulation of SIOD in model organisms. At both the molecular and genetic levels, SMARCAL1 plays a role in modulating gene expression. One model for the penetrance of biallelic mutations of SMARCAL1 orthologs is shown in Figure . In this model, SMARCAL1 orthologs modulate random fluctuations in gene expression and thereby potentiate or capacitate phenotypic changes induced by genetic or non-genetic insults, whereas the absence of the SMARCAL1 orthologs creates a chromatin environment permissive for such insults, pushing gene expression beyond a threshold of disease (Fig. ).