RFX transcription factors are essential for hearing in mice

Abstract

Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-like cells. Importantly, although the transcriptional regulators of embryonic HC development have been described, little is known about the postnatal regulators of maturating HCs. Here we apply a cell type-specific functional genomic analysis to the transcriptomes of auditory and vestibular sensory epithelia from early postnatal mice. We identify RFX transcription factors as essential and evolutionarily conserved regulators of the HC-specific transcriptomes, and detect Rfx1,2,3,5 and 7 in the developing HCs. To understand the role of RFX in hearing, we generate Rfx1/3 conditional knockout mice. We show that these mice are deaf secondary to rapid loss of initially well-formed outer HCs. These data identify an essential role for RFX in hearing and survival of the terminally differentiating outer HCs.

Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression

“…Previous studies have found that proximal regulatory regions of genes expressed in motile ciliated cells are enriched in Rfx binding sites[34,35] and that in Xenopus , Rfx2 binding is found extensively in association with cilia genes. [22] Consistent with these observations, the binding site for the Rfx proteins was by far the most enriched motif identified when sequences (+/-100 bases) around the TSS of the core MCC genes (verified by H3K4me3, S6 Fig) were examined for overrepresented motifs using an unbiased approach (Fig 3A).…”

“…[22,48,56] In addition, the expanded Rfx family in vertebrates clearly has major roles in enabling gene expression that serves non-cilia functions,[57] based on single family member mutants (S2 Fig) as well as compound mutants. [34] The Rfx family also appears to have broad functions based on the high occurrence of Rfx binding motifs within non-coding regions that are conserved within mammalian genomes. [58] Thus, the analysis of MCC gene promoters suggests that Rfx factors are major players in MCC gene expression but other observations suggest they act by facilitating the action of other TFs.…”

ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits

“…Involvement of RFX proteins is supported by ChIP-Seq data from other studies, for example for murine Rfx1 and Rfx3 in neural progenitors and Min6 insulinoma cells, respectively [100, 101] (data accessed via the Cistrome Data Browser [102]). Vertebrate RFX2 and RFX3 have well-established roles in regulating ciliary genes in various tissues [103], while RFX1 has recently been reported to stimulate transcription of key ciliogenic genes downstream of leptin in hypothalamic neurons and to regulate other ciliary genes [104, 105].…”

Development and regeneration of vestibular hair cells in mammals

“…A number of high throughput methods are being used to profile the transcriptome and proteome during processes like hair cell differentiation [24, 184–186], growth of the hair bundle [187, 188], the cellular response to ototoxic insult [189], and hair cell regeneration in non-mammals [190–192]. As applied to differentiation and regeneration, single-cell transcriptional profiling is particularly powerful, since it characterizes these processes for distinct cell types and subtypes in an unbiased manner.…”