ATP-binding cassette protein ABCF1 couples gene transcription with maintenance of genome integrity in embryonic stem cells

Abstract

OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell-specific gene expression programs. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here we report the identification of ATP-binding cassette subfamily F member 1 (ABCF1) as a critical coactivator for OCT4/SOX2. ABCF1 is required for pluripotency gene expression and stem cell self-renewal. ABCF1 binds co-dependent coactivators XPC and DKC1 via its intrinsically disordered region and stimulates transcription by linking SOX2 to the transcription machinery. Furthermore, in response to pathogen infection and DNA damage, ABCF1 binds intracellular DNAs accumulated in cells, concomitant with loss of SOX2 interaction and pluripotency gene transcription. This results in spontaneous differentiation of compromised stem cells and elimination from the self-renewing population. Thus, ABCF1 directly couples pluripotency gene transcription with sensing aberrant DNAs and acts as a checkpoint for self-renewal to safeguard stem cell fidelity and genome integrity.

Low complexity domains, condensates, and stem cell pluripotency

“…Most if not all of the regulatory factors described thus far are utilized by many transcription factors to activate their target genes in both ESCs and somatic cells. Our work and others indicated that robust transcriptional activation by OCT4 and SOX2 in ESCs requires additional coactivators that are distinct from Mediator[ 30 , 86 - 88 ]. Using a fully reconstituted in vitro transcription assay, we detected multiple novel coactivators that work in concert with OCT4 and SOX2 to activate pluripotency gene transcription.…”

“…In addition, the flexible nature of LCDs is thought to facilitate their interaction with multiple protein partners, by rapidly adopting an ensemble of conformations[ 27 , 28 ] Indeed, LCD’s ability to bind multiple proteins, also known as multivalency, is a major driving force of LLPS by lowering threshold concentration[ 29 ]. It is worth emphasizing that while LCDs are unstructured sequences, they do not always bind promiscuously to any proteins; instead, they can be selective for binding partners[ 30 - 32 ]. More importantly, because these selective multivalent interactions are usually weak and transient, as opposed to the high affinity (but low valency) “lock-and-key” interactions found in ligand-receptor complexes, they allow dynamic regulation of LLPS properties, condensate composition, and biochemical reactions that take place inside these bodies.…”

“…Using a fully reconstituted in vitro transcription assay, we detected multiple novel coactivators that work in concert with OCT4 and SOX2 to activate pluripotency gene transcription. Biochemical purification of these coactivators led to the discovery of three stem cell-specific coactivators - the nucleotide excision repair protein xeroderma pigmentosum, complementation group C (XPC)[ 87 - 90 ], dyskerin (DKC1) ribonucleoprotein complex[ 86 ], and the ATP-binding cassette subfamily F member 1 (ABCF1)[ 30 ] (Figure 1B ). We found that the ability of XPC and DKC1 to stimulate OCT4/SOX2-activated transcription is strongly dependent on ABCF1, indicating a pivotal role of ABCF1 in mediating stem cell-specific transcription.…”

“…However, because ESCs lack a canonical innate immune response to DNAs[ 170 - 172 ], the functional consequence of DNA sensing by ABCF1 in ESCs is unknown. Our identification of ABCF1 as a critical stem cell coactivator prompted us to examine whether ABCF1 can couple DNA sensing with stem cell transcription in response to DNA damage[ 30 ] (Figure 5A ). We found that ABCF1 specifically binds double-stranded (ds) but not single-stranded (ss) DNAs in an LCD-dependent manner.…”