ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation

Abstract

Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5′ splice site motifs within nuclear speckles

“…This is in agreement with previous results where the tethering of U1-70K to a reporter mRNA promoted nuclear retention without targeting the transcript to nuclear speckles ( Takemura et al 2011 ). Recently, it has been shown that the amino-terminal domain of ZFC3H1 forms phase-separated nuclear compartments, which partially overlap with nuclear speckles ( Wang et al 2021 ). The formation of these phase-separated compartments is thought to be required for the nuclear retention of substrate RNAs, which get trapped in these structures ( Silla et al 2018 ; Wang et al 2021 ).…”

“…Recently, it has been shown that the amino-terminal domain of ZFC3H1 forms phase-separated nuclear compartments, which partially overlap with nuclear speckles ( Wang et al 2021 ). The formation of these phase-separated compartments is thought to be required for the nuclear retention of substrate RNAs, which get trapped in these structures ( Silla et al 2018 ; Wang et al 2021 ). It remains possible that the 5′SS motif targets mRNAs to structures that only partially overlap with speckles, and this may explain why the nuclear speckle localization of some IPA transcripts, such as the PCF11 IPA transcript ( Supplemental Fig.…”

“…While MTR4 is found in other complexes and generally targets RNAs to the nuclear exosome (Schilders et al 2007;Ogami et al 2018), ZFC3H1 is thought to form the core of the PAXT complex and specifically recognize certain RNA substrates. Although it contains a zinc-finger domain and a coiled-coil region, it is largely unstructured and can promote phase-separation when expressed in cells (Wang et al 2021).…”

“…While MTR4 is found in other complexes and generally targets RNAs to the nuclear exosome ( Schilders et al 2007 ; Ogami et al 2018 ), ZFC3H1 is thought to form the core of the PAXT complex and specifically recognize certain RNA substrates. Although it contains a zinc-finger domain and a coiled-coil region, it is largely unstructured and can promote phase-separation when expressed in cells ( Wang et al 2021 ). PABPN1 binds to poly(A)-tails and has been implicated in many different aspects of RNA metabolism, not only in PAXT-dependent RNA surveillance but also in nuclear export and nonsense-mediated decay ( Sato and Maquat 2009 ; Apponi et al 2010 ).…”

Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function

“…Although the full composition of the polyA+ RNA foci is yet to be determined, it at least includes all the PAXT components as well as SNHG RNAs and exosome target mRNAs [34,35]. The formation of the foci depends on the condensation activity of ZFC3H1 through its N-terminal intrinsically disordered region [36], and the depletion of ZFC3H1 results in disruption of the nuclear polyA+ foci formed upon exosome inactivation [35,36]. Therefore, ZFC3H1 functions not only as a degradation factor but also as a nuclear RNA retention factor.…”