Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains

Abstract

The low-complexity (LC) domains of the products of the fused in sarcoma (FUS), Ewings sarcoma (EWS), and TAF15 genes are translocated onto a variety of different DNA-binding domains and thereby assist in driving the formation of cancerous cells. In the context of the translocated fusion proteins, these LC sequences function as transcriptional activation domains. Here, we show that polymeric fibers formed from these LC domains directly bind the C-terminal domain (CTD) of RNA polymerase II in a manner reversible by phosphorylation of the iterated, heptad repeats of the CTD. Mutational analysis indicates that the degree of binding between the CTD and the LC domain polymers correlates with the strength of transcriptional activation. These studies offer a simple means of conceptualizing how RNA polymerase II is recruited to active genes in its unphosphorylated state and released for elongation following phosphorylation of the CTD.

Figure 1. Correlation Between Transcriptional Activation and Hydrogel Binding of Native and Mutated Derivatives of the LC Domain of FUS

(A) The LC domain of FUS was linked to the DNA binding domain of GAL4 and assayed for activation of a GAL4 reporter gene in transiently transfected U20S cells. Activity of the native LC sequence was compared with 43 variants wherein different number of tyrosine residues were randomly mutated to serine (see text). Identities of specific tyrosine-to-serine changes in each mutant are shown in Table S1. Expression levels for all test protein were assayed by western blotting as shown below histograms. (B) The GFP-linked LC domains of FUS carrying the same mutations as (A) were exposed to mCherry:FUS hydrogels (left) and initial binding rates were measured (right). (C) A correlation plot between the transactivation activity and hydrogel binding rate of the individual LC mutants. Note that there is but one significant outlier indicated by a red circle. This is the “2A mutant” and described in more detail in the text and Figure 5.

Figure 2. Biotinylated Isoxazole Preferentially Precipitates Unphosphorylated CTD of RNA polymerase II

Western blot of total cell extract (T) or b-isox pellet (P) with different CTD antibodies. Bands shown in the four panels correspond in size to the largest subunit of RNA polymerase II (217 kD). The 8WG16 antibody recognizes the unphosphorylated CTD, the 3E10 antibody recognizes serine 2 phosphorylated CTD, the 3E8 antibody recognizes serine 5 phosphorylated CTD, and the 4E12 antibody recognizes serine 7 phosphorylated CTD. B-isox significantly precipitates only unphosphorylated CTD of Pol II. See also Figure S1.

Figure 3. Selective Binding of GFP:CTD to mCherry:TAF15 Hydrogel Droplets

(A) Hydrogels composed of LC domains of mCherry:TAF15, mCherry:FUS, mCherry:EWS, mCherry:hnRNPA2 and mCherry:CIRP were incubated with a soluble form of GFP linked to the C-terminal 26 heptad repeats of the CTD of mammalian RNA polymerase II. Little or no retention of the GFP:CTD_C26 protein was observed for the mCherry:hnRNPA2 or mCherry:CIRBP hydrogel droplets, and weak binding was observed for mCherry:FUS and mCherry:EWS hydrogels. By contrast, strong retention was observed for mCherry:TAF15 hydrogel droplets. See also Figure S2. (B) The degenerate C-terminal half of the CTD (GFP:CTD_C20) binds mCherry:TAF15 hydrogel stronger than the highly conserved, N-terminal half of the CTD (GFP:CTD_N20). (C) The binding intensity of the GFP:CTD degenerate repeats to mCherry:TAF15 hydrogel correlates with the number of heptad repeats, with no binding observed for GFP:CTD_C5, weak binding for GFP:CTD_C10 and strong binding for GFP:CTD_C15, GFP:CTD_C20 and GFP:CTD_C26.

Figure 4. CDK7-mediated Release of GFP:CTD_C26 from mCherry:TAF15 Hydrogel Droplets

(A) The GFP:CTD_C26 trapped by mCherry:TAF15 hydrogel was released upon addition of CDK7 or CDK9 in the presence of ATP in an enzyme concentration-dependent manner. (B) Hydrogel droplets of mCherry:TAF15 (red) were exposed to GFP:CTD_C26 (green). Chamber slides containing individual hydrogel droplets were exposed to CDK7 plus ATP (top row), CDK7 alone (middle row) or ATP alone (bottom row). Samples exposed to both CDK7 and ATP revealed the time-dependent release of GFP:CTD_C26. See also Movie S1. (C) Western blot analysis of materials released into the well of chamber slides revealed progressive increases in the presence of soluble, phosphorylated CTD (top) and soluble GFP:CTD_C26 (bottom). See also Figure S3.

Figure 5. Hydrogels Formed from the 2A Mutant of FUS LC Domain Display Enhanced CTD Binding

(A) 2A mutant of FUS LC domain, which exhibits enhanced transactivation activity relative to the wild type protein (Figure 1C), carries tyrosine-to-serine mutations at tyrosine within the 16^th and 20^th [G/S]Y[G/S] triplet repeats (Figure 5B). The 2A mutant LC domain was fused with mCherry, and hydrogel binding assays were carried out with GFP:CTD fusions carrying different numbers of heptad repeats. Compared with hydrogel droplets formed with the native LC domain of FUS, those formed from the 2A mutant showed enhanced binding to GFP:CTD_C20 and GFP:CTD_C26. See also Figure S4. (B) Alignment of [G/S]Y[G/S] triplet repeats in low complexity domains of FUS (left) and TAF15 (right). The two tyrosineto-serine mutations causing FUS to suffer a gain-of-function enhancement in transcriptional activation and CTD binding are highlighted in blue. All triplet repeats of TAF15 carrying an aspartic acid or glutamic acid adjacent to tyrosine are highlighted in green. Canonical [G/S]Y[G/S] triplet repeats of both LC domains are shown in red.

Figure 6. DNA-dependent Enhancement of Fiber Formation of FUS-FLI Fusion Protein

(A) mCherry:FUS LC domain-FLI DNA-binding domain fusion protein (0.5 μM) was incubated with microsatellite DNA (20 nM) in the presence of 35% glycerol. After 1 hr incubation, materials in the solution were visualized by transmission electron microscopy. FUS-FLI fibers grew long and became large sleave. (B) mCherry:FUS-FLI protein was incubated in the presence of 35% glycerol (no DNA). Small amounts of spontaneous nucleation and fiber growth were observed. All scale bars indicate 0.5 μm. See also Figure S5.

Figure 7. Polymerization of the LC Domain of TAF15 is Required for Both Transcriptional Activation and CTD Binding

(A) 48 tyrosine-to-serine mutations were randomly introduced into the LC domain of TAF15 (Table S4). Mutants were assayed for transcriptional activation capacity as GAL4 fusion proteins. Expression levels for individual test proteins were monitored by Western blotting as displayed below histogram depictions of transcriptional activation measurements. (B) mCherry fusion proteins linked to the native LC domain of TAF15 (WT), the 1F mutant, the 2H mutant and the 3K mutant were incubated under conditions favorable for polymerization (Experimental Procedures). Fluorescence microscopy was employed as an assay for fiberization of the four test proteins. See also Movie S2. (C) Co-immunoprecipitation assay was conducted by mixing Flag-tagged GFP:CTD_C26 with HA-tagged versions of mCherry linked to the native form of the TAF15 LC domain, or to the 1F, 2H or 3K tyrosine-to-serine mutants. Following HA-mediated immunoprecipitation, samples were run on a denaturing SDS-PAGE gel and subjected to Western blotting using either anti-Flag or anti-HA antibodies. See also Figure S6. (D) Schematic Concept of RNA Polymerase II Recruitment by LC Domain Polymers. 1) The C-terminal domain (CTD) of RNA polymerase II does not bind to monomers of the unstructured LC domain of FET protein fused to the ETS DNA-binding domain. 2) Once the ETS DNA-binding domain of the fusion protein binds to the GGAA repeats on microsatellite DNA, the LC domains of FET protein form fibrous polymer that can recruit RNA polymerase II via direct interaction with the CTD. 3) Phosphorylation of serine residues 2, 5 and 7 of the CTD heptad repeats by CDK7 or CDK9 facilitates release of RNA polymerase II from the FET LC domain polymer.