Figure 7. Primary cells from prostate tumours are more sensitive to ML-60218 than adjacent non-cancerous cells from the ... Figure 7. Primary cells from.

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Figure 7. Primary cells from prostate tumours are more sensitive to ML-60218 than adjacent non-cancerous cells from the ... Figure 7. Primary cells from prostate tumours are more sensitive to ML-60218 than adjacent non-cancerous cells from the same tissues. (A) Means of cell numbers from tumours (left) and non-cancerous tumour-adjacent samples (right) from patients H646, H643, H627 and H637 during culture for 3 days in the presence or absence of 20 μM ML-60218. (B) Means of the number of viable cells, as determined using alamar blue, after 2 days of exposure of tumour samples (left) and non-cancerous tumour-adjacent samples (right) from patients H646, H643, H627 and H637 to the indicated concentrations of ML-60218, in three independent experiments. * indicates P < 0.05 relative to control by t-test; ** indicates P < 0.01; *** indicates P < 0.005. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. Effects of DR2 Alu RNA on differentiation and proliferation of PC-3 cells. (A) Northern blot of RNA harvested ... Figure 4. Effects of DR2 Alu RNA on differentiation and proliferation of PC-3 cells. (A) Northern blot of RNA harvested from PC-3 cells after 48 h treatment with or without 20 μM ML-60218 and hybridized with probes for U2 snRNA (pol II-transcribed control) and each strand of NANOG-Alu-Sx RNA. (B) Means of the relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG, as determined by RT-qPCR in 3–5 independent experiments, in PC-3 cells harvested 48 hrs after transfection with a 33nt synthetic RNA corresponding to part of the NANOG-Alu-Sx sequence. (C) Western blot of NANOG and actin protein expression in PC-3 cells 48 h after mock transfection (control) or transfection with a 33nt synthetic RNA corresponding to forward or reverse strands of part of the NANOG-Alu-Sx sequence. (D) Means of PC-3 cell numbers over 3 days following transfection with a 33nt synthetic RNA corresponding to part of the NANOG-Alu-Sx sequence, as indicated, in 4 independent experiments. (E) Means of the percentage of PC-3 cells staining positively for Ki67 proliferation marker 48 h after mock transfection or transfection with a 33nt synthetic RNA corresponding to part of the NANOG-Alu-Sx sequence or a 56nt synthetic RNA corresponding to part of the DR2 Alu consensus sequence. (F) Means of the relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG, as determined by RT-qPCR in three independent experiments, in PC-3 cells harvested 48 h after transfection with a 56nt synthetic RNA corresponding to part of the DR2 Alu consensus sequence. (G) Means of PC-3 cell numbers over 3 days following transfection with a 56nt synthetic RNA corresponding to part of the DR2 Alu consensus sequence, as indicated, in three independent experiments. * indicates P < 0.05 relative to control by t-test; ** indicates P < 0.01; *** indicates P < 0.005. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Benign PNT2C2 prostate cells express less POLR3G and are less sensitive to ML-60218 than PC-3 cells. (A) ... Figure 5. Benign PNT2C2 prostate cells express less POLR3G and are less sensitive to ML-60218 than PC-3 cells. (A) Normalized relative levels of POLR3A, POLR3G and POLR3GL mRNAs in PNT2C2 and PC-3 cells, as determined by RT-qPCR in two independent experiments. (B) Western blot of POLR3A, POLR3G, POLR3GL and actin proteins in PC-3 and PNT2C2 cells. (C) Means of the relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG in PNT2C2 cells harvested 48 hrs after treatment with or without 20μM ML-60218, as determined by RT-qPCR in three independent experiments. (D) Means of PNT2C2 cell numbers over 3 days in presence or absence of 20μM ML-60218, in three independent experiments. (E) Western blot of POLR3G and actin in PNT2C2 cells harvested 48 h after transfection with control or POLR3G-targeting siRNAs. (F) Means of PNT2C2 cell numbers over 3 days following transfection with control or POLR3G-targeting siRNAs, as indicated, in three independent experiments. (G) Means of the percentage of viable PNT2C2 and PC-3 cells, as determined using Alamar blue, after 2 days exposure to the indicated concentrations of ML-60218, in three independent experiments. * indicates P < 0.05 relative to control by t-test; *** indicates P < 0.005. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Primary cells from prostate tumours differentiate in response to ML-60218. (A) Relative changes in normalized ... Figure 6. Primary cells from prostate tumours differentiate in response to ML-60218. (A) Relative changes in normalized expression of the indicated transcripts, as determined by RT-qPCR, when tumour cells from patients H646, H643, H627 and H637 were treated for 48 h with or without 20 μM ML-60218. Means are indicated by horizontal lines and values for each patient are indicated by symbols. (B) Normalized relative levels of POLR3A, POLR3G and POLR3GL mRNAs in normal and cancer cells from patients H646, H643, H627 and H637, as determined by RT-qPCR. * indicates P < 0.05 relative to normal by t-test. Error bars represent S.E.M. (C) Relative changes in expression of the indicated transcripts, as determined by RT-qPCR, when cells from non-cancerous tumour-adjacent cells from patients H646, H643, H627 and H637 were treated for 48 h with or without 20 μM ML-60218. Means are indicated by horizontal lines and values for each patient are indicated by symbols. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 1. Differential response of PC-3 cells to RNAi-mediated depletion of pol III subunits. (A) Western blot of ... Figure 1. Differential response of PC-3 cells to RNAi-mediated depletion of pol III subunits. (A) Western blot of POLR3G and actin in PC-3 cells harvested 48 hrs after transfection with control or POLR3G-targeting siRNAs. (B) Mean relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG in PC-3 cells harvested 48 hrs after transfection with control or POLR3G-targeting siRNAs, as determined by RT-qPCR in 3–4 independent experiments. (C) Western blot of POLR3GL and actin in PC-3 cells harvested 48 h after transfection with control or POLR3GL-targeting siRNAs. (D) Mean relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG in PC-3 cells harvested 48 hrs after transfection with control or POLR3GL-targeting siRNAs, as determined by RT-qPCR in 3–4 independent experiments. (E) Mean PC-3 cell numbers over 3 days following transfection with control siRNA or siRNAs targeting POLR3G or POLR3GL, as indicated, in 5 independent experiments. (F) Western blot of POLR3A and actin in PC-3 cells harvested 48 h after transfection with control or POLR3A-targeting siRNAs. (G) Mean relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG in PC-3 cells harvested 48 hrs after transfection with control or POLR3A-targeting siRNAs, as determined by RT-qPCR in 3–4 independent experiments. (H) Mean PC-3 cell numbers over 3 days following transfection with control or POLR3A-targeting siRNAs, as indicated, in three independent experiments. * indicates P < 0.05 relative to control siRNA by t-test; ** indicates P < 0.01; *** indicates P < 0.005. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Response of PC-3 cells to pol III inhibitor ML-60218 Figure 2. Response of PC-3 cells to pol III inhibitor ML-60218. (A) Mean relative changes in normalized expression of ... Figure 2. Response of PC-3 cells to pol III inhibitor ML-60218. (A) Mean relative changes in normalized expression of unprocessed pre-tRNA<sup>Tyr</sup> and mRNAs encoding CK8, CK14, CK18, SYP, NSE, GRP78, CD55, CD59, CD63 and NANOG in PC-3 cells harvested 48 hrs after treatment with or without 20 μM ML-60218, as determined by RT-qPCR in 3–6 independent experiments. (B) Western blot of NSE, SYP and tubulin in PC-3 cells harvested 48 h after treatment with or without 20 μM ML-60218. (C) Means of PC-3 cell numbers over 3 days with or without 20 μM ML-60218, in six independent experiments. (D) Means of the percentage of PC-3 cells staining positively for Ki67 proliferation marker 2 days after treatment with or without 20 μM ML-60218, in three independent experiments. (E) Western blot of POLR3A, POLR3G, POLR3GL and actin in PC-3 cells harvested 48 h after treatment with or without 20 μM ML-60218. (F) Antiserum to POLR3A was used to immunoprecipitate pol III from PC-3 cells cultured for 48hrs without or with 20 μM ML-60218; panels show western blots of immunoprecipiated protein probed with antibodies to POLR3A, POLR3G and POLR3GL, as indicated. (G) Representative northern blot of U2 snRNA (pol II-transcribed control), unprocessed pre-tRNA<sub>i</sub><sup>Met</sup> and mature tRNA<sub>i</sub><sup>Met</sup> in PC-3 cells harvested 48 hrs after duplicate treatment with or without 20 μM ML-60218. * indicates P < 0.05 relative to control by t-test; ** indicates P < 0.01; *** indicates P < 0.005. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Effects of POLR3G RNAi and ML-60218 on DR2 Alu Figure 3. Effects of POLR3G RNAi and ML-60218 on DR2 Alu. (A) Mean relative changes in normalized expression of DR2 Alu ... Figure 3. Effects of POLR3G RNAi and ML-60218 on DR2 Alu. (A) Mean relative changes in normalized expression of DR2 Alu RNA in PC-3 cells harvested 48 hrs after transfection with control siRNA or siRNAs targeting POLR3G or POLR3GL, as determined by RT-qPCR in three independent experiments. (B) Mean relative changes in normalized expression of NANOG mRNA in PC-3 cells harvested 48 h after transfection with control siRNA or siRNAs targeting POLR3G or POLR3GL, as determined by RT-qPCR in three independent experiments. (C) Mean relative changes in normalized expression of NANOG-Alu-Sx RNA in PC-3 cells harvested 48 h after transfection with control siRNA or siRNAs targeting POLR3G or POLR3GL, as determined by RT-qPCR in three independent experiments. (D) Mean relative changes in normalized expression of NANOG-Alu-Sx RNA in PC-3 cells harvested 48 h after treatment with or without 20 μM ML-60218, as determined by RT-qPCR in three independent experiments. (E) Mean relative changes in normalized expression of NANOG-Alu-Sx RNA in PC-3 cells harvested 48 h after treatment with or without 20μM ML-60218, as determined by RT-qPCR in 3 independent experiments. Black bars indicate samples that were exposed to 10μg/ml α-amanitin for 4 h prior to harvesting. (F) Mean ratios relative to input of NANOG-Alu-Sx DNA immunoprecipitated using antibodies against POLR3A, POLR2A, H3K79me2 and TAF<sub>I</sub>48 (negative control) with chromatin from PC-3 cells harvested 48 h after treatment with or without 20 μM ML-60218, as determined by ChIP-qPCR in six independent experiments. (G) Mean ratios relative to input of gene desert DNA immunoprecipitated using antibodies against POLR3A, POLR2A, H3K79me2 and TAF<sub>I</sub>48 (negative control) with chromatin from PC-3 cells harvested 48 h after treatment with or without 20 μM ML-60218, as determined by ChIP-qPCR in 6 independent experiments. * indicates P < 0.05 relative to control by t-test; ** indicates P < 0.01; *** indicates P < 0.005. # indicates P < 0.05 by t-test for +α-amanitin relative to –α-amanitin. Error bars represent S.E.M. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 8. Transient exposure to ML-60218 can diminish tumour initiation in vivo. (A) Relative changes in normalized ... Figure 8. Transient exposure to ML-60218 can diminish tumour initiation in vivo. (A) Relative changes in normalized expression of the indicated transcripts, as determined by RT-qPCR, when dissociated tumour cells from CRPC patient H455 were treated for 48 hrs with or without 20 μM ML-60218. (B) Percentages of viable cells, as determined using alamar blue, after 2 days exposure of H455 tumour samples to the indicated concentrations of ML-60218. (C) Growth rates of tumours, following injection of 10<sup>5</sup> H455 cells pre-treated for 48 hrs with (triangles) or without (circles) 20 μM ML-60218 (n = 4 mice per group). The relative value of 100% refers to a volume of ∼50 mm<sup>3</sup>. (D) Numbers of mice developing tumours after groups of four mice were injected subcutaneously with the indicated numbers of viable H455 tumour cells after 48 h pre-treatment without (con) or with (test) 20 μM ML-60218. Calculated tumour initiation frequencies and percentages of tumour-forming cells are shown for treatment and control arms. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 9. Model to explain the observed response of prostate cancer cells to POLR3G depletion following RNAi or ... Figure 9. Model to explain the observed response of prostate cancer cells to POLR3G depletion following RNAi or ML-60218 treatment. Undifferentiated cells express NANOG, which has been shown to bind the promoter of the POLR3G gene and stimulate its expression. Pol III associated with POLR3G binds DR2 Alu SINEs but does not transcribe them efficiently. When POLR3G is depleted by RNAi or treatment with ML-60218, levels of pol III at DR2 Alu SINEs decrease whereas levels of pol II increase; transcription of these loci rises, generating transcripts that are processed by dicer into repeat-induced small RNAs (riRNA) that target NANOG mRNA for AGO-mediated degradation; falling levels of NANOG trigger differentiation. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz128, https://doi.org/10.1093/nar/gkz128 The content of this slide may be subject to copyright: please see the slide notes for details.