In mammalian cells, the MYC oncoprotein binds to thousands of promoters. During mitogenic stimulation of primary lymphocytes, MYC promotes an increase in the expression of virtually all genes. In contrast, MYC-driven tumour cells differ from normal cells in the expression of specific sets of up- and downregulated genes that have considerable prognostic value. To understand this discrepancy, we studied the consequences of inducible expression and depletion of MYC in human cells and murine tumour models. Changes in MYC levels activate and repress specific sets of direct target genes that are characteristic of MYC-transformed tumour cells. Three factors account for this specificity. First, the magnitude of response parallels the change in occupancy by MYC at each promoter. Functionally distinct classes of target genes differ in the E-box sequence bound by MYC, suggesting that different cellular responses to physiological and oncogenic MYC levels are controlled by promoter affinity. Second, MYC both positively and negatively affects transcription initiation independent of its effect on transcriptional elongation. Third, complex formation with MIZ1 (also known as ZBTB17) mediates repression of multiple target genes by MYC and the ratio of MYC and MIZ1 bound to each promoter correlates with the direction of response.

Transcription in eukaryotic nuclei is carried out by DNA-dependent RNA polymerases I, II, and III. Human RNA polymerase III (Pol III) transcribes small untranslated RNAs that include tRNAs, 5S RNA, U6 RNA, and some microRNAs. Increased Pol III transcription has been reported to accompany or cause cell transformation. Here we describe a Pol III subunit (RPC32β) that led to the demonstration of two human Pol III isoforms (Pol IIIα and Pol IIIβ). RPC32β-containing Pol IIIβ is ubiquitously expressed and essential for growth of human cells. RPC32α-containing Pol IIIα is dispensable for cell survival, with expression being restricted to undifferentiated ES cells and to tumor cells. In this regard, and most importantly, suppression of RPC32α expression impedes anchorage-independent growth of HeLa cells, whereas ectopic expression of RPC32α in IMR90 fibroblasts enhances cell transformation and dramatically changes the expression of several tumor-related mRNAs and that of a subset of Pol III RNAs. These results identify a human Pol III isoform and isoform-specific functions in the regulation of cell growth and transformation.T ranscription in eukaryotes is mediated by three nuclear DNAdependent RNA polymerases (Pol I, Pol II, and Pol III) (1, 2). Pol III directs transcription of small noncoding RNAs that are involved in translation, splicing, and other cellular processes. Transcription by Pol III is directed by at least three distinct promoter types. Type 1 (5S RNA) and type 2 [tRNA, Alu RNA, and adenoviral viral-associated (VA) RNA] promoters are internal to the gene. Type 3 (U6 and 7SK RNA) promoters are located 5′ to the transcription initiation site (3). The transcription factors that directly recognize these promoters [type 1 by gene-specific TFIIIA and general initiation factor TFIIIC; type 2 by TFIIIC; and type 3 by gene-specific PSE-binding transcription factor/small nuclear RNA-activating protein complex (PTF/SNAPc)] have been well characterized and shown to recruit general initiation factor TFIIIB to their cognate promoters (reviewed in ref. 4). Overall, the multisubunit compositions of TFIIIC and TFIIIB have been conserved from yeast to human (5, 6), but two distinct isoforms of TFIIIB have been identified in human cells-one (TFIIIB-β) active in transcription of type 1 and type 2 promoters and one (TFIIIB-α) active in transcription of type 3 promoters (7). This functional difference reflects the presence of BRF1 in TFIIIB-β and of its paralogue BRF2 in TFIIIB-α (8, 9).Pol III is highly conserved from yeast to humans and composed of 17 subunits. Of these subunits, five are common to all three polymerases, two are shared by Pol I and Pol III, and five are paralogous to subunits found in Pol I and Pol II. However, five subunits are specific to Pol III without a counterpart in Pol I or Pol II (reviewed in refs. 5 and 10). Three of these five Pol III-specific subunits (RPC32, RPC39, and RPC62) form a dissociable ternary subcomplex that is specifically required for transcription initiation (11). This ternary complex...

RSC is an essential, multisubunit chromatin remodeling complex. We show here that the Rsc4 subunit of RSC interacted via its C terminus with Rpb5, a conserved subunit shared by all three nuclear RNA polymerases (Pol). Furthermore, the RSC complex coimmunoprecipitated with all three RNA polymerases. Mutations in the C terminus of Rsc4 conferred a thermosensitive phenotype and the loss of interaction with Rpb5. Certain thermosensitive rpb5 mutations were lethal in combination with an rsc4 mutation, supporting the physiological significance of the interaction. Pol II transcription of ca. 12% of the yeast genome was increased or decreased twofold or more in a rsc4 C-terminal mutant. The transcription of the Pol III-transcribed genes SNR6 and RPR1 was also reduced, in agreement with the observed localization of RSC near many class III genes. Rsc4 C-terminal mutations did not alter the stability or assembly of the RSC complex, suggesting an impact on Rsc4 function. Strikingly, a C-terminal mutation of Rsc4 did not impair RSC recruitment to the RSC-responsive genes DUT1 and SMX3 but rather changed the chromatin accessibility of DNases to their promoter regions, suggesting that the altered transcription of DUT1 and SMX3 was the consequence of altered chromatin remodeling.Transcription occurs in the crowded context of the nucleus in which genes are wrapped in chromatin. The first step in gene expression involves the modification and/or the remodeling of repressive chromatin by specialized complexes. For polymerase II (Pol II)-transcribed genes, these steps are followed by the recruitment of Mediator, the general transcription factors (GTFs) and the Pol II itself, although in an order that can vary from one promoter to another (9, 34). The pathway leading from silent chromatin to transcription by Pol I and Pol III has not been studied as thoroughly but is globally similar, with an additional contribution of cognate GTFs. In yeast and human cells, the Pol III-specific transcription factor TFIIIC has been found to be required for the proper nucleosomal organization of Pol III genes (4, 23, 32). In the case of Pol I transcription, the mammalian termination factor TTF-I is able to activate transcription by promoting chromatin remodeling in synergy with ATP-dependent cofactors in vitro (24). Transcription initiation is not the only step at which chromatin might interfere with transcription. Nucleosomes residing in the transcribed region can inhibit the movement of RNA polymerases during elongation. To contend with this, the FACT complex helps human Pol II transcribe through nucleosome-induced blocks (28, 38). These observations suggest that factors that relieve the repressive effect of nucleosomes might act in conjunction with the transcription machinery at the successive stages of the transcription cycle.The repressive effect of nucleosomes is overcome by two cooperative mechanisms. The first involves the covalent modification of the histones, including the acetylation of specific histone tail lysines by acetyl transferases (...

1 that share the task of transcribing the information contained in genes into mobile RNA entities. In humans, Pol I transcribes the precursor of the large ribosomal 45S RNA, Pol II transcribes all messenger RNAs, most snRNAs, snoRNAs and micro RNAs and Pol III transcribes a diverse group of small untranslated RNAs that participate in the regulation of transcription, splicing and translation. After transcription, Pol III transcripts are either directly degraded or modified for participation in the regulation and execution of processes in the nucleus and cytoplasm (transcription regulation; RNA processing; ribosome assembly; translation) that ultimately lead to protein synthesis. In the past few years, in part due to the discovery of novel classes of regulatory RNAs such as micro (mi) RNAs and small interfering (si)RNAs, it has become clear that the three classical eukaryotic RNA polymerases have acquired additional layers of complexity during evolution from unicellular to multicellular eukaryotes. For instance, derivatives of Pol II that fulfill specific functions in transcription of siRNAs (Pol IV) or of noncoding RNAs at target loci (Pol V) have been found in Arabidopsis. rNA polymerase iii transcribes small untranslated rNAs that fulfill essential cellular functions in regulating transcription, rNA processing, translation and protein translocation. rNA polymerase iii transcription activity is tightly regulated during the cell cycle and coupled to growth control mechanisms. Furthermore, there are reports of changes in rNA polymerase iii transcription activity during cellular differentiation, including the discovery of a novel isoform of human rNA polymerase iii that has been shown to be specifically expressed in undifferentiated human H1 embryonic stem cells. Here, we review major regulatory mechanisms of rNA polymerase iii transcription during the cell cycle, cell growth and cell differentiation.

ObjectiveTo identify the genetic cause of hypomyelinating leukodystrophy in 2 consanguineous families.MethodsHomozygosity mapping combined with whole-exome sequencing of consanguineous families was performed. Mutation consequences were determined by studying the structural change of the protein and by the RNA analysis of patients' fibroblasts.ResultsWe identified a biallelic mutation in a gene coding for a Pol III–specific subunit, POLR3K (c.121C>T/p.Arg41Trp), that cosegregates with the disease in 2 unrelated patients. Patients expressed neurologic and extraneurologic signs found in POLR3A- and POLR3B-related leukodystrophies with a peculiar severe digestive dysfunction. The mutation impaired the POLR3K-POLR3B interactions resulting in zebrafish in abnormal gut development. Functional studies in the 2 patients' fibroblasts revealed a severe decrease (60%–80%) in the expression of 5S and 7S ribosomal RNAs in comparison with control.ConclusionsThese analyses underlined the key role of ribosomal RNA regulation in the development and maintenance of the white matter and the cerebellum as already reported for diseases related to genes involved in transfer RNA or translation initiation factors.

The 17-subunit human RNA polymerase III (hPol III) transcribes small, untranslated RNA genes that are involved in the regulation of transcription, splicing and translation. hPol III subunits hRPC62, hRPC39 and hRPC32 form a stable ternary subcomplex required for promoter-specific transcription initiation by hPol III. Here, we report the crystal structure of hRPC62. This subunit folds as a four-tandem extended winged helix (eWH) protein that is structurally related to the transcription factor TFIIEα N terminus. Through biochemical analyses, we mapped the protein-protein interactions of hRPC62, hRPC32 and hRPC39. In addition, we demonstrated that hRPC62 and hRPC39 bind single-stranded and duplex DNA, respectively, in a sequence-independent manner. Overall, we shed light on structural similarities between the hPol III-specific subunit hRPC62 and TFIIEα and propose specific functions for hRPC39 and hRPC62 in transcription initiation by hPol III.

RNA polymerase (pol) III occurs in two forms, containing either the POLR3G subunit or the related paralogue POLR3GL. Whereas POLR3GL is ubiquitous, POLR3G is enriched in undifferentiated cells. Depletion of POLR3G selectively triggers proliferative arrest and differentiation of prostate cancer cells, responses not elicited when POLR3GL is depleted. A small molecule pol III inhibitor can cause POLR3G depletion, induce similar differentiation and suppress proliferation and viability of cancer cells. This response involves control of the fate-determining factor NANOG by small RNAs derived from Alu short interspersed nuclear elements. Tumour initiating activity in vivo can be reduced by transient exposure to the pol III inhibitor. Untransformed prostate cells appear less sensitive than cancer cells to pol III depletion or inhibition, raising the possibility of a therapeutic window.

The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.