An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping

Abstract

Transcription factors (TFs) bind DNA in a sequence-specific manner and are generally cell type-specific factors and/or developmental master regulators. In contrast, general TFs (GTFs) are part of very large protein complexes and serve for RNA polymerases’ recruitment to promoter sequences, generally in a cell type-independent manner. Whereas, several TFs have been proven to serve as anchors for the 3D genome organization, the role of GTFs in genome architecture have not been carefully explored. Here, we used ChIP-seq and Hi-C data to depict the role of TFIIIC, one of the RNA polymerase III GTFs, in 3D genome organization. We find that TFIIIC genome occupancy mainly occurs at specific regions, which largely correspond to Alu elements; other characteristic classes of repetitive elements (REs) such as MIR, FLAM-C and ALR/alpha are also found depending on the cell’s developmental origin. The analysis also shows that TFIIIC-enriched regions are involved in cell type-specific DNA looping, which does not depend on colocalization with the master architectural protein CTCF. This work extends previous knowledge on the role of TFIIIC as a bona fide genome organizer whose action participates in cell type-dependent 3D genome looping via binding to REs.

Structural insights into human TFIIIC promoter recognition

“…The observation that TFIIIC dimerizes under cryo-EM conditions should be treated with care because we were unable to evaluate TFIIIC110 dimerization in solution due to a limited amount of protein sample. Because TFIIIC also functions in 3D genome organization ( 22 , 23 ), one could, nevertheless, speculate that DNA-bound τB dimerizes at tRNA gene clusters and ETC sites, where it may help to stabilize long-range chromatin loops. For the following molecular description of human τB, we will, however, only focus on the τB monomer.…”

“…Independently of its role in recruiting Pol III to its target genes, TFIIIC recognizes "extra TFIIIC" (ETC) sites in various eukaryotes (13)(14)(15) and functions in genome organization by acting as a chromatin insulator (16,17) and via interaction with the architectural proteins cohesin and condensin (18)(19)(20)(21). TFIIIC also has histone acetylation activity and, together with the insulator protein CCCTC-binding factor, was shown to mediate long-range chromatin looping (22,23).…”

TFIIIC as a Potential Epigenetic Modulator of Histone Acetylation in Human Stem Cells

“…Given that hESCs are typically cultured in serum-free media [ 10 ], and taking into account our previous analyses ( Figure 1 A–D), we speculated that H3K18ac in hESCs could, at least in part, be deposited by TFIIIC. To provide evidence for this hypothesis, we first analyzed published TFIIIC genome-wide occupancy in H9 hESCs [ 15 ] and compared it to H3K18ac and H3K27ac profiles [ 16 ].…”

“…Surprisingly, TFIIIC is also bound to genes associated with neuronal differentiation ( Figure 2 B), suggesting that a general transcription factor of the Pol III machinery may potentially play a role in the early stages of neuronal development from naïve hESCs. To support this observation, we employed GIGGLE score analysis [ 18 ] to screen ~90,000 available ChIP-seq datasets, from several cell lines and tissues, for transcription factors and chromatin regulators [ 15 , 16 ], and in silico predict the presence of these factors at TFIIIC-bound regions devoid of p300 in H9 hESCs. We found significant enrichment for various neuronal factors such as ADNP, whose mutations underlie a complex neurological disorder (Helsmoortel–Van der Aa syndrome; OMIM#615873), and that interact with TFIIIC in mouse ESCs [ 19 ]; CHD4, a chromatin-remodeling enzyme-regulating genome architecture in mouse brain [ 20 ], and Polycomb proteins such as RNF2, RYBP, EZH1, EZH2, KDM2B and JARID, all important regulators of neurogenesis and known interactors of TFIIIC in differentiated cells [ 21 , 22 ] ( Figure 2 D).…”

Structural insights into human TFIIIC promoter recognition

“…Independently of its role in recruiting Pol III to its target genes, TFIIIC recognizes 'extra TFIIIC' (ETC) sites in various eukaryotes [13][14][15] and functions in genome organization by acting as a chromatin insulator 16,17 and via interaction with the architectural proteins cohesin and condensin [18][19][20][21] . TFIIIC also possesses histone acetylation activity and, together with the insulator protein CTCF, was shown to mediate long-range chromatin looping 22,23 .…”