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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 have been proven to serve as anchors to the 3D genome organization. These TFs are generally cell type-specific factor and/or developmental master regulators. General TFs (GTFs) which serve RNA polymerase recruitment to specific promoter sequences, however, can be part of very large protein complexes but their roles in genome architecture have not been carefully explored. Here, we used a bio-informatic approach of ChIP-seq and Hi-C data analysis to depict the role of one GTF of the RNA polymerase III system (TFIIIC) in several human cell lines, both normal and transformed. We find that TFIIIC occupancy within the genome mainly occurs at specific regions which largely correspond to Alu elements but also at characteristic classes of repetitive elements (REs) such as MIR, FLAMC and ALR/alpha, depending on the cell’s developmental origin. We then show that these TFIIIC-enriched regions are involved in cell type-specific DNA looping within the genome and do not depend on colocalization with the master architectural protein CTCF. This work extends previous knowledge about the role of TFIIIC as a bona fide genome organizer whose action can lead to cell type-dependent 3D genome looping via binding to REs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE195499 | GEO | 2022/02/22

REPOSITORIES: GEO

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Project description:Summary: Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their targets in a temporal manner remains largely elusive. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and the association to 3D enhancer rewiring and the transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts to (MEFs) to PSCs. Inducible depletion of KLF factors in PSC caused a genome-wide decrease in connectivity of enhancers and disruption of KLF4 binding site from PSC-specific enhancers was sufficient to reduce expression of genes within the enhancer hub partly by impairing long-range contacts. Our study provides an integrative view of the intricate activities of a master regulator during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding. Purpose: We captured on a genome-wide scale the binding of KLF4 during iPSC formation and its effects on chromatin state, transcriptional activity and chromatin topology around its targets. Methods: We used a well-characterized reprogramming system to apply genome-wide assays that map KLF4 binding (ChIP-seq), chromatin accessibility (ATAC-seq), enhancer and gene activity (H3K27ac ChIP-seq and RNA-seq), enhancer connectivity (H3K27ac Hi-ChIP) as well as KLF4-centric chromatin looping (KLF4 Hi-ChIP) at different stages during acquisition of pluripotency. Results: Integrative analysis of our results generated a reference map of stage-specific chromatin changes around KLF4 bound loci and established strong links with enhancer. rewiring and concordant transcriptional changes. Genetic manipulation of KLF4 binding from a PSC enhancer further supported the ability of KLF4 to function both as a transcriptional regulator and a chromatin organizer. Conclusions: Our study offers novel insights into the intricate roles of a master regulator during cell fate transition.

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

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