RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors

Ravi K Alla,Bradley R Cairns,Costanza Emanueli

doi:10.1371/journal.pone.0085648

Ravi K Alla, Bradley R Cairns + Show 1 more

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https://doi.org/10.1371/journal.pone.0085648

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Abstract

Recent genomic approaches have revealed that the repertoire of RNA Pol III-transcribed genes varies in different human cell types, and that this variation is likely determined by a combination of the chromatin landscape, cell-specific DNA-binding transcription factors, and collaboration with RNA Pol II. Although much is known about this regulation in differentiated human cells, there is presently little understanding of this aspect of the Pol III system in human ES cells. Here, we determine the occupancy profiles of Pol III components in human H1 ES cells, and also induced pluripotent cells, and compare to known profiles of chromatin, transcription factors, and RNA expression. We find a relatively large fraction of the Pol III repertoire occupied in human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs). In ES cells we find clear correlations between Pol III occupancy and active chromatin. Interestingly, we find a highly significant fraction of Pol III-occupied genes with adjacent binding events by pluripotency factors in ES cells, especially NANOG. Notably, in human ES cells we find H3K27me3 adjacent to but not overlapping many active Pol III loci. We observe in all such cases, a peak of H3K4me3 and/or RNA Pol II, between the H3K27me3 and Pol III binding peaks, suggesting that H3K4me3 and Pol II activity may “insulate” Pol III from neighboring repressive H3K27me3. Further, we find iPSCs have a larger Pol III repertoire than their precursors. Finally, the active Pol III genome in iPSCs is not completely reprogrammed to a hESC like state and partially retains the transcriptional repertoire of the precursor. Together, our correlative results are consistent with Pol III binding and activity in human ES cells being enabled by active/permissive chromatin that is shaped in part by the pluripotency network of transcription factors and RNA Pol II activity.

Highlights

Nuclear transcription is carried out by three distinct RNAPolymerases: RNA Polymerase I (Pol I), RNA Polymerase II (PolII) and RNA Polymerase III (Pol III)
Our correlative results are consistent with Pol III binding and activity in human ES cells being enabled by active/permissive chromatin that is shaped in part by the pluripotency network of transcription factors and RNA Pol II activity
Our study aims to understand the relationship of human ES cell chromatin and transcription factors, especially pluripotency factors with Pol III

Summary

Introduction

Nuclear transcription is carried out by three distinct RNAPolymerases: RNA Polymerase I (Pol I), RNA Polymerase II (PolII) and RNA Polymerase III (Pol III). Nuclear transcription is carried out by three distinct RNA. Pol I transcribes a single long ribosomal RNA (pre-rRNA) transcript which is processed into. Pol II transcribes primarily messenger RNA (mRNA) that code for proteins, as well as a variety of non-coding RNAs (ncRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and micro RNAs (miRNAs) that are involved in gene regulation, RNA processing and chromatin organization. Pol III transcribes ncRNAs [1] that are mostly involved in translation, such as 5S ribosomal RNA, RNase P, RNase MRP and tRNAs. In addition Pol III transcribes U6 RNA (involved in splicing); VA-I and VA-II (involved in Pol II transcription); BC1 (involved in spermatogenesis); Vault RNA (implicated multidrug resistance) and Y RNA (component of the Ro ribonuclear protein complex) [2].

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