hnRNP-K Targets Open Chromatin in Mouse Embryonic Stem Cells in Concert with Multiple Regulators

Abstract

The transcription factor Oct4 plays a key regulatory role in the induction and maintenance of cellular pluripotency. In this article, we show that ubiquitous and multifunctional poly(C) DNA/RNA-binding protein hnRNP-K occupies Oct4 (Pou5f1) enhancers in embryonic stem cells (ESCs) but is dispensable for the initiation, maintenance, and downregulation of Oct4 gene expression. Nevertheless, hnRNP-K has an essential cell-autonomous function in ESCs to maintain their proliferation and viability. To better understand mechanisms of hnRNP-K action in ESCs, we have performed ChIP-seq analysis of genome-wide binding of hnRNP-K and identified several thousands of hnRNP-K target sites that are frequently co-occupied by pluripotencyrelated and common factors (Oct4, TATA-box binding protein, Sox2, Nanog, Otx2, etc.), as well as active histone marks. Furthermore, hnRNP-K localizes exclusively within open chromatin, implying its role in the onset and/or maintenance of this chromatin state.Results of this study showed that the poly(C)-binding protein hnRNP-K occupies in embryonic stem cells (ESCs) both distal and proximal enhancers of the Oct4 gene via CT-rich elements. Genome-wide analysis revealed many colocalizations of hnRNP-K with TATA-box binding protein (TBP), Oct4, Otx2, and active histone marks. Also, comparison of hnRNP-K ChIP-seq data with MNase-seq and ATAC-seq revealed that this protein exclusively targets open chromatin of ESCs.

Phase separation of RNA-binding protein promotes polymerase engagement and transcription

“…We have used the following published datasets in our analysis. GSM2988821 WDR43 ChIP-seq, GSM2988831 Pol II 8WG16 ChIP-seq, GSM2988824 Pol II Ser2P ChIP-seq, GSM2988827 Pol II Ser5P ChIP-seq 77 ; GSM1941467 pan-Pol II ChIP-seq; GSM3713432 hnRNPK ChIP-seq 101 ; GSM3407052 SRSF2 ChIP-seq 102 ; GSM1893472 NONO ChIP-seq 103 ; GSM1693793 DDX21 ChIP-seq; GSM1915715 LIN28A ChIP-seq 104 ; GSM2424700 METTL3 ChIP-seq 105 ; GSM560347 MED1 ChIP-seq; GSM1082340 OCT4 ChIP-seq; GSM288356 c-MYC ChIP-seq; GSM1082341 SOX2 ChIP-seq; GSM611197 SIN3A ChIP-seq; GSM1023124 TET2 ChIP-seq; GSM918750 P300 ChIP-seq; GSM480162 SUZ12 ChIP-seq; GSM480161 EZH2 ChIP-seq; GSM769008 H3K4me3 ChIP-seq; GSM1000089 H3K27me3 ChIP-seq; GSM1000099 H3K27ac ChIP-seq; GSM769009 H3K4me1 ChIP-seq; GSM1000109 H3K36me3 ChIP-seq. ;…”

“…RNA-binding proteins (RBPs) constitute a major family of regulators that process and metabolize RNA transcripts from their synthesis to function and to decay 48 . A number of RBPs such as WDR43, DDX21/18/5, SRSF1/2, FUS, hnRNPK/U/L, NCL, and NONO, have been implicated in modulating transcriptional, epigenetic, and signaling responses in various cellular contexts [49][50][51][52][53][54][55][56][57][58][59][60][61][62][63] . Yet, the direct involvement of RBPs and their interplay with RNA in transcription regulation remain to be proven.…”

The functional diversity of the POUV-class proteins across vertebrates

“…2 kb 5′ from TSS), the proximal enhancer (approx. 1 kb 5′ from TSS), and the proximal promoter—targets of a variety of transcriptional regulators [ 2 , 90 , 106 – 108 ]. The distal enhancer is active in the pluripotent epiblast of preimplantation embryos and, as expected, in its cultured counterparts, ESCs, while the proximal enhancer is active in the epiblast of post-implantation embryos and the cells derived thereof, EpiSCs [ 109 ].…”

Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer

“…It is known now that the chromatin conformation at the supranucleosome and higher levels of the genome architecture is much a subject of the biophysical processes which assemble the active and inactive chromatin in two separate self-organizing high-order domains [89][90][91][92][93]. Self-organization is an important driving force of evolution [94].…”