Drosha regulates gene expression independently of RNA cleavage function

Abstract

Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription-dependent manner. This binding is not associated with miRNA production or RNA cleavage. Drosha knockdown in HeLa cells downregulated nascent gene transcription, resulting in a reduction of polyadenylated mRNA produced from these gene regions. Furthermore, we show that this function of Drosha is dependent on its N-terminal protein-interaction domain, which associates with the RNA-binding protein CBP80 and RNA Polymerase II. Consequently, we uncover a previously unsuspected RNA cleavage-independent function of Drosha in the regulation of human gene expression.

Graphical abstract

Figure 1

Drosha Binds 5′ Ends of Human Genes in a Transcription-Dependent Manner (A) (i) Metagene profiles of Drosha binding around transcriptional start sites (TSS, top) and transcriptional termination sites (TxEnd, bottom) based on Drosha ChIP-on-chip analysis in HeLa cells using ENCODE array. (ii) Average Drosha ChIP enrichment over input (log2) for probes overlapping miRNAs, intergenic regions, gene bodies, TSSs, and TxEnds. Error bars represent SEM. Number of probes covering each region is indicated above the bars. TSS signal is significantly enriched (p < 0.001, t test) compared to all intergenic gene bodies or TxEnd regions. (B–D) Pol II and Drosha ChIP analyses on γ-actin (B) and GAPDH (C) genes and the miR-330 genomic locus, compared to β-actin ex 4 (D) in HeLa cells. ChIP amplicons are shown above the gene diagrams. (E) (i) qRT-PCR analysis of γ-actin, β-actin and GAPDH pre-mRNAs from HeLa cells mock-treated or treated with 5 μg/ml actinomycin D for 6 hr, normalized to 5S rRNA. The amount of RNA in the untreated cells was taken as 1. Drosha (ii) and H3 (iii) ChIPs on γ-actin gene and miR-330 gene locus in HeLa cells, mock-treated or treated with 5 μg/ml of actinomycin D for 6 hr. Bars in (B)–(E) represent the average values from at least three biological experiments ±SD. See Figures S1–S5.

Figure 2

DGCR8 Binds Promoter-Proximal Regions of Human Genes (A) DGCR8 ChIP analysis on γ-actin, GAPDH, and SELENBP1 genes and the miR-330 genomic locus in HeLa cells. SELENBP1 gene diagram is in Figure S2A. Bars represent the average values from at least three biological experiments ±SD. (B) DGCR8 HITS-CLIP. Distribution of significant sense (green) and antisense (red) reads mapping around transcription start sites (TSSs; top panels) and transcription termination regions (TTSs; bottom panels) of protein coding genes, as determined by CEAS software, using FDR < 0.01. The y axis shows the number of genes detected as a percentage, whereas the x axis represents the location in relation to the position of TSS and TTS. (C) Distribution of sense and antisense DRCG8 CLIP binding sites. 1,101 DGCR8 binding sites in the sense orientation correspond to 967 genes, and 196 DGCR8 antisense binding sites correspond to 174 genes. (D) Drosha in vitro processing reactions in HeLa nuclear extracts with β-actin promoter-proximal region and miR17-18-19a sequences. Arrows indicate the positions of pre-miRNAs. See also Figures S6 and S7.

Figure 3

Drosha Depletion Causes Transcriptional Downregulation and Decreases Pre-mRNA and Poly(A)+ RNA Levels (A) Western blot analysis of protein extracts (50 μg) from mock-treated and Drosha siRNA-treated HeLa cells, probed with Drosha and GAPDH antibodies (i). Pol II ChIP across γ-actin (ii) and GAPDH (iii) genes in mock-treated and Drosha-depleted HeLa cells. (B) qRT-PCR analysis of pre-mRNA (i) and poly(A)+ RNA (ii) in mock-treated and Drosha-depleted cells. The level of RNA in mock-treated samples was taken as 1. (C) Br-UTP NRO analysis carried out in mock-treated and Drosha-depleted cells. Amount of nascent Br-UTP RNA was calculated by subtracting the background of U-RNA produced over a specific gene probe. The level of Br-UTP RNA in mock-treated samples was taken as 1. (D) Diagram of β-actin/EGFP plasmid. Promoter, exon 1, and intron 1 sequences are derived from the human β-actin gene, indicated by dashed line. qRT-PCR primers are shown above the diagram. SV40 3′ UTR contains a poly(A) signal, indicated with an arrow. qRT-PCR analysis of Drosha (i) and EGFP (ii) mRNAs in mock-treated and Drosha-depleted HeLa cells. (E) Top, domain structure of Drosha protein. Double-stranded RNA-binding (dsRBD), RNaseIII (RIIIa, RIIIb), proline-rich, and serine-arginine (RS) domains are shown. Positions of catalytic E110aQ (aQ) mutation and Δ390 deletion of the N-terminal proline-rich and RS-rich domains are indicated above the diagram. Bottom, qRT-PCR analysis of Drosha mRNA (i) and EGFP mRNA (iii) in Drosha-depleted 293T cells, overexpressed with RNAi-resistant Flag, Drosha WT, aQ, and Δ390 constructs. The level of Drosha (i) or EGFP (iii) mRNA in cells, overexpressed with Flag was taken as 1. siRNA2, targeting 3′ UTR of endogenous Drosha mRNA, was used for Drosha depletion in overexpression experiments. (ii) Western blot of total protein extracts (50 μg) from 293T cells, overexpressed with Flag, Drosha WT, aQ, and Δ390 plasmids, probed with Flag antibody. The positions of the marker are indicated on the left. Bars in (A)–(E) represent average values from at least three independent experiments ±SD. In (B), (D), and (E), the levels of RNA were normalized to 5S rRNA.

Figure 4

Drosha Regulates Human Gene Expression through Its Interaction with CBP80 and Pol II (A) Pull-down experiments performed with anti-Flag in 293 cells, overexpressed with Flag and Drosha WT-Flag constructs. Western blots were probed with Pol II, Ars2, and CBP80 antibodies. Input represents 1% of material added to IP. (B and C) CBP80 ChIP analyses across γ-actin (B) and GAPDH (C) genes and miR-330 gene locus in HeLa cells. Bars represent average values from at least three independent experiments ±SD. (D) Pull-down experiments performed with anti-Flag in 293 cells, overexpressed with Flag, Drosha WT, aQ, Δ390, and Δ390 aQ constructs. Input represents 1% of material added to IP. Western blot was probed with CBP80 (top panel) and Pol II (middle panel) and FLAG (bottom panel) antibodies. Asterisks indicate full-length proteins. (E) Pull-down experiments performed with anti-Flag in 293 cells, overexpressed with Drosha WT construct. Cell extracts were nontreated (−) or treated (+) with 50 μg/ml of RNase A. Input represents 1% of material added to IP. Western blot was probed with CBP80 (top panel) and Pol II (bottom panel) antibodies. (F) Model for the function of Drosha in the regulation of human gene expression. Following transcription of nascent RNA by Pol II, Drosha, most probably in a complex with DGCR8, binds GC-rich hairpins at the promoter-proximal regions of human genes. Drosha does not cleave such hairpins, but it interacts with Pol II and CBP80 through its N-terminal proline-rich domain. Drosha can enhance gene expression, independently of its RNA cleavage function. Depletion of Drosha results in decrease of nascent transcription and subsequent decrease in the amount of nascent and poly(A)+ mRNA.