A large fraction of extragenic RNA pol II transcription sites overlap enhancers

Abstract

Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are products of RNA genes, however, is still unclear. Here we have characterized transcription sites located outside protein-coding genes in a highly regulated response, macrophage activation by endotoxin. Using chromatin signatures, we could unambiguously classify extragenic Pol_II binding sites as belonging to either canonical RNA genes or transcribed enhancers. Unexpectedly, 70% of extragenic Pol_II peaks were associated with genomic regions with a canonical chromatin signature of enhancers. Enhancer-associated extragenic transcription was frequently adjacent to inducible inflammatory genes, was regulated in response to endotoxin stimulation, and generated very low abundance transcripts. Moreover, transcribed enhancers were under purifying selection and contained binding sites for inflammatory transcription factors, thus suggesting their functionality. These data demonstrate that a large fraction of extragenic Pol_II transcription sites can be ascribed to cis-regulatory genomic regions. Discrimination between lncRNAs generated by canonical RNA genes and products of transcribed enhancers will provide a framework for experimental approaches to lncRNAs and help complete the annotation of mammalian genomes.

Figure 1. Sites of regulated extragenic transcription upstream of LPS-inducible genes.

(A) Pol_II ChIP-Seq data from unstimulated and LPS+γIFN-stimulated macrophages at the Ccl5 gene and surrounding genomic regions. The extragenic Pol_II peaks (indicated as −1, −2, and −3) and the genomic annotations (mm9) are shown. The y-axis indicates the number of ChIP-Seq tags. (B) Phosphorylated Ser5 Pol_II ChIP-Seq data at the same genomic region. UT, untreated macrophages.

Figure 2. Inducible upstream extragenic transcription frequently precedes the activation of the adjacent protein-coding gene.

Kinetics of induction of Ccl5 (A) and Cxcl11 (B) mRNAs relative to those of the upstream extragenic transcripts. Extragenic Ccl5 transcripts (#−1, −2, and −3) correspond to the Pol_II peaks shown in Figure 1. Cxcl11 transcripts #−1 and #−2 correspond to the regions in Figure S1A. Cells were stimulated with LPS+γIFN as indicated. y-axes indicate mRNA (left) or ncRNA (right) levels relative to those of a housekeeping gene (TBP). (C) Kinetics of mRNA induction of a panel of protein-coding genes together with the associated extragenic transcripts. The corresponding Pol_II ChIP_seq data (2h LPS+γIFN stimulation) are shown on the right. Shaded areas indicate the extragenic Pol_II peaks. For Trim25 and Zcchc2, amplicons correspond to the Pol_II peak closest to the 5′ of the gene.

Figure 3. Characterization of the extragenic transcripts generated upstream of LPS-inducible genes.

(A) Polyadenylation of extragenic Ccl5 transcripts. Total RNA was reverse-transcribed using oligo-dT primers. cDNA was then amplified with primers corresponding to regions −1, −2, and −3 upstream of Ccl5 (as in Figure 1). (B) Upstream extragenic transcripts are nuclear RNAs. Macrophages were fractionated before RNA extraction. RNA from the cytoplasmic and nuclear fractions was then reverse transcribed and amplified with the indicated primers. Neat1 is a nuclear non-coding RNA that was used as a control of the fractionation procedure. (C) Extragenic transcription upstream of Ccl5 generates long unspliced transcripts. RNA was reverse transcribed using antisense primers in the region just upstream of Ccl5 TSS, as indicated. cDNA was then PCR-amplified using primers in the extragenic region −1 (as in Figure 1A). (D) Extragenic Ccl5 and Cxcl11 transcripts are very unstable. Cells were stimulated with LPS for 2 h, followed by a 30 min actinomycinD (5 µg/ml) chase. mRNAs for Ccl5 and Cxcl11 and the corresponding extragenic transcripts were measured by quantitative PCR. UT, untreated. (E) DRB insensitivity of extragenic Ccl5 and Cxcl11 transcripts. Macrophages were stimulated with LPS for 2 h in the presence or absence of DRB (50 µg/ml), as indicated. UT, untreated.

Figure 4. Identification of enhancer-associated and promoter-associated extragenic Pol_II transcription sites.

(A) Pie chart showing the three groups of extragenic Pol_II peaks (classified on the basis of Pol_II changes after stimulation) in untreated and LPS+γIFN-treated macrophages. Numbers refer to Pol_II peaks before SVM classification, clusterization, and filtering against Ensembl protein-coding genes. (B) The pie chart shows the results of the machine-learning approach used to classify extragenic Pol_II clusters as belonging to promoters or enhancers. Numbers refer to Pol_II peaks after clusterization and filtering against Ensembl protein-coding genes. (C) Enhancer and promoter predictions. Regions of extragenic Pol_II transcription were classified as enhancers or promoters/TSSs using a machine-learning algorithm recognizing alternative H3K4me3/H3K4me1 patterns. Each line represents a 5 kb region centered around the summit of a Pol_II peak (±2.5 kb). Peaks are shown from chromosome 1 (top) to chromosome X (bottom). (D) Examples of predicted promoters and enhancers. ChIP-Seq profiles at regions containing representative extragenic transcription sites belonging to the two groups are shown. The coordinates indicate the position of the Pol_II peak. The green square indicates a CpG island. (E) Association of predicted enhancers and promoters with CpG islands. Expected and observed fractions are shown. (F) Correlation between LPS-induced Pol_II changes at predicted transcribed enhancers and at the neighboring protein-coding gene. Inducible enhancers (upper panel) and repressed enhancers (lower panel) are shown. Observed (obs) and expected (exp) fractions for each group of genes (constitutive, repressed, and inducible genes) are shown together with the respective p value (the p value may refer to either an over- or an under-representation). Expected fractions were calculated on the basis of the relative frequency of each group (constitutive, induced, repressed genes) with respect to all Pol_II positive genes. n.s., non-significant.

Figure 5. Evidence for active transcription at Pol_II-associated enhancers.

(A) Distribution of the median distance between CAGE tags clusters overlapping the regions predicted as either enhancers or promoters. (B) Correlation between total and active Pol_II (phosphorylated at Ser5 of the CTD) at enhancers. The graphs illustrate the distance between extragenic Pol_II peaks predicted as enhancers and the closest P-Ser5 Pol_II peak. (C) Extragenic regions associated with RNA_Seq signals display higher Pol_II occupancy than those without RNA-Seq signals.

Figure 6. Signatures of functionality at enhancer-associated extragenic transcription sites.

(A) Sequence conservation at extragenic Pol_II transcription sites. Average conservation scores (phastCons score per bp) in the enhancer, promoter, and unpredictable groups are shown. Pol_II peaks were centered around their summit. (B) Statistical significance of sequence conservation in the three groups was evaluated as compared to random sets. The y-axis indicates the p value of the deviation from random. The horizontal grey line indicates the threshold for statistical significance (set to p<0.01). (C) Functional evaluation of predicted enhancers in reporter assays. The indicated regions were subcloned in the pGL3 promoter vector, which bears a minimal promoter, and transfected in Raw264.7 macrophage cells. Cells were stimulated with LPS for 16 h before harvesting. Errors bars, S.D. (D) Overlap of extragenic transcription sites with an enhancer-associated chromatin signature with experimentally determined binding sites of the hematopoietic transcription factor PU.1. PU.1 peaks ± 500 bp (identified in a ChIP-Seq experiment in untreated macrophages) were considered. Black numbers refer to Pol_II clusters, while blue numbers refer to PU.1 peaks.

Figure 7. Enrichment of transcription factor binding sites in enhancer-type extragenic Pol_II transcription sites.

(A) TFBSs enriched in the set of inducible, enhancer-type extragenic transcription sites. Enrichment was evaluated using two reference datasets (see Methods). Each vertical column in the heat-plot represents a Pol_II peak, while each row corresponds to an enriched PWM. Data are shown after hierarchical clustering. Selected enriched PWMs for inflammatory TFs (IRFs, STAT1, NF-kB) are shown on the right. Increasing red color represents increasing probabilities for a PWM to have a match in the region as compared to randomized sequences with the same nucleotide composition . (B) IRF3 and NF-kB are required for extragenic transcription upstream of Ccl5. Raw264.7 cell lines constitutively expressing a dominant negative Irf3 (IRF3DN) or a general inhibitor of NF-kB (IkBα super-repressor, IkBαDN) were stimulated with LPS as indicated and Ccl5 mRNA or upstream extragenic transcripts were measured by RT Q-PCR. (C) Binding of NF-kB to the Ccl5 promoter and to a region corresponding to the −1 Pol_II peak. NF-kB binding was measured using an anti-p65 ChIP.

Figure 8. Functional consequences of transcriptional inhibition on extragenic histone acetylation at the Ccl5 and Cxcl11 loci.

(A) H3K9 acetylation at the transcribed region (about 5 kb) upstream of Ccl5 was measured by ChIP in the absence or presence of CHX (10 µg/ml) or ActD (5 µg/ml) as indicated. UT, untreated macrophages. Position of the amplicons (transcription start site [TSS] and five extragenic amplicons indicated by progressive numbers) is indicated. (B) Left panel: inhibition of transcription but not translation blocks the activation of the primary response gene Ccl5 . Conversely, Pol_II recruitment to the TSS of the secondary gene IL-6 is equally sensitive to CHX and ActD. Right panel: ActD does not inhibit Pol_II recruitment to IkBα and CD40. (C) Transcription is required for inducible H3K9 hyperacetylation at the transcribed region upstream of Cxcl11. The position of amplicons at the TSS and upstream of the gene are indicated.