The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
Almost all eukaryotic mRNA precursors undergo a co-transcriptional modification at the 3ʹ end, which includes two coupled steps, cleavage and polyadenylation [1, 2]. Cleavage/polyadenylation (C/P) involves recognition of upstream and downstream cis elements around the C/P site (known as pA) by the C/P complex [3, 4]. While a relatively simple signal sequence in the precursor mRNA is required for the reaction, many interactions between a large number of protein factors are necessary for the correct formation of the C/P complex . In addition to factors in the core C/P complex, it has been shown that splicing factors can play roles in 3ʹ end processing. U1 snRNP (or U1) has been implicated in inhibition of C/P via poly(A) polymerase [5,
Well over half of the mammalian genes contain more than one pA, leading to expression of alternative cleavage and polyadenylation (APA) isoforms . APA is highly dynamic across tissue types [12, 13], in cell proliferation and differentiation [14, 15], and in response to extracellular cues . Most APA sites are located in the 3ʹ untranslated region (3ʹUTR) of mRNA . As 3ʹUTRs contain various cis elements for post-transcriptional control, such as microRNA target sites and AU-rich elements, 3ʹUTR-APA can significantly impact mRNA metabolism. In addition, a sizable fraction of genes harbor pAs in introns . Intron-APA can result in change of coding sequences of mRNA, impacting the proteome. The core mammalian C/P machinery and additional cis elements around the pA are responsible for the selection among APA sites [18,
The DNA damage response (DDR) occurs on a number of environmental exposures, such as ultraviolet (UV) irradiation, and involves functional and structural changes in a number of nuclear proteins, resulting in a coordinated control of gene expression and DNA repair. One key aspect of the response is the transient decrease of the cellular levels of mRNA following UV irradiation and its recovery [22, 23]. Although the mechanisms involved in this response are still not completely resolved, it has been determined that the UV-induced inhibition of both transcription  and mRNA 3ʹ processing  are responsible for the decrease in mRNA levels. Both 3ʹ end formation and transcription are affected in a similar time frame after DNA damage, resulting in a general, transient decrease of the cellular levels of polyadenylated transcripts . mRNA levels of genes involved in DDR appear to be specifically regulated at the 3ʹ-end processing step . Tumor suppressors and DNA repair factors whose expression is commonly compromised in most cancers, such as BARD1 and p53, have functional interactions with the 3ʹ end processing factor CstF-50 and PARN deadenylase, resulting in the regulation of mRNA 3ʹ processing during DDR [25, 27,
Here we explore the mechanisms and consequences of APA on UV-induced DNA damage. Using 3ʹ region extraction and deep sequencing (3ʹREADS), we show widespread changes of intron-APA and 3ʹUTR-APA on UV treatment in mammalian cells. Distinct APA changes at different time points after UV treatment affect many genes involved in DDR and cancer. Intron-APA upregulation correlates with a decrease in U1 snRNA levels after UV-induced DNA damage. Importantly, overexpression of U1 snRNA reverses UV-induced intron-APA and mitigates the apoptosis caused by UV. Our results indicate that the U1–APA axis is an important part of gene regulatory mechanism in DDR.
Analysis of UV-induced APA by 3ʹREADS
Previous studies indicated that 3ʹ end processing is regulated during DDR [25, 27,
To simplify the analysis of APA in 3ʹ-most exons, where a variable number of pAs can exist , we selected top two 3ʹUTR-APA isoforms for each gene with the most number of reads and examined their relative expression. For RKO cells, we identified 1 278 and 1 317 genes that displayed isoform expression changes in the 0–0.5 h and 0.5–2 h time windows, respectively (Fisher exact test, P<0.05; Figure 1c). For RKO-E6, we identified 728 and 755 genes with significant 3ʹUTR-APA changes in the 0–0.5 h and 0.5–2 h time windows, respectively (Figure 1d). The fact that fewer genes underwent 3ʹUTR-APA in RKO-E6 cells than in RKO cells suggests a potential role of p53 in impacting the extent of 3ʹUTR-APA regulation during DDR. Overall, for both cell lines, the number of genes which had upregulated distal pA isoform was similar to that of genes which had upregulated proximal pA isoform in both windows, indicating that there was no global direction for 3ʹUTR length changes under these conditions. It is noteworthy that in both time windows and for both cells lines, upregulation of proximal pA isoforms was accompanied with a similar magnitude downregulation of distal pA isoforms and vice versa (similar x-axis and y-axis median values for blue and red dots in Figure 1c and d), indicating that APA isoform expression regulation was generally due to changes of pA choice rather than differences in isoform stability (which would cause different magnitudes of regulation).
Interestingly, the APA pattern in the 0–0.5 h window was largely different than the 0.5–2 h window for both cell lines (Figure 1e); a group of pAs in fact had an opposite regulatory trend between the two time windows. This result indicates widespread and dynamic 3ʹUTR-APA regulation during the progression of DDR. Consistently, Gene Ontology (GO) analysis indicated that different biological processes were affected by 3ʹUTR-APA in the two windows (Supplementary Table S1). For example, APA regulation was significantly enriched for genes associated with ‘cell redox homeostasis’, ‘cellular homeostasis’ and ‘regulation of cellular component organization’ in the 0.5–2.0 h window, whereas ‘protein localization to endoplasmic reticulum’, ‘negative regulation of transport’ and ‘membrane protein proteolysis’ were found to be associated with genes with APA regulation in the 0–0.5 h window. Three example genes are shown in Supplementary Figure S1.
A large fraction of human pAs are located in introns . We next compared expression of isoforms using intronic pAs with those using 3ʹ-most exon pAs for RKO and RKO-E6 cells. As with 3ʹUTR-APA events, fewer genes underwent intron-APA in RKO-E6 cells than in RKO cells, suggesting a role of p53 in the regulation (Figure 2a and b). Much to our surprise, intronic pA isoforms were greatly upregulated compared with 3ʹ-most exon pA isoforms in both cell lines. This trend was much more conspicuous in the 0.5–2 h window than the 0–0.5 h window, in which 4.3- and 1.8-fold more genes had upregulated intronic pA isoforms than had upregulated 3ʹ-most exon pA isoforms, respectively (Figure 2a). A similar trend was observed for RKO-E6 cells albeit to a lesser extent (2.8- and 1.5-fold, Figure 2b). In contrast to 3ʹUTR-APA regulation, the magnitude of upregulation of intronic pA isoforms in both cell lines was greater than that of downregulation of 3ʹ-most exon pA isoforms (different x-axis and y-axis median values for blue and red dots in Figure 2a and b), in line with the fact that intronic pAs isoforms are typically expressed at much lower levels than 3ʹUTR pA isoforms. Consistently, greater numbers of intronic pAs were detected in 2 h samples than in 0 or 0.5 h samples by 1.9- and 1.6-fold for RKO and RKO-E6, respectively (Figure 2c). Six example genes are shown in Supplementary Figure S2. Together, these results suggest that while p53 expression may impact the extent of APA regulation, it does not affect the direction of regulation.
Similar to the 3ʹUTR-APA result, genes with regulated intronic pAs in the two time windows analyzed are largely different (Figure 2d). GO analysis (Supplementary Table S2) indicated that upregulated intronic pAs in the 0–0.5 h window were enriched for genes associated with several GO terms, such as ‘regulation of protein kinase B signaling cascade’ and ‘modification of morphology or physiology of other organism involved in symbiotic interaction’, and those in the 0.5–2 h window were enriched for genes associated with ‘regulation of transcription from RNA polymerase II promoter’, ‘response to DNA damage stimulus’, ‘nucleocytoplasmic transport’ and so on. A significant number of regulated intronic APA events overlapped between RKO and RKO-E6 cells (P=2.4×10−5, Fisher’s exact test, Figure 2e, right panel), suggesting that the effect of UV treatment on intronic APA is not cell type specific. Notably, the extent of overlap is greater than that for 3ʹUTR-APA (P=0.14, Fisher’s exact test, Figure 2e, left panel), suggesting that intron-APA is less regulated by p53 than is 3ʹUTR-APA.
We then asked how intron-APA regulation was related to gene expression (Figure 3a and b, Supplementary Figure S6). Our data indicate that genes with intronic pA activation between 0.5 and 2 h were more likely to be downregulated in the same period, as compared with other genes (Figure 3a), suggesting that intronic APA can inhibit gene expression by generating truncated transcripts. Interestingly, we also found that the same genes with intronic pA activation between 0.5 and 2 h were also more likely to be upregulated between 0 and 0.5 h after UV treatment (Figure 3b), suggesting that intronic APA might serve as a mechanism to regulate gene expression of factors involved in the response, such as POLR2A and cyclin-dependent kinase inhibitor 1A (CDKN1A), assuring that cells react to damage response in a controlled and timely manner. Consistent with this and the results shown in Supplementary Table S2, Ingenuity Pathway Analysis showed that genes with significant intronic APA regulation in both RKO and RKO-E6 cells were associated with pathways highly relevant to DDR (Figure 3c and d).
Validation of UV-induced APAs detected by 3ʹ READS
To validate our genome-wide analysis, we examined 3ʹUTR- and intron-APAs for genes following the strategies shown in Figure 4a. To further confirm that the effect of UV treatment on intronic APA is not a cell type-specific effect, we extended our study to colon carcinoma HCT116 cells. Briefly, after recovery from UV treatment, nuclear RNA was isolated from colon carcinoma HCT116 and RKO cells and complementary DNA (cDNA) was synthesized by reverse transcription using oligo(dT) primers. Quantitative reverse transcription–PCR (qRT–PCR) was performed with these cDNA as template. HCT116 results are shown in Figure 4b and c. Three primers were used to detect intron-APA products (short isoform) and full-length mRNAs (long isoform): the forward primers were located in the upstream exons of regulated intronic pAs of studied genes and the two reverse primers corresponded to either the intron containing the pA (for detection of short isoform) or the downstream exon (for detection of long isoform). A similar strategy was used to detect 3ʹUTR-APA products: a common forward primer in the 3ʹUTR and the two reverse primers corresponded to either upstream (for detection of total 3ʹUTR-APA) or downstream (for detection of distal-APA isoforms) from the used pA. The values for the proximal APA were calculated by subtracting the distal-APA values from the total 3ʹUTR-APA values.
As shown in Figure 4b, our analysis for 3ʹUTR-APAs included genes involved in different biological pathways (Supplementary Table S1) with functions in DDR and cancer, such as small nuclear ribonucleoprotein polypeptide B (SNRPB2) [36, 37], endoplasmic reticulum protein retention receptor 1 (KDELR1) [38, 39]; Notch homolog 1 translocation-associated (NOTCH1) [40, 41] and dual specificity phosphatase 6 (DUSP6) [42, 43]. Consistent with the 3ʹREADS results (Figure 1c), the analysis of UV-induced 3ʹUTR-APA in the 0–0.5 h window indicated that each individual gene did not show a major change in the distal/proximal ratio. However, UV treatment in the 0–2 h window induced changes in the usage of pA for individual genes, favoring either distal (KDELR1, NOTCH1 and DUSP6) or proximal (SNRPB2) pAs. The analysis shown in Figure 1c might represent the overall behavior of the total genes analyzed, indicating that there was no global direction of 3ʹUTR length changes under these conditions.
Our analysis for intron-APAs included genes with important functions in DDR and cancer (Figure 4c), namely cyclin-dependent kinase inhibitor 1A (CDKN1A, p21) [44, 45], polymerase (RNA) II (DNA directed) polypeptide A (POLR2A, RNA polymerase II) [46, 47], Ephrin B2 (EFNB2) [48, 49], E2F transcription factor 1 (E2F1) [50, 51] and Down syndrome critical region gene 3 (DSCR3) [52, 53]. Importantly, based on IPA analysis, CDKN1A and POLR2A were at the hub of the networks significantly associated with intronic pA activation in the 0.5–2 h window (Supplementary Figure S3A and B). Consistent with the 3ʹREADS analysis results, UV treatment induced the formation of intron-APA transcripts that were polyadenylated (Figure 4b and c). Interestingly, the increase in intron-APA isoforms was observed from 2 to 6 h after UV treatment, but these shorter isoforms decrease after 10 h, reaching the levels of untreated cells (Figure 4c). Similar results were observed with RKO cells (not shown), suggesting that UV-mediated regulation of intronic APA is not a cell type-specific effect. The transient nature of these intron-APA isoforms is consistent with previously characterized responses to DNA damage [25, 30]. The sequences of the second intron was not detected in any of the mRNAs samples analyzed (Supplementary Figure S4A), indicating that intron-APA was induced within the first intron of the target mRNAs. Together, these results indicate the UV treatment induce the usage of intronic pAs of genes involved in DDR, suggesting a possible role for these intron-APA events in controlling gene expression during the response.
Features of UV-induced intronic APA events
We next examined features of introns that harbor activated pAs in DDR in our 3ʹREADS data. Strikingly, we found the activated intronic pAs are highly enriched (>1.5-fold above background) in 5ʹ introns, with the most notable enrichment being pAs in the first intron in the 0.5–2 h window (2-fold above background) (Figure 5a). Consistently, we found that the distance from the activated pAs in the 0.5–2 h window to transcription start site (TSS) was significantly shorter than those in control cells (P=3×10−12) (Figure 5b), a trend not seen for activated pAs in the 0–0.5 h window (P=0.4). Further analysis of intron features indicated that introns harboring activated pAs are larger and had stronger 5ʹ splice site (5ʹSS) compared with other introns (Supplementary Figure S5). However, these distinct features were not significantly different from other first introns. Note that the upregulated intronic pAs of POLR2A and EFNB2 are both located in the first intron, and the APA event of CDKN1A was either in the first intron or a 5ʹ intron depending on the TSS (Supplementary Figure S2). Interestingly, in addition to the sense strand pAs, we also noticed in the 0.5–2 h window a general upregulation of transcripts using pAs within 4 kb from the TSS on the anti-sense strand (Figure 5c). These transcripts were previously named upstream anti-sense RNA (uaRNA) or PROMPTs [54, 55]. Their activation in the 0.5–2 h window suggests a unique mechanism regulating RNAP II activity around the TSS in this phase of DDR response. We also determined the distribution of nucleotides around the 3ʹUTR and intronic pAs identified by 3ʹREADS (Figure 5d). The base composition profiles upstream and downstream from the pA for these two groups of pAs were highly similar and consistent with those of known pAs , indicating that the 3ʹUTR and intronic pAs detected by 3ʹREADS were genuine pAs with similar surrounding cis elements.
Role of U1 RNA levels in intronic APA events during DDR
The activation of promoter-proximal pAs in 2 vs 0.5 h is reminiscent of APA regulation by U1 snRNP: functional depletion of U1 RNA shortens mRNAs due to usage of promoter-proximal cleavage and polyadenylation signals . Earlier studies have shown a decrease in U1 and U2 small RNA levels in HeLa cells on UV treatment . Therefore, we examined whether intronic APA was triggered by U1 RNA reduction in response to UV irradiation. First, we detected the effect of UV treatment on the levels of U1 RNA by qRT–PCR using HCT116 and RKO cells (Figure 6a). Cells were treated with UV irradiation and allowed to recover for the indicated time points. Consistent with the studies of Eliceiri and Smith , our qRT–PCR analysis of nuclear RNA samples from these cells showed a transient decrease in U1 RNA levels on UV treatment (Figure 6a). Although a decrease in U1 RNA was detected as early as 0.5 h after UV treatment, the lowest level of U1 RNA was observed 6 h after UV treatment for both cell lines. The levels of U1 RNA increased 24 h after UV treatment, reaching the levels of untreated cells. Extending those studies, we analyzed the levels of other components of the U1 and U2 snRNPs by qRT–PCR. After UV treatment, a decrease was also observed in U2 RNA, U1A and U1-70K mRNAs of U1 snRNP (Figure 6b). No significant changes were observed in U1C levels. Thus, among all the molecules examined, U1 snRNA levels (Figure 6a) correlated the best with the changes in intronic/full-length APA levels (Figure 4c). Previous studies indicate that U1 snRNPs, such as U1A and U1-70K, are inhibitors of 3ʹ end processing and intronic APA (reviewed in 57). Our studies indicate that the decrease of these U1 snRNPs early in DDR might increase intronic APA. However, only U1 snRNA levels correlate with the decrease in intronic APA later in the response, suggesting that other components of U1 snRNP might not be at the rate-limiting level during DDR.
Importantly, functional depletion of U1 RNA using morpholino oligonucleotides increased significantly the ratio of intron/full-length APA isoforms for POLR2A, CDKN1A and EFNB2 (Figure 6c). Strikingly, using low concentrations of U1 snRNA AMO, the changes in the intronic/full-length ratio by U1 RNA depletion were similar in magnitude to that observed after UV treatment (compare Figures 4b and 6c). As previously described , we did not detect sequences of the second intron in any of the mRNA samples analyzed at low concentrations of U1 snRNA AMO (Supplementary Figure S4B), indicating that the moderate functional decrease in U1 levels was insufficient to inhibit splicing. However, at higher concentrations, second intron inclusion was observed for the genes analyzed (Supplementary Figure S4B). U2 RNA depletion using morpholino did not increase the usage of examined intronic pAs (Figure 6c). This is consistent with previous studies showing that decrease of U2 snRNP levels has a different impact on intronic APA . Supporting these results, overexpression of U1 snRNA reverses the UV-induced increase of intron-APA (Figure 6d) and apoptosis (Figure 6e). Together, these results indicate that the UV-induced downregulation of U1 snRNA, not other components of the U1 snRNP, is chiefly responsible for the activation of intronic APA sites during DDR.
Here we report significant activation of intronic pAs on UV treatment in mammalian cells, adding a new layer of gene regulation in the cellular response to UV-induced DNA damage. At the center of this mechanism is U1 snRNA, one of the component of U1 snRNP, which has previously been shown to play an important role not only in splicing but also in 3ʹ end processing [5, 20]. Our data for the first time provides a cellular response/pathway that is affected by the U1–APA axis and shows that downregulation of the U1 snRNA level is the controlling step for intronic APA in DDR. This mechanism results in activation of pAs located near TSS, mostly in the first intron, and serves as a rapid (within 2 h after UV) strategy to regulate expression of affected genes. Given the different correlations between intronic pA activation and gene expression changes in 0.5 vs 2 h and 0 vs 0.5 h windows, it is plausible that this mechanism assures that the expression of factors involved in the response, such POLR2A and CDKN1A, occurs in a controlled and timely manner. Consistent with this, genes with significant intronic APA regulation belong to pathways activated during DDR and downregulation of gene expression was more likely to be associated with intronic APA.
Our results indicate that similar changes in APA events occur in different cell lines in a similar timeframe, suggesting that UV-mediated regulation of intronic APA and 3ʹUTR-APA are not a cell type-specific effect. However, our results also indicate that p53 expression may impact the extent of APA regulation during DDR. This is not surprising given that p53 is involved in different aspects of gene expression regulation during DDR, such as controlling transcription, mRNA stability and/or translation [58, 59]. Further experiments are needed to reveal the exact role of p53 in APA regulation in DDR.
Although transcriptional and protein level changes of POLR2A and CDKN1A are known mechanisms of UV response in mammalian cells, the UV-induced regulation of their APA isoforms and steady-state levels of their transcripts have never been reported. A fraction of the largest subunit of POLR2A decreases by DNA damage-induced ubiquitination followed by proteasomal degradation in mammalian cells [60, 61]. This modification can be detected within 15 min after exposing cells to UV irradiation and persists for about 8–12 h . POLR2A ubiquitination requires C-terminal domain phosphorylation, which is a characteristic of elongating POLR2A [61, 62]. Interestingly, the polyadenylation factor CstF associated to the tumor suppressors BRCA1/BARD1 play a role in the proteasome-mediated degradation of POLR2A during DDR [27, 63]. Both the interaction of CstF and BRCA1/BARD1 complex [24, 27, 31] and the proteasome-mediated degradation of POLR2A [27, 63] contribute to the inhibition of 3ʹ end processing that occurs after DNA damage. Those studies suggested the existence of several, possibly redundant, mechanisms to explain the inhibitory effect of UV irradiation on mRNA 3ʹ processing. The studies presented here add another level of complexity indicating that the UV-induced decrease in POLR2A protein levels might be due to intronic APA, which results in a decrease in full-length POLR2A mRNA, supporting the idea that U1 snRNA plays a role in this response. The cellular function of this shorter form of POLR2A protein in cellular transcription as well as other factors involved in intronic APA during DDR will be addressed in future studies. Notably, it has been shown that UV damage switches the usage of pAs from the proximal to the distal one in the 3ʹUTR for the yeast largest subunit of POLR2A gene . How APA-medicated regulatory mechanisms vary in different species is another subject of future investigation.
Although it is known that a differential regulation of genes involved in DDR occurs during the progression of DDR, the mechanisms driving this differential regulation are not completely understood. One example is the p53 pathway. Although p53 binds to the promoter of all of its target genes not all these genes are activated with same stimulus at the same time of the response [65,
Together, our study reveals a significant gene-specific regulatory scheme in DDR where U1 snRNA impacts gene expression via APA.
Materials and Methods
Tissue culture methods
RKO, RKO-E6 and HCT116 cell lines were cultured in Eagle's minimal essential medium and Dulbecco’s modified Eagles medium, respectively. Media were supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin antibiotic.
Ninety percent confluent cultures were exposed to UV and harvested at the indicated times. UVC doses (40 J m−2) were delivered in two pulses using a Stratalinker (Stratagene, La Jolla, CA, USA). Prior to pulsing, medium was removed and replaced immediately after treatment.
Colon carcinoma RKO cells were treated with UV irradiation and allowed to recover for 0.5 or 2 h. Nuclear RNA was purified using the RNeasy kit (Qiagen, Valencia, CA, USA) following manufacturer’s protocol, followed by 3ʹREADS analysis as described in ref. 33. Briefly, after RNA fragmentation, poly(A)-containing RNA fragments were captured onto magnetic beads coated with a chimeric oligonucleotide (oligo CU5T45), which contained 45 thymidines (Ts) at the 5′ portion and 5 uridines (Us) at the 3′ portion, and were released from the beads by RNase H treatment, which also eliminated most of the As of the poly(A) tail. Eluted RNA was ligated to 5′ and 3′ adapters, followed by reverse transcription, PCR amplification and deep sequencing.
Reads from 3ʹREADS were aligned to the genome using Bowtie2 , and those with at least two non-genomic As at the 3′ end were considered as PolyA site-supporting reads, which were used for APA analysis. We used the Fisher’s exact test to compare isoform expression between two samples. For 3ʹUTR-APA analysis, the two most abundant 3ʹUTR pA isoforms were compared; for intron-APA analysis, we either compared each intronic pA isoform with all isoforms using pAs in the 3ʹ-most exon or combined all intronic pA isoforms and compared them with all isoforms using pAs in the 3ʹ-most exon. We used P-value<0.05 and relative abundance change>5% to select significantly regulated APA events. GO analysis (http://www.geneontology.org) were carried out using Fisher’s exact test. IPA analysis was carried out using default values (www.qiagen.com/ingenuity). Features of introns with regulated pAs were based on RefSeq annotations. 5ʹSS and 3ʹSS scores were based on the maximum entropy method .
Analysis of endogenous mRNAs or APA isoforms abundance
Nuclear RNA was purified from different cell lines using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions. RNA concentrations of the samples obtained under different conditions were equalized. Equivalent amounts of purified RNA (2 μg) were used as a template to synthesize cDNA using either random hexamer primers or oligo-d(T) primers and GoScript reverse transcriptase (Promega, Madison, WI, USA) according to the manufacturer’s protocol. PCR was performed using the reverse transcriptase products and Taqman master mix (Applied Biosystems, Foster City, CA, USA). The primers used to detect intron/full-length and distal/proximal mRNA isoforms are described in Supplementary Table S3. Commercially available primers for GAPDH (Applied Biosystems) were used in the qRT–PCR reactions to normalize qRT–PCR reactions. SYBR green master mix (Applied Biosystems) was used in the qRT–PCR reactions. Relative levels were calculated using ΔCτ method. Genomic DNA was prepared from HCT116 cells as in ref. 74. For detection of second introns the following primers were used: POLR2A: forward primer 5ʹ- GGGAAGCAGGCTGGAATTGG-3ʹ, reverse primer 5ʹ- GTCTGCATTGTACGGAGTT-GTC-3ʹ. CDKN1A: forward primer 5ʹ- GAGTGGACGTTCCCCGAGTT-3ʹ, reverse primer 5ʹ- GTCAGCCAGGCCAAGAAGAAG-3ʹ. Ephrin B2: forward primer 5ʹ- GCCAGGAAGGAGGTATAATTGGG-3ʹ, reverse primer: 5ʹ- ACCTTTCTTCTCCCCTGCTAC-3ʹ.
Depletion and overexpression of U1 snRNA
HCT116 cells were transfected with either 10 nmol of control oligo or U1 snRNA targeting morpholino oligonucleotides according to the manufacturer’s instructions (Gene Tools, Philomath, OR, USA) using scrape delivery method. After addition of morpholino nucleotides, cells were scraped and transferred to a new six-well plate. The plasmid overexpressing U1 snRNA was kindly provided by Dr Gunderson (Rutgers University). HCT116 cells were transfected with this plasmid using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Cells were harvested 48 h after transfection and nuclear RNA was isolated. cDNA was prepared and used in qRT–PCR reactions as described above.
Nuclear extract preparation
Cell death ELISA assay
Fragmentation of DNA after induction of apoptosis was determined by photometric enzyme immunoassay (Cell Death Detection ELISAPLUS; Roche, Indianapolis, IN, USA) as recommended by the manufacturer.
Availability of supporting data
The data sets supporting the results of this article are available in the NCBI’s Sequence Read Archive: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71801.
We thank Dr Gunderson for U1 snRNA-encoding plasmids. This work is supported by National Institute of Health grants R21 CA175794-02 to FEK and R01 GM084089 to BT.
About this article
Nature Reviews Molecular Cell Biology (2017)