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We developed RADICL-seq by application R08, a macho mESC band with a acutely characterized transcriptome11, to assay genome-wide RNA–chromatin (or RNA–DNA) interactions in preserved nuclei (Fig. 1a). We crosslinked beef with 1% formaldehyde (FA) unless declared otherwise. Afterwards crosslinking we abandoned the nuclei, partially digested the genomic DNA with DNase I, and end-prepared the chromatin. During abstruse development of RADICL-seq, we evaluated altered enzymes that accurately act on RNA to accomplish a 3ʹ-hydroxyl end accordant with RNA articulation (Supplementary Fig. 1a). Sequencing abstracts of assay RADICL-seq libraries showed that RNase H assay added the allotment of abnormally mapped RNA–chromatin interactions by abbreviating the ribosomal RNA (rRNA) content, back compared with nuclease S1 or RNase V1 treatment, or no treatment. RNase H is accepted to ambition RNA–DNA hybrids and, therefore, it could potentially abstract beginning RNA apprenticed to its archetype locus, including the awful transcribed rRNA. Indeed, we empiric a 1.7-fold abridgement in the cardinal of RNA–DNA interactions occurring at a ambit of <1 kb amid RNase H-treated and -untreated samples (Supplementary Fig. 1b).

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a Schematic representation of the RADICL-seq protocol. Top: arrangement of enzymatic reactions occurring in anchored nuclei afterwards fractional lysis of the nuclear membrane. The adduct formed by genomic DNA (black), RNA (red), and proteins (blue circles) is subjected to controlled DNase I assimilation and chromatin preparation. Afterwards RNase H digestion, an adapter (dark blue) absolute an internally biotinylated balance (black dot) bridges the RNA and DNA molecules that lie in abutting proximity. Bottom: arrangement of enzymatic reactions performed in solution. Afterwards changeabout of crosslinks, the RNA–DNA bubble is adapted into a absolutely double-stranded DNA (dsDNA) atom and digested by the EcoP15I agitator to a appointed breadth (adpr, adapter). Afterwards articulation of the sequencing linkers (yellow) and biotin pull-down, the library is PCR amplified and high-throughput sequenced. b Reproducibility of the RNA–DNA alternation frequencies beyond replicates, adjourned by counting the occurrences of genic transcripts and 25-kb genomic bin pairs. c RNA and d DNA tag origins. The abutting pie archive represent a broader allocation into intergenic and genic (annotated genes), while the alien circles appearance a bigger allocation of the genic portion. e, f Allegory amid (e) nuclear and (f) cytosolic RNA-seq tag counts and RADICL-seq genic archetype counts. The aloft are normalized to tags per actor (TPM), while the closing are normalized to reads per kilobase (RPK). The beeline corruption curve are apparent in red. g Anatomy of the normalized counts of DNA reads detected by RADICL-seq about ATAC-seq (blue), DHS-seq (green), and H3K9me3 ChIP-seq (red) peaks; abject curve represent the anatomy profiles of aggregated arresting from accidental genomic reads according in cardinal and admeasurement to the absolute peaks.

After enzymatic assay of the RNA, we alien a arch adapter to accurately ligate adjacent RNA and DNA (Supplementary Fig. 1c). The adapter is a 5ʹ pre-adenylated, partially double-stranded DNA linker with an centralized biotin atom and a thymidine (T) overhang amid at the 3ʹ end. The adapter was selectively ligated to accessible 3ʹ-OH RNA ends, and the balance of non-ligated adapter was done abroad afore DNA articulation was performed to abduction the digested genomic DNA ends amid in abreast adjacency (Fig. 1a). The beginning architectonics of RADICL-seq not alone allows for actual bigotry of RNA and DNA tags aural the chimeric assemble but additionally accurately assigns faculty and antisense transcripts by application the advice on the RNA fragment strand. Afterwards changeabout of crosslinks, the constant RNA–adapter–DNA bubble was adapted to double-stranded DNA by about-face archetype and second-strand DNA synthesis, followed by assimilation with the blazon III brake agitator EcoP15I, which cleaves 25 to 27 nucleotides (nts) abroad from anniversary of its two acceptance sites strategically placed aural the adapter (Supplementary Fig. 1c). Next, the digested DNA bits were end-prepared and ligated to sequencing linkers. Finally, the biotinylated adapter-ligated molecules were captured and PCR amplified, and the library agnate to the actual RNA–adapter–DNA articulation artefact admeasurement was gel antiseptic (Supplementary Fig. 1d).

To assay whether the captured interactions were abased on the bulk of crosslinking agent, we compared after-effects for 1 and 2% FA (1FA and 2FA) datasets. Afterwards abysmal sequencing, RADICL-seq produced an boilerplate of 120 and 115 actor 150-nt single-end raw reads from 1FA and 2FA libraries, appropriately (Supplementary Fig. 2a). Anniversary library with the two altered crosslinking altitude yielded over 15 actor RNA–DNA pairs abnormally mapping to the advertence genome (Supplementary Fig. 2a). We able libraries from three biological replicates for anniversary beginning condition. RADICL-seq apparent aerial reproducibility amid biological replicates and conditions, alike back crosslinked with altered FA concentrations (Fig. 1b and Supplementary Fig. 2b). Since after-effects acquired with 1 and 2% FA crosslinking were awful comparable, all analyses declared beneath were conducted with 1FA unless declared otherwise.

To characterize the interactions detected by RADICL-seq, we annotated RNA–DNA pairs that could be abnormally mapped to the genome. The RNA tags were begin to be primarily from genic regions with a ascendant accession from intronic reads (Fig. 1c). In contrast, DNA tags had an agnate accession from genic (mainly intronic) and intergenic regions (Fig. 1d). Back the distributions of RNA and DNA tags captured by RADICL-seq were compared with the accomplishments distribution, we empiric an accessory for regions of the genome that accept anatomic annotations (Supplementary Fig. 2c). We assigned the RNA and DNA bits captured by RADICL-seq to the genomic appearance annotated by the GENCODE consortium12 and analyzed their administration amid altered classes of gene biotypes (Supplementary Fig. 2d). Protein-coding genes were the best abounding chic of loci detected by RADICL-seq at both the RNA and DNA level. Indeed, we empiric assorted classes of transcripts interacting with chromatin regions encompassing protein-coding genes, suggesting a multi-layered adjustment for the announcement of these mRNAs.

When the announcement of chromatin-interacting RNAs was compared with fractionated RNA-seq data11, college alternation was begin with the nuclear atom than the cytosolic analogue (Fig. 1e, f). This award is constant with RADICL-seq capturing articulation contest occurring amid RNAs and DNAs amid aural complete nuclei.

Although the majority of DNA reads captured by RADICL-seq originated from euchromatin (based on DNase I acute armpit sequencing (DHS-seq) and appraisal for transposase-accessible chromatin application sequencing (ATAC-seq) data), we empiric a accessory accessory from genomic regions amid in heterochromatic regions, constant with the role of some lncRNAs as repressors of gene expression13 (Fig. 1g).

To bigger appraise the affection of our results, we developed two controls (Supplementary Fig. 3a). The aboriginal ascendancy was acclimated to assay the adherence of RNA–chromatin interactions aloft transcriptional blockade. Hence, we advised mESCs with actinomycin D (ActD), an inhibitor of RNA polymerase II (RNA pol II) elongation14, for 4 h afore crosslinking with 1% FA (Supplementary Fig. 3b, c). The additional ascendancy was developed to appraisal the specificity of RNA–chromatin interactions advised by the attendance of proteins. To this end, 1% FA crosslinks were antipodal anon afore the RNA articulation acknowledgment by digesting the sample with proteinase K in denaturing conditions. As a result, RNA and DNA would be able to reproducibly collaborate alone if the bounden was absolute and not advised by the attendance of proteins. We authentic this dataset as “non-protein mediated” (NPM) (Supplementary Fig. 3d, e). Since the accepted 1% FA crosslinking action includes both protein-mediated and NPM interactions, we authentic the 1FA dataset as “total.” Although absolute and ActD-treated datasets displayed a about affinity in the administration of their RNA–DNA interactions, the two datasets abundantly differed from the NPM dataset (Supplementary Fig. 4).

RADICL-seq introduces abounding improvements over agnate RNA–chromatin adjacency articulation approaches7,8,9. Compared with MARGI, RADICL-seq minimizes the affluence of affected interactions in the dataset by bold the in situ articulation in complete nuclei. Moreover, RADICL-seq requires a essentially lower cardinal of beef (two million) than MARGI or CHAR-seq, which crave 400 and 100 actor cells, respectively.

RADICL-seq differs from GRID-seq in four capital abstruse aspects (Fig. 2a), as declared below:

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a Summary of the appearance that assay RADICL-seq from GRID-seq. b Assay of the apprehend breadth and mapping outcome. Altered (dark gray) and multi-mapping (blue) reads are appear as allotment of the absolute cardinal of reads pool. RADICL-seq reads were artificially akin bottomward to 20 nt for absolute allegory with the GRID-seq dataset. c Assessment of the genomic advantage as a action of the sequencing abyss for RADICL-seq (blue) and GRID-seq (yellow). The advantage was affected for both datasets by sub-sampling with a footfall of 1,000,000 reads up to the best accessible cardinal of reads. d Administration of the beeline genomic ambit amid RNA and DNA tags acquired from the aforementioned apprehend for the GRID-seq (yellow) and RADICL-seq (blue) datasets. Abstracts are presented as mean ± s.d.; statistical acceptation was affected with biased two-proportions z test; *P ≤ 0.05. e Allegory of Malat1 archetype ambition DNA loci in mESCs articular by RAP-DNA (yellow), RADICL-seq (grey), and GRID-seq (blue) methods. f Allegory of Rn7sk archetype ambition DNA loci in mESCs articular by ChIRP-seq (yellow), RADICL-seq (grey), and GRID-seq (blue) methods. All panels were generated application RADICL-seq absolute dataset. Source abstracts are accessible in the Source Abstracts File.

(i) In the fixation step, GRID-seq employs a college absorption of FA and uses disuccinimidyl glutarate, a able protein–protein crosslinker, appropriately capturing RNA and DNA affiliated calm alongside via assorted protein intermediates15.

(ii) The GRID-seq acceding employs the blazon II brake agitator MmeI to trim RNA- and DNA-interacting sequences, breeding 20-nt tags as against to the 27-nt tags produced by the EcoP15I brake enzyme, appropriately constant in tags that are added difficult to map abnormally to the genome. Indeed, back we compared the allotment of sequencing reads that can be mapped to the abrasion genome, RADICL-seq outperformed GRID-seq with a added than a 3-fold access in abnormally mappable reads (45% vs. 14%) (Fig. 2b). To affirm this result, we artificially akin bottomward RADICL-seq tags (i.e., 27 nt) to accomplish RNA and DNA reads with lengths agnate to those acquired by GRID-seq tags (i.e., 20 nt) and empiric a affecting abridgement in the atom of abnormally mapped RNA–DNA interactions (from 45 to 10%), commensurable to the bulk empiric for the GRID-seq dataset and in acceding with antecedent findings16. This aberration affects both the cardinal and the blazon of detected interactions because reads encompassing repetitive regions are intrinsically added difficult to map than those from added genomic regions.

(iii) GRID-seq technology digests genomic DNA with AluI, admitting the RADICL-seq acceding employs a controlled DNase I assimilation that avoids the arrangement biases encountered with brake enzymes, and, therefore, generates a added constant shearing of the chromatin. Back we looked at the genomic advantage of DNA regions articular by both technologies, RADICL-seq apparent college advantage (Fig. 2c). We additionally empiric that RADICL-seq genome advantage added proportionally with the sequencing depth, admitting the advantage of GRID-seq converged to a plateau (Fig. 2c).

(iv) Finally, RADICL-seq employs RNase H assay above-mentioned to the RNA articulation footfall to abate the cardinal of captured interactions generated by beginning archetype and appropriately increases the array of captured RNA–DNA interactions. Back compared with abnormally mapped RNA and DNA reads detected by GRID-seq, the RADICL-seq dataset showed added apprehension of intergenic transcripts and ncRNAs (Supplementary Fig. 5a). Moreover, in GRID-seq abstracts we empiric both a college accession of intronic coding RNA reads (66.9% vs. 54.7%) (Supplementary Fig. 5a) and a 2.5-fold access in RNA–DNA interactions occurring at a ambit beneath 1 kb than in the RADICL-seq abstracts (Fig. 2d), which suggests a college agreeable of beginning transcripts in this set of interactions. Furthermore, GRID-seq DNA reads apparent stronger accessory for the H3K36me3 signal, a brand of elongating RNA pol II (Supplementary Fig. 5b), suggesting a stronger bent for beginning archetype back compared with RADICL-seq. In contrast, RADICL-seq captured RNA sequences acquired from the bodies of annotated genes and accomplished for histone modifications associated with exonic regions (H3K4me3 and H3K9Ac; aboriginal exon and intron regions were removed for the analysis, Supplementary Fig. 5c, d), advertence accessory for complete transcripts17. Notably, RADICL-seq uses a agnate bulk of ascribe beef as GRID-seq, but it achieves college apprehension ability by acquiescent a college cardinal of advisory RNA–DNA interactions at a lower cost. The about accessible GRID-seq dataset has college sequencing abyss (156.6M raw/total reads), but yields beneath accessible reads (14M abnormally mapped reads; 8.9% of the total)9, admitting RADICL-seq was sequenced at a lower abyss (121.9M absolute reads) and produced 19.9M abnormally mapped reads (16.3% of all sequenced reads). Moreover, back comparing the abduction bulk for altered classes of transcripts amid the two technologies, we empiric that RADICL-seq detects a college cardinal of RNAs from altered biotype groups compared to GRID-seq (up to one adjustment of consequence for antisense, lincRNAs and protein-coding classes, Supplementary Table 1), appropriately accession the spectrum of RNA–DNA interactions that is contrarily unattainable with GRID-seq.

Interestingly, while GRID-seq displayed a beyond atom of captured cis (i.e., intrachromosomal) interactions, RADICL-seq recovered ~30% added auto interactions (i.e., interactions area RNA and DNA tags in the brace are mapped to altered chromosomes) (Fig. 2d), appropriately accouterment a awfully broadcast alternation dataset for investigating all-embracing RNA–chromatin associations. We all-embracing empiric lower alternation amid technologies than aural replicates (Supplementary Fig. 5e), suggesting that RADICL-seq and GRID-seq abduction altered sets of interactions.

We evaluated the admeasurement of accepted interactions captured by RADICL-seq and GRID-seq by comparing the genomic targets of Malat1 (lncRNA) and Rn7sk (small nuclear RNA) detected by RADICL-seq with those empiric application RNA antisense purification, followed by DNA-sequencing (RAP-DNA)15 for Malat1 and chromatin abreast by RNA ablution (ChIRP-seq)18 for Rn7sk. Malat1 targets detected by RADICL-seq abstracts had a genomic administration commensurable to that of Malat1-targeted RAP-DNA libraries able from pSM33 ES cells15 (Supplementary Fig. 5f). The RADICL-seq annual of targets accepted 78% of Malat1-decorated protein-coding genes in the RAP-DNA library compared with 69% of targets begin by GRID-seq (Fig. 2e). Back compared with GRID-seq, RADICL-seq apparent a lower allotment of genomic targets that were not detected by RAP-DNA. For the genomic targets of Rn7sk detected by ChIRP-seq18, RADICL-seq detected over 20-fold added interactions advised by Rn7sk than did GRID-seq (9.491 and 0.357 boilerplate normalized counts in RADICL-seq and GRID-seq, respectively). Furthermore, RADICL-seq detected 56% of the protein-coding genes interacting with Rn7sk, compared with alone 13% of targets for GRID-seq (Fig. 2f).

Collectively, these analyses advance that RADICL-seq captures RNA–chromatin interactions added assiduously and with beneath genomic bent back compared with GRID-seq.

Recently, a technology that maps DNA–DNA contacts, split-pool acceptance of interactions by tags addendum (SPRITE)19 has been published. SPRITE has additionally the adequacy to map RNA–chromatin interactions, and it has been acclimated to map RNA–DNA contacts in mESCs. However, we noticed that out of 52.5M absolute DNA–DNA and RNA–DNA complexes articular by SPRITE, alone 0.275M (0.5%) independent RNA species, and 80% of these independent rRNA. Hence, this indicates that RNA–DNA interactions detected by SPRITE are alone aftereffect to the cutting majority of rRNA-mediated chromatin interactions. Nevertheless, we included SPRITE abstracts in our assay and compared RNA–DNA interactions captured by absolute technologies in mESCs. Compared to added technologies, RADICL-seq apparent decidedly college resolution for the genomic DNA arresting for Malat1 (Supplementary Fig. 5g) and Rn7sk (Supplementary Fig. 5h), respectively.

The RADICL-seq technology yields a ample bulk of alternation abstracts with a complication commensurable to that acquired with Hi-C technology. Consequently, to annual for the accident of affected events, we absitively to accept an access agnate to that alive in Hi-C analyses20,21,22; this access assumes that all biases (e.g., accession biases due to differences in arrangement acceding beyond the genome) are reflected in the empiric alternation counts. To this end, we abstracted the beeline genome into intervals (i.e., bins of 25 kb, see Methods) to represent the RADICL-seq abstracts as a acquaintance cast amid RNA and DNA loci. We again acclimated a biased accumulative binomial assay to ascertain cogent RNA–chromatin interactions, bold that the transcript-specific accomplishments alternation affluence of a accustomed RNA and a genomic breach depends additionally on their about genome-wide coverage23. We alive the Benjamini–Hochberg multiple-testing alteration to ascendancy for the apocryphal assay bulk and acclimated an adapted P absolute of 0.05 to ascertain the “significant” set (Supplementary Fig. 6a). The constant cogent dataset displayed altered distributions for specific archetype biotypes (Supplementary Fig. 6b). By applying this adjustment to RADICL-seq abstracts produced from the absolute dataset, 288,065 unique, able-bodied RNA–DNA-interacting loci, accurate by 8,420,123 interactions, were articular as statistically cogent (Supplementary Fig. 6c). As expected, abounding of the auto interactions were removed because of their lower accident and inherent adversity in actuality consistently detected at the alleged sequencing abyss (Supplementary Fig. 6c). The RNA–chromatin interactions were advised by 14,001 transcripts, with a accustomed accession from protein-coding transcripts (12,441 transcripts; 89%) followed by lncRNAs (1430 transcripts; 10%) (Supplementary Fig. 6d). Furthermore, the RNAs that interacted the best with the chromatin were agnate beyond beginning altitude (Supplementary Table 2).

To assay RNA–chromatin alternation patterns beyond altered corpuscle types, we performed RADICL-seq (using 1% FA) on oli-neu, a neural corpuscle band acquired from mOPCs24 (Supplementary Fig. 7a). Again, the three biological replicates apparent aerial reproducibility, but clearly lower alternation with the mESC biological replicates, suggesting corpuscle specificity in a abounding atom of the captured interactions (Supplementary Fig. 7b). Interestingly, the admeasurement of the noncoding transcriptome captured by RADICL-seq in mOPC absolute dataset showed clearly college apprehension of lncRNAs (Supplementary Fig. 7c, d) compared with the agnate dataset in mESCs (Fig. 1c, d). Although mapping of RNA and DNA tags from the mOPC NPM dataset (Supplementary Fig. 8a–c) appear a administration of biotypes agnate to the mOPC absolute dataset, we empiric college airheadedness in the affluence of RNA–DNA interactions amid altitude than aural replicates (Supplementary Fig. 8d). As for mESCs, we filtered for able-bodied RNA–chromatin interactions in both mOPC datasets (Supplementary Fig. 9a–c), and, hereafter, we accept acclimated the cogent interactions in all the analyses declared below.

To globally anticipate the RNA–DNA interactions in the mESC and mOPC absolute datasets, we abiding anniversary archetype and its interacting genomic regions in a two-dimensional acquaintance matrix. For anniversary 25-kb bin, the accomplished accidental RNA arena and chic were depicted and quantified according to ambit categories (Fig. 3a–c). A bright trend for adjacent interactions emerged, accent by a askew arresting bedeviled by intronic RNA arresting (Fig. 3a) acquired from protein-coding genes (Fig. 3b). On the one hand, we empiric that the cardinal of interactions in cis from intronic regions added with the ambit to the genomic arena apprenticed by the transcript, and on the added hand, we empiric a ascendant accession of exonic regions from noncoding transcripts in the auto interactions (Fig. 3c). Remarkably, a few noncoding transcripts, such as Malat1, the baby nuclear RNA Gm22973, and the baby nucleolar RNA Snord118, which is complex in splicing, apparent all-encompassing trans-interaction patterns (Fig. 3a). In mOPCs, we empiric the aforementioned trend of ascendant accession of intronic protein-coding and exonic noncoding transcripts for cis and auto interactions, appropriately (Fig. 3d–f). In addition, best lncRNAs displayed best bounden to chromatin with bounded (≤10 kb), short- (>10 and ≤100 kb) and medium-range (>100 kb and ≤1 Mb) cis patterns in both corpuscle types (Supplementary Table 3).

a, b RNA–DNA interactions in mESCs apparent as a distinct point per 25-kb bin and black (see key in c) by the most-represented RNA arena or RNA class, respectively, in that bin. c RNA–DNA interactions in mESCs, quantified according to genomic ambit amid RNA and DNA tags. d, e RNA–DNA alternation cast for mOPCs, agnate to that apparent in a, b. f RNA–DNA interactions in mOPCs, quantified according to genomic ambit amid RNA and DNA tags. All panels were generated application cogent absolute datasets.

To added strengthen the abounding aberration amid RADICL-seq and GRID-seq technologies, we proceeded by allegory their datasets of cogent interactions. We accepted that RADICL-seq retains a abounding college genomic advantage than GRID-seq alike back we accede alone cogent interactions (Supplementary Fig. 10a). In adjustment to investigate whether GRID-seq abstracts would be able to acquisition agnate after-effects to those acquired with RADICL-seq (Fig. 3), we alleged cogent interactions from GRID-seq abstracts by application the aforementioned statistical access we alive for RADICL-seq. Then, we advised the admeasurement of specific RNA biotypes for altered intervals of RNA–DNA alternation distances (Supplementary Fig. 10b). The allegory amid the two technologies shows that GRID-seq captures appreciably beneath all-embracing cis and auto RNA–chromatin interactions, accurately those advised by ncRNAs (Supplementary Fig. 10c).

Global patterns of interactions adumbrated bright differences amid the two corpuscle types for both cis and auto interactions. Specifically, we empiric ample domains of cis interactions broadcast forth anniversary chromosome with assorted transcripts interacting with ample regions of the chromosome from which they arise in a cell-type-specific address (Supplementary Fig. 11a, b). For example, Pvt1 contacted ample portions of its chromosome of agent in both corpuscle types, admitting Malat1 interacted broadly beyond the genome with cell-type-specific patterns, and Gm22973 contacted assorted chromosomes but alone in mESCs (Supplementary Fig. 11a, b).

We approved to investigate whether the DNA bounden could be affiliated to the transcriptional levels of the RNAs complex in the interactions. Accordingly, we generated cap assay of gene announcement (CAGE) abstracts from the nuclear atom of mESCs and mOPCs, and disconnected the genic transcripts into announcement quartiles (I: lowest; IV: highest). Back we advised the cardinal of interactions as a action of the ambit to the gene anatomy in the absolute datasets of both corpuscle types, we empiric a bluff adulteration bulk for transcripts that were bidding at lower levels, suggesting that the announcement plays a role in the enactment of RNA–DNA contacts adjacent to the archetype locus (Supplementary Fig. 12a, b). However, we noticed that a atom of cis interactions occurring at ample ambit from the gene anatomy were still present afterwards assay with ActD, which suggests that factors added than transcriptional action ability comedy a role in the accumulation of such contacts (Supplementary Fig. 12a). Indeed, in ActD-treated mESCs, we still empiric a accustomed intronic RNA arresting from protein-coding genes in cis interactions (Supplementary Fig. 13a–c); however, the inhibition of RNA pol II addendum resulted in a able burning of the arresting in long- (>1 Mb and ≤10 Mb, 1.4% vs. 9.1% in absolute dataset) and acute all-embracing (>10 Mb, 0.5% vs. 1.8% in absolute dataset) cis interactions (Supplementary Fig. 13c). Furthermore, the accession of ncRNAs was added in the subset of acute all-embracing cis interactions, and, interestingly, a cogent cardinal of auto interactions were preserved (Supplementary Fig. 13a, b) and appeared in the aforementioned regions of the genome as in the absolute dataset (Fig. 3a, b).

In the NPM datasets of both corpuscle types, the adorning of the arresting from the askew empiric in the absolute datasets (Fig. 3a, b) was absolutely absent (Supplementary Fig. 13d, e, g, h), suggesting a accordant accession of proteins in the enactment of RNA–chromatin interactions. Genome-wide bounden of specific noncoding transcripts was absent, although we empiric genomic regions awful apprenticed by RNAs with cis and auto contacts. Moreover, we empiric a affecting bead in auto interactions involving exonic RNAs from noncoding genes, which suggests that best of these interactions are protein advised (Supplementary Fig. 13f, i).

To added investigate the attributes of absolute bounden amid RNA and DNA molecules, we advised the administration of the distances amid interacting RNA and DNA tags in the mESC and mOPC NPM datasets (Supplementary Fig. 14a). We empiric a ascendant accession (>85%) of interactions area both RNA and DNA tags were commutual to anniversary added (distance of <1 kb) compared with alone 4.5% in the absolute datasets (Supplementary Fig. 14a, b). Next, we looked at the overlap of DNA tags captured by the NPM and absolute datasets with accessible DRIP-seq abstracts that maps the area of R-loops genome-wide in mESCs25 (Supplementary Fig. 14c). There was a about accessory of RADICL-seq DNA tags beyond DRIP-seq peaks in the NPM dataset compared with the absolute dataset, possibly advertence an over-representation of R-loops. As the actual atom of absolute RNA–DNA interactions in the NPM dataset could not be explained by complementarity of RNA and DNA strands, we advised whether these interactions could be advised by the accumulation of triple-helical nucleic acerbic structures26. To this end, we analyzed the interactions of lncRNAs that are accepted to anatomy amateur helices with DNA26,27, namely Malat1 and Meg3. We begin that these transcripts were amid the lncRNAs with the accomplished cardinal of auto contacts (Supplementary Table 4) and that they are acceptable to anatomy triplexes in abutting adjacency to these contacts (Supplementary Fig. 14d–i).

To bigger accept the accord amid the interactions captured by RADICL-seq and the 3D architectonics of the genome (i.e., DNA–DNA contacts and/or genomic distance), we leveraged Hi-C abstracts produced from agnate corpuscle types (mESCs and neural antecedent cells)28. At 25-kb resolution, the frequencies of cis RNA–DNA contacts in the absolute datasets moderately activated with normalized Hi-C DNA–DNA contacts (Pearson’s alternation coefficient = 0.56 for both corpuscle types, Supplementary Fig. 15). However, about 30% of the about-face (based on the aloft alternation coefficient) in the cis RNA–DNA acquaintance affluence could be explained by genomic architecture. The actual ~70% of about-face in RNA–DNA contacts is best acceptable a aggregate of babble and accurate arresting that is not linearly abased on spatial ambit amid genomic loci.

We advised the administration of DNA tags with account to topologically advertence domains (TADs) articular in the aloft Hi-C data28 and begin a bright arresting accessory at TAD boundaries in both corpuscle types absolute and NPM datasets (Fig. 4a, b). This award was replicated additionally in the mESC ActD dataset. (Supplementary Fig. 16a). Furthermore, we empiric accessory for RNA tags at TAD boundaries primarily in the NPM action in both corpuscle types (Fig. 4c, d and Supplementary Fig. 16b). Interestingly, we acquired a agnate accessory for DRIP-seq signal25 at the TAD boundaries, possibly suggesting a accord amid TAD accumulation and the bearing of R-loops (Supplementary Fig. 16c). These after-effects accentuate the accent of including the NPM action to abduction biological appearance that ability be contrarily disregarded by alone application absolute datasets. Finally, we surveyed RNA–DNA interactions amid in A and B compartments (i.e., preferentially accessible and bankrupt chromatin, respectively) for both the mESC and mOPC absolute datasets (Supplementary Fig. 16d). Although we did not beam cogent accessory of RNA classes (protein coding or lncRNA) for any compartment, the after-effects showed a bright allegory of A and B compartments with transcripts basic from one alcove mainly complex in interactions aural the aforementioned compartment.

a–d Metadata profiles assuming the boilerplate advantage of a, b DNA tags or c, d RNA tags at the boundaries of TADs in mESCs (a, c) and mOPCs (b, d) for the adumbrated conditions. e, f Boilerplate RNA-binding arresting at TAD boundaries in absolute mESCs and mOPCs, respectively. The arresting was breach based on whether the RNA originated aural or alfresco of the TAD. Advantage ambit from the TAD is about to the agnate TAD width. g, h Allotment of RNA–DNA interactions in absolute RADICL-seq libraries from mESCs and mOPCs, respectively, disconnected into incremental RNA–DNA distances and with RNA tags aggregate by the character of intersected echo elements. NR, RNA tags not mapped on any repeat. Statistical acceptation was affected with the two-tailed Student’s t test. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001. All panels were generated application cogent datasets. Source abstracts are accessible in the Source Abstracts File.

Next, we asked whether RNAs basic from loci positioned aural or alfresco TADs showed specific DNA-binding patterns, possibly dictated by genomic structural constraints. Back we looked at the administration of the arresting for RNAs transcribed aural TADs in the mESC and mOPC absolute datasets, we begin it to badly bead alfresco the area regions, admitting the arresting from transcripts transcribed alfresco TADs showed the adverse trend (Fig. 4e, f), appropriately suggesting a barrier aftereffect for the RNA clearing into or out of TADs that prevents chargeless diffusion. Collectively, our after-effects highlight a accepted role for TADs in abstraction RNA–chromatin interactions in mESCs, mOPCs, and possibly added corpuscle types.

Repeat elements (REs) accept emerged in contempo years as key contributors to genomic adjustment and organization29. In the mESC and mOPC absolute datasets we empiric that ~12% and ~8%, respectively, of the abnormally mapped genic RNA tags intersected with REs as authentic by RepeatMasker30 (Supplementary Fig. 17). In mESCs, the best abounding classes of intragenic REs were baby nuclear RNA (snRNA) (~39%) and SINE (short interspersed elements) (~35%), followed by LINE (long interspersed elements) and LTR (long terminal repeat) (both ~9%) (Supplementary Fig. 18). In mOPCs the best abounding classes were SINE (~48%) followed by LINE (~20%) and LTR (~15%); intriguingly, the affluence of snRNAs complex in RNA–DNA interactions was badly lower in mOPCs (<1%) than in mESCs (Supplementary Fig. 18). We annotated non-self RNA–chromatin interactions for the best abounding classes of intragenic REs beyond accretion distances from the armpit of transcription. Back we compared them to interactions not involving REs, we begin a appreciably categorical RE-specific arrangement of cis interactions that was reproducible in both corpuscle types (Fig. 4g, h). In acceding of differences amid altered RE families, RNA–DNA pairs area the RNA mapped to SINE were begin to be accomplished at ambit intervals of ≥10 kb and <1 Mb, admitting RNAs that mapped to LINE and LTR were proportionally depleted at beeline distances of <100 kb, but decidedly accomplished at best ambit intervals (Fig. 4g, h) alike in the absence of beginning archetype (Supplementary Fig. 19). Although pairs area the RNA mapped to SINE, LINE, or LTR displayed no auto interactions, those mapping to snRNAs apparent all-encompassing auto interactions (>95%, Fig. 4g, h and Supplementary Fig. 19). Collectively, these analyses appearance that transcripts absolute REs are affianced in cis interactions with the chromatin, which is in acceding with antecedent studies that appear their affiliation with euchromatin29.

To bigger accept the captivation of RNA in genome alignment and the fine-tuning of cell-specific gene expression, we compared genome-wide RNA–DNA bounden profiles and abduction ante amid mESCs and mOPCs. For anniversary transcript, we affected the Jaccard ambit amid the RNA–DNA bounden profiles as a action of the aberration in RADICL-seq abduction rate, actuality advised a proxy for gene announcement (Fig. 5a). As expected, there was a bright accord amid cogwheel archetype affluence and differences in RNA–DNA bounden profiles. However, alike at commensurable announcement levels, we empiric a assortment of alternation patterns amid assorted transcripts amid the two corpuscle types (e.g., Hunk and Ralgapa2, Supplementary Fig. 20a–d). Back transcripts were disconnected into cogwheel announcement deciles, for genes with <40% aberration in gene announcement amid the two corpuscle types, we begin no articulation amid cogwheel gene announcement and changes in genome-wide bounden contour (Supplementary Fig. 20e). These after-effects advance that, although announcement plays a role in free the bounden arrangement of a transcript, the DNA bounden contour for genes bidding at agnate levels may be absolute by added factors, such as 3D chromatin architectonics or epigenomic state.

a For anniversary gene, the Jaccard ambit amid the genome-wide RNA–DNA bounden profiles in mESCs and mOPCs is compared with the aberration in abduction bulk (proxy for gene expression) amid the two corpuscle types. b Administration of the log2 ratios of RADICL-seq mESC to mOPC DNA normalized tag counts for targeted gene apostle regions, which are authentic as ±2 kb about the TSS. Cell-type-specific brand gene positions are accent for both mESCs (red) and mOPCs (blue). Counts were normalized by library size. c RADICL-seq counts of altered genomic targets per interacting RNA in mESCs vs. mOPCs. d, e Circos plots depicting Neat1 genomic interactions in mESCs and mOPCs, respectively. f, g Circos plots depicting Fgfr2 genomic interactions in mESCs and mOPCs, respectively. Anniversary band represents the alternation amid the genic archetype and the contacted genomic bin, while its blush indicates log2 of the RADICL-seq count. The chromosome of agent of the RNA beneath analysis is apparent continued (gray shading) on the larboard allocation of anniversary circos plot. All panels were generated application cogent absolute datasets.

Next, we adjourned whether RADICL-seq can be acclimated to discriminate biologically accordant differences amid corpuscle types. To this end, we calm from the abstract a annual of brand genes that are accurately bidding in mESCs or mOPCs (Supplementary Table 5) and acclimated RADICL-seq to assay patterns of RNA–chromatin adjustment at the genomic regions absolute these markers. To assay cell-specific RNA–chromatin interactions at the gene level, we acclimated the absolute datasets to account the mESC/mOPC arrangement of the normalized RADICL-seq counts of apprenticed RNAs for the apostle regions (defined as ±2 kb about the archetype alpha armpit [TSS]) of all genes. We advised the positions of the cell-specific markers in the administration of these mESC/mOPC ratios and begin that they absolute appear the cape of the administration according to the corpuscle band in which they were accepted to be added awful bidding (Fig. 5b). Our after-effects advance that the technology is able to discriminate cell-type-specific features.

To investigate in greater detail whether RNA–chromatin interactions could comedy a role in gene expression, we alive CAGE abstracts to comment de novo promoters in mESCs and mOPCs. For both absolute datasets, we compared the administration of altered RNAs interacting with apostle regions of genes that are transcriptionally alive with those that are inactive. We did not beam any bright aberration amid the two groups in either corpuscle blazon (Supplementary Fig. 21a, b), advertence that gene announcement does not assume to be abased on the cardinal of altered interacting RNAs. However, the top 100 promoters of the genes that interacted with the accomplished cardinal of altered RNAs amassed in altered chromosomes in the two corpuscle types: predominantly in chromosomes 8 and 11 in mESCs and in chromosome 5 in mOPCs (Supplementary Fig. 21c, d).

When comparing the cardinal of altered genomic targets for anniversary archetype detected in the absolute datasets for mESCs vs. mOPCs, we empiric a beeline alternation with the attendance of some outliers (Fig. 5c). Amid the RNAs that showed ample deviations from the askew (i.e., transcripts that had antithetical patterns of interactions amid the corpuscle types), we called Neat1 and Fgfr2 as adumbrative examples of transcripts accepting college RADICL-seq counts in mOPCs and mESCs, respectively. The nuclear lncRNA Neat1 is one of the capital apparatus of paraspeckles, membrane-less compartments present in the basis of differentiated cells31. In mESCs, Neat1 exists as a beneath isoform, which is clumsy to advance the accumulation of paraspeckles, admitting its best isoform is bidding in differentiated cells32,33. Constant with these observations, RADICL-seq RNA reads mapped alone to the beneath isoform in mESCs, admitting the arresting covered the accomplished amount of the best isoform in mOPCs (Supplementary Fig. 22a). Furthermore, the genomic bounden arrangement of Neat1 apparent affecting differences amid the two corpuscle types, with the lncRNA interacting mostly in cis in mESCs as against to the all-encompassing auto interactions advised in mOPCs (Fig. 5d, e). Assay of the DNA-binding regions of Neat1 accepted the alternative for bounden to the 5ʹ ends of the ambition genes empiric previously34 (Supplementary Fig. 22b, c). Fgfr2 is a protein-coding gene with an important role in pluripotency; mutations affecting its announcement aftereffect in aboriginal beginning accident due to abutting corpuscle accumulation defects35. Unlike the localized arrangement apparent in mOPCs, Fgfr2 displayed all-encompassing cis interactions in mESCs, accoutrement aloft 30% of the chromosome from which it is transcribed (Fig. 5f, g and Supplementary Fig. 11a). The RADICL-seq after-effects appropriately advance a potentially structural role for Fgfr2 in mESCs.

Finally, we angry our absorption to auto RNA–DNA interactions. To assay the admeasurement of overlap amid the two corpuscle types, we affected the circle of RNA–chromatin interactions categorized by beeline ambit in the absolute datasets (Supplementary Fig. 23). To our surprise, we begin 3414 altered (12.2%) auto RNA–DNA pairs aggregate by both corpuscle types; this allotment of overlap was agnate to that for cis RNA–chromatin interactions afar by a beeline ambit of ≥1 Mb and <10 Mb (Supplementary Fig. 23). Furthermore, these auto interactions captured in both corpuscle types were advised by 14 transcripts with a above accession from Malat1 (Supplementary Table 6). These after-effects highlight the accession of Malat1 in the alignment of accepted attempt of RNA–chromatin interactions.

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