www.nature.com/scientificreports OPEN Highly interacting regions of the human genome are enriched with enhancers and bound by DNA Received: 24 July 2018 Accepted: 12 February 2019 repair proteins Published: xx xx xxxx Haitham Sobhy 1, Rajendra Kumar 2,3, Jacob Lewerentz1, Ludvig Lizana2,3 & Per Stenberg4,5 In specifc cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identifed by Chromosome Conformation Capture (such as Hi-C) analyses. In eforts to elucidate their characteristics and functions, we have identifed highly interacting regions (HIRs) using intra- chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identifed HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements. Te chromatin in eukaryotic cells is not randomly organized, as various domains have been shown to occupy distinct ‘territories’ within the nucleus1–4. To decipher the chromatin architecture and three-dimensional (3D) organization within the nucleus, chromosome conformation capture techniques (such as 3C, 4C, 5C and Hi-C) have been developed5–7. In these techniques, chromatin segments in close spatial proximity are crosslinked, the crosslinked chromatin is digested and ligated, then the DNA is purifed and sequenced. Te chromatin segments identifed as being in close physical proximity in this manner are considered as interacting loci. Finally, fre- quencies of interactions between pairs of loci are quantifed. Visualization of chromosome conformation data as heat maps has revealed that the genome is partitioned into 3D compartments, inter alia topological associated domains (TADs) and A/B compartments8–10. Loci located within such domains tend to interact highly with each other and TADs’ boundaries are reportedly enriched in insulators and highly expressed genes8,9,11–13. It has also been observed in other types of experiments that distant regions of the genome can interact14, and there are observations indicating that expressed genes tend to co-localize in the nucleus, forming so called tran- scription factories5,15–18. In Drosophila it has been shown that Polycomb repressed regions can also co-localize in foci5,13,19–21. In addition, DNA double strand breaks, were shown through fuorescence labelling to travel within the nucleus22 and breaks have also been shown to cluster together23. Teoretically, there are obvious advantages in moving genomic regions that require similar factors into close three-dimensional proximity. However, bringing distant regions of the genome into proximity strongly raises risks of detrimental rearrangements if any DNA damage that occurs in such regions is not quickly repaired. Accordingly, there are indications that chromosomal rearrangements tend to occur in regions that are brought into three-dimensional proximity24. 1Department of Molecular Biology, Umeå University, Umeå, Sweden. 2Integrated Science Lab, Umeå University, Umeå, Sweden. 3Department of Physics, Umeå University, Umeå, Sweden. 4Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden. 5Department of Ecology and Environmental Science (EMG), Umeå University, Umeå, Sweden. Correspondence and requests for materials should be addressed to H.S. (email: [email protected]) or L.L. (email: [email protected]) or P.S. (email: [email protected]) SCIENTIFIC REPORTS | (2019) 9:4577 | https://doi.org/10.1038/s41598-019-40770-9 1 www.nature.com/scientificreports/ www.nature.com/scientificreports Tus, the functional advantages of long-range interactions and associated 3-D conformations of DNA presum- ably outweigh the selective disadvantages of such risks. However, despite the eforts summarized above, knowl- edge of the nature and functions of many of the interactions is still rudimentary. Terefore, the aims of this study were to computationally defne regions of the genome that form high numbers of long-range intra-chromosomal contacts using Hi-C data and investigate their properties using ENCODE data. For this purpose, we developed a new method to transform two-dimensional Hi-C contact maps into one-dimensional profles. Tis method difers from TAD and A/B-fnding techniques involving the construction of correlation matrices then fnding clusters with Principal Component Analysis (PCA)25. Instead, our method involves direct use of Hi-C data (afer a simple element-wise manipulation), and extraction of the eigenvector for the smallest eigenvalue (here, unity), where the values are proportional to the interactivity (or number of contacts) for a particular genomic region. Using this method, we fnd that in line with previous observations some regions cluster by functions such as active transcription and Polycomb repression. In addition, we fnd that predicted enhancers and super-enhancers are potentially involved in long-range interactions and interestingly that most genomic regions with a high num- ber of contacts are bound by DNA damage repair factors. Material and Methods Stationary distribution. To calculate the interactivity (or numbers of contacts) of genomic regions we con- sider each chromatin segment as a node in a network. Te segment’s length is determined by the resolution of the Hi-C map, which thus also governs the numbers of nodes and links in the network. Te links represent physical interactions. Since these interactions are not uniform across the genome, we assign weights to the links that are proportional to the frequencies that pairs of chromatin segments are physically close to each other in a cell population. We restrict the analysis to intra-chromosomal contacts (i.e. contacts within the same chromosome), since data on inter-chromosomal contacts in Hi-C are too sparse to include. Te raw frequencies produced from a cell population could be directly taken as weights. However, contact frequency decays as a function of distance between chromatin loci, and contact frequencies are higher for neighbouring loci than for distant loci. Terefore, we derive weights from the raw Hi-C maps by subtracting each contact frequency with expected contact fre- quency, defned as the median contact frequency at each particular distance (Supplementary Information SI-1, 2 and Fig. S1). In the study reported here, Hi-C maps for GM12878 human lymphoblastoid cells at two resolutions (100 and 5 kb) were downloaded from the GEO database7. Next, we transformed the raw maps to ‘observed – expected’ maps using the gcMapExplorer package26 (https://github.com/rjdkmr/gcMapExplorer). From the ‘observed – expected’ map, we construct a transition probability matrix W, where every entry is the probability to jump from one node to any other node in the network. To calculate W, we divide every row in the ‘observed – expected’ map by its sum (shown as a network in Fig. S1 and Supplementary Information SI-2). Based on W, we then formulate a Markov model for how a particle randomly jumps between nodes in the network. Denoting Pn12(),(Pn), ...,(PnN ) as the probability that the particle is in node 1,2, …N at time n, we calculate Pn12(1++), Pn(1), ...,(PnN + 1) as a simple one-step process. pn(1+=)(pn),W where pn()= [(Pn12), Pn(),,... PnN()] From this, we are interested in the stationary probability distribution p()np=∞ = ∞, which we obtain from the equation p∞∞= pW. Tis means that p∞ is the normalised eigenvector of W associated with the eigenvalue one. In this study, to calculate p∞ we used the Scipy Python library to eigendecompose the transition probability matrix W, and extracted the eigenvector with the largest eigenvalue (one in this case). Te above method is imple- mented in the gcMapExplorer package26 (https://github.com/rjdkmr/gcMapExplorer), and the user can easily calculate the stationary distribution from a raw Hi-C map in a few steps. When the raw Hi-C map was directly used to calculate the Transition Probability Matrix (TPM), the dynamic range in the resulting stationary probability distribution (SPD) was limited due to the inclusion of both expected neighbouring and short-range contacts as well as long-range contacts (Fig. S2). Observed/expected’ normaliza- tion did not improve the dynamic range of the resulting SPD. When ‘observed-expected’ normalization was used to calculate the TPM, the SPD had a very similar profle but larger dynamic range (Fig. S2), thus it was applied in further analyses. Chromatin-related datasets and correlation. We downloaded ChIP-seq data for 177 chromatin-related datasets (available for GM12878 cells) from the ENCODE project website (https://www.encodeproject.org/), last updated in 2016. Te ENCODE dataset contains ChIP-seq data for 87 chromatin-bound proteins (listed in SI-3), as well as various histone modifcations, CG methylation, DNA accessibility (DNase-seq) and nucleosome den- sity (MNase-seq), hereafer ENCODE factors (177 in total). We used these data to calculate global correlations between