Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
© The Author(s) 2017
Received: 23 July 2017
Accepted: 13 September 2017
Published: 20 September 2017
Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed.
Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, k-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish.
This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning.
Eukaryotic genomes are organized into chromatin, a DNA–protein complex, together with epigenetic information such as nucleosome position, histone modification, and DNA methylation. A nucleosome is a basic packaging unit of chromatin consisting of 147 base pairs (bp) DNA wrapped around a histone octamer . Positioning of nucleosomes affects accessibility of regulatory proteins to DNA and thereby influences gene transcription . Histone modification and DNA methylation also play critical roles in transcriptional regulation, and regulatory DNA regions such as promoters and enhancers are characterized by specific histone modifications, DNA hypomethylation, and accessible nucleosome organization [3–7].
Using next generation sequencing techniques, many studies have attempted to identify the basic principle for nucleosome positioning and have found that nucleosomes have DNA sequence preference. For example, nucleosome formation tends to occur at 10-bp periodic repeat of AT/TA dinucleotides and also GC-rich sequences, whereas poly(dA:dT) sequences tend to evict nucleosomes and thus reside in the linker region [8, 9]. Indeed, a periodic DNA sequence pattern associated with nucleosome has been found in genomes . Furthermore, genome-wide nucleosome mapping in yeast and C. elegans revealed that the position of nucleosomes on the genome is accurately predictable from DNA sequences , suggesting a certain dependency of nucleosome positioning on local DNA sequences in these organisms. However, in more complex organisms such as vertebrates the prediction from DNA sequence has not been successful [12, 13]. These facts suggest that the sequence dependency of nucleosome positioning varies among species.
The promoter region is unique in the genome, because nucleosomes at gene promoters are known to be stably positioned and strongly phased, which is one of the widely conserved features of nucleosome organization in eukaryotes including vertebrates [13–18]. In spite of these characteristics, the prediction of nucleosome positions in promoter regions from DNA sequence has not been successful even in yeast [11–13], suggesting that nucleosome positioning in promoter regions relies on other rules. Indeed, a transacting factor-mediated mechanism has been proposed in the promoter region [8, 18, 19]. One exception reported so far is tetrahymena, in which nucleosome positioning downstream of TSSs coincides significantly with GC content . However, the logic underlying nucleosome positioning at promoters remains elusive for other organisms.
In vertebrates, the majority of the genome is maintained methylated, and hypomethylated domains (HMDs) are predominantly found in the region around gene promoters . HMDs are mostly enriched with specific histone modifications such as H3K4me and required for gene transcription [21–23]. Recent studies have utilized a supervised machine learning algorithm, the k-mer support vector machine (SVM), and showed that HMDs can be accurately predicted from DNA sequence alone in Xenopus embryos and that these HMD regions are highly enriched with specific k-mers . Importantly, the link between epigenetic modifications and nucleosome positioning has been also reported [13, 18, 25, 26], and epigenetic modification could be one of the key factors which affect nucleosome positioning. Given that majority of gene promoters are overlapped with HMDs, vertebrate promoter regions are distinct from the rest of the genomic regions in terms of both epigenetic modification and DNA sequence composition. Thus, distinct mechanism for nucleosome positioning might exist in promoter regions.
Here, we investigated the nucleosome organization and the contribution of DNA sequences to nucleosome positioning in HMDs using the medaka (Japanese killifish). We found that the nucleosome linkers in HMDs are specifically accessible, and their positions can be precisely mapped using DNase I-seq in medaka embryos. The nucleosome linkers in HMDs are longer than typical ones in the methylated medaka genome, and the average nucleosome spacing changes sharply at the boundary of HMDs (200 bp in HMDs and 180 bp in methylated regions). Unlike the previous notion, the nucleosome positioning within HMDs was found to be highly predictable from DNA sequence using k-mer SVM, suggesting that nucleosome positioning in HMDs depends significantly on its proximal linker sequence. Surprisingly, this sequence feature was opposite from the previously reported global sequence preference of nucleosome in yeast. Finally, the specific sequence occurrence in hypomethylated linkers was also observed in zebrafish, a distantly related teleost species. Taken together, we propose a novel epigenetic modification-dependent and sequence-based rule for nucleosome positioning at teleost promoters.
HMD have specific nucleosome organization
To examine if the periodic DNase I-seq pattern reflects the array of nucleosome linkers in HMDs and if the nucleosome linker length is specifically longer in HMDs than in methylated regions, we compared the periodic DNase I cleavage pattern with our previous MNase-seq data in medaka blastula embryos . To clarify the difference in nucleosome organization between HMDs and methylated regions, the DNase I-seq peak summits that reside at the most end of the HMD were designated as the base position. As nucleosomes are known to show strong phasing especially downstream of TSSs [2, 30], we wanted to distinguish the change in nucleosome phasing at HMD boundaries from TSS-dependent phasing. To this end, we oriented each HMD boundary by the direction of transcriptions from its nearest TSS (i.e., if the direction of the transcription was from the methylated side toward hypomethylated side, the boundary was classified as 5′ boundary, and 3′ boundary in the opposite case). First, we confirmed that the periodic pattern of DNase I-seq is inversely correlated with the nucleosome position estimated from the MNase-seq data (Fig. 1c; top and middle). In some cases, MNase-seq data could be affected by nonhistone DNA binding proteins . However, we confirmed that the periodic patterns of DNase I-seq and MNase-seq are consistent with our previously published histone ChIP-seq pattern  (Additional file 1). These results indicate that the periodic DNase I-seq signals indeed reflected the nucleosome linkers in HMDs. Next, we observed that TSSs were most frequently found at the accessible linker located at the 5′ edge of HMDs, i.e., on the base position (Fig. 1c; bottom left). On the other hand, at 3′ boundary of HMDs, several peaks of TSS counts appear at linkers upstream of the base position (Fig. 1c; right bottom), probably reflecting TSSs at the 5′ boundary in short HMDs. Surprisingly, we found that the average spacing of nucleosomes changed clearly at the HMD boundary irrespective of the direction of transcription; in the methylated region, nucleosomes showed approximately 180-bp spacing, but in HMDs, the spacing was approximately 200 bp (Fig. 1c; Additional file 2). The spacing at 5′ HMD boundary was especially long (~250 bp), which is reminiscent of the fact that nucleosome-depleted region (NDR) exists at TSSs [2, 18]. Taken together, HMDs have distinct nucleosome organization, and our DNase I-seq data preferentially detect nucleosome linkers in HMDs that are longer (~200 bp) than typical linkers (~180 bp) in medaka embryos.
Prediction of nucleosome positioning by k-mer SVM
Specific 6-mers periodically distribute with 200-bp intervals in the linker regions of HMDs
The SVM outputs a weight for each k-mer which corresponds to the degree it contributes to the prediction  (Additional file 5). In this case, 6-mers with large positive weights were most frequently found in linker sequences, whereas those with large negative weights tended to be excluded from linkers but present in nucleosome core sequences. We noticed that the top positive 6-mers have larger absolute weights than top negative ones (Additional file 5), suggesting that a few number of specific 6-mers in linkers have strong contribution to nucleosome positioning. To test whether the high SVM-weight 6-mers appear periodically in a single HMD, we examined the distances between every pairs of top 10 high-weight 6-mers of SVMDNaseI within HMDs. The histogram of all distances between the top 6-mer pairs showed clear enrichment at 200 bp (Fig. 2c), indicating that those top 6-mers tend to distribute with approximately 200-bp intervals within a HMD.
Previously, the global sequence preference of nucleosome has been proposed to predict in vivo genome-wide nucleosome positioning in yeast and C. elegans . However, this model has limited performance when applied to human and zebrafish genomes [12, 13]. To test whether this model can be applied to the nucleosome positioning in HMDs, we calculated the Kaplan occupancy (expected nucleosome occupancy) around HMD boundaries. As shown in Fig. 3, the Kaplan occupancy showed the clear periodic pattern similar to that of the SVM score. This result was surprising, because the Kaplan occupancy is known to predict the nucleosome core position, but the SVM score correlates with the linker region in HMDs. Thus, nucleosomes in medaka HMDs have the sequence preference opposite to the global tendency in yeast.
Linker-specific 6-mers distribute preferentially in HMDs
Taken together, accessible nucleosome organization in HMDs might uniquely depend on DNA sequence, which is directed by specific short sequences preferentially distributed with approximately 200-bp intervals in HMDs, longer than those in methylated regions (~180 bp) (Fig. 4d).
Similar sequence preference of nucleosome positioning in zebrafish HMDs
Thus far, prediction of the nucleosome position on the basis of DNA sequence has not been successful in vertebrate genomes, in particular, gene promoter regions. In vertebrates, most gene promoters reside in HMDs, and in the present study, we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. DNase I-seq was recently applied to genome-wide mapping of nucleosome positions in yeast and human , but in medaka embryos, DNase I was found to preferentially digest long linker DNA in HMDs. This feature allowed us to unveil the clear transition in nucleosome spacing length at the HMD boundary; from closed (180-bp interval in methylated) to open (200-bp in HMD) nucleosome organization. More importantly, with this precise map of linkers in HMDs, we identified the novel sequence-based rule that allows us to accurately predict the positions of nucleosomes in vertebrate HMDs harboring gene promoters. The 200-bp periodic occurrence of the predictable 6-mers accounts for longer spacing of nucleosomes in HMDs, and thereby promoters in HMDs could maintain accessibility to regulatory proteins (Fig. 4d). In general, the majority of hypomethylated promoters persist throughout cell differentiation and sustain gene expression of housekeeping genes and early developmental genes [7, 43, 44]. Thus, DNA sequence directed long nucleosome linkers could contribute to their transcriptional regulation by constitutively maintaining accessible nucleosome organizations at those promoters. On the other hand, cell-type specifically hypomethylated promoters may not depend on the predictable 6-mers identified in blastula embryos, as they are activated by cell-type-specific transcription factors and epigenetic modifications. Notably, this HMD-specific rule was at least conserved among teleosts, as the similar tendency was observed in zebrafish which is evolutionarily long diverged from medaka. However, this rule holds true only in HMDs, and the co-occurrence of the specific 6-mers and nucleosome linker is not observed in methylated regions. Since the HMD constitutes only 3% of the entire genome, despite its crucial role in gene regulation, the HMD-specific rule could have been overlooked in previous genome-wide analyses.
The strong phasing of nucleosome positions downstream of TSSs is widely conserved among eukaryote genomes, but the degree of sequence contribution to the nucleosome positioning varies among species [11, 13, 14]. Surprisingly, the novel HMD-specific rule in medaka clearly contradicts the global sequence preference previously reported (poly(dA:dT) for linkers and GC-rich for nucleosome cores) ; the predictable short sequences enriched in medaka HMD linkers are relatively GC-rich, and the Kaplan occupancy, which was originally used to predict the global nucleosome occupancy in yeast, exhibits the opposite tendency in HMDs. At the moment, the reason for the reverse sequence preference of nucleosomes and the function of high SVMDNaseI-weight 6-mers remain speculative. Those 6-mers may be intrinsically unfavorable for nucleosome formation in HMDs, although we cannot rule out the possibility that unknown proteins bind to those 6-mers and influence nucleosome positioning. To examine whether the 6-mers alone can direct nucleosome positioning, it would be informative to perform in vitro reconstitution of chromatin from histone octamers and naked medaka genomic DNA. Importantly, however, it has been reported in zebrafish that the strongly phased nucleosome array at gene promoters does not exist in early embryos, but appears during the zygotic genome activation (ZGA) stage, correlating with the emergence of H3K4me3, a histone modification specific to HMDs [13, 21, 45, 46]. This indicates that nucleosome positioning in promoter regions is not solely determined by DNA sequence, but may require specific chromatin environment (e.g., modifications such as H3K4me3 or binding of chromatin factors which function at the ZGA stage). Therefore, it is likely that the specific epigenetic environment override the normal sequence preference of nucleosome in HMDs.
In summary, although the molecular mechanisms by which identified short sequences are translated into nucleosome positioning remain elusive, the present study focusing on the HMD provides novel insights into a hypomethylated DNA-specific regulation of nucleosome positioning in the vertebrate genome.
Materials and methods
We used medaka d-rR strain as wild type. Medaka fishes were maintained and raised under standard condition.
DNase I-seq was performed as previously described  with modifications. 5000 d-rR strain medaka blastula embryos were dechorionated and dissociated by forcing the embryos through a 21G needle using a syringe, and cells were harvested by centrifugation at 500g for 5 min. After washing with PBS, cells were resuspended in 500 μl of buffer A [15 mM Tris–HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 1 mM PMSF]. Cells were isolated using a cell-strainer (Falcon, 352235), centrifuged at 500g for 10 min, and resuspended in 1.5 ml of lysis buffer [buffer A with 0.1% IGEPAL CA-630]. After a 1-min incubation at 4 °C, nuclei were collected by centrifugation at 500g for 10 min. Nuclei were washed in buffer A, then resuspended in nuclear storage buffer [20 mM Tris–HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% (v/v) glycerol, 1 mM DTT, and 0.1 mM PMSF], and stored at −80 °C. For DNase I digestion, frozen nuclei were thawed on ice, washed in buffer A with 0.5 mM spermidine and 0.3 mM spermine, incubated for exactly 2 min at 37 °C in 3.5 ml of buffer D [1 volume of 10× DNase I digestion buffer with 9 volume of Buffer A] containing 480 U of DNase I. The reaction was stopped by adding stop buffer [50 mM Tris–HCl, pH 8.0, 100 mM NaCl, 0.1% SDS, 100 mM EDTA, 20 μg/ml RNase A, 0.5 mM spermidine, and 0.3 mM spermine] and proteinase K, and incubated at 55 °C overnight. Digested DNA was purified by phenol chloroform, sucrose fractionated, and fragments below 1 kb were collected, end-repaired, ligated with adapters compatible with the Illumina sequencing platform and sequenced as single-end tags on HiSeq 1500 platform (Illumina).
ATAC-seq was performed as previously described  with some modifications. Embryos were homogenized in PBS, and cells were harvested by centrifugation at 500g for 5 min. Approximately 5000 cells were used. After washing with PBS, cells were resuspended in 500 μl of cold lysis buffer [10 mM Tris–HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630], centrifuged for 10 min at 500g, and supernatant was removed. Tagmentation reaction was performed as described previously  with Nextera Sample Preparation Kit (Illumina). After DNA was purified using MinElute kit (Qiagen), two sequential PCR were performed to enrich small DNA fragments. First, 9-cycle PCR were performed using indexed primers from Nextera Index Kit (Illumina) and KAPA HiFi HS ReadyMix, and amplified DNA was size selected (less than 500 bp) using AMPure XP beads. Then, a second 7-cycle PCR were performed using the same primer as the first PCR, and purified by AMPure XP beads. Libraries were sequenced using the Illumina HiSeq 1500 platform.
DNase I-seq and ATAC-seq data processing
The sequenced tags were aligned to the medaka reference genome by BWA , and tags with mapping quality larger than 20 were used for further analyses. Before the peak detection, each read position was shifted toward 5′ side with 50 bp. Then, MACS2 (version 184.108.40.20620913)  was used to identify regions that are significantly enriched (FDR 0.1%, fold enrichment > 5) with sequence tags (DHSs) using following options: –keep-dup all –nomodel –shiftsize 50 –q 0.01 –nolambda –call-summits –B –SPMR. For visualization and further analyses, signals per million reads data produced by MACS2 were used.
Nucleosome organization and sequence profiles around HMD boundaries
We used HMDs identified in the previous study . To calculate the average chromatin profile around HMD boundaries, we needed to set the base position (position x = 0) in each HMD. For this, we first determined DNase I-seq peak summits that locate within HMDs and selected the summit nearest to the boundary (the first low-methylated CpG in the HMD) as the base position. Then, the boundaries were classified by the orientation relative to the direction of transcription from the nearest TSS. HMDs that have TSSs within 1 kb distance were used for this analysis. Kaplan nucleosome occupancy was calculated using the model previously reported . SNP rate was calculated using the genome sequences of two medaka species, Hd-rR and HNI. SNPs identified in previous study  were used.
To estimate the average spacing of nucleosomes, we calculated the autocorrelation of nucleosome dyad score using acf function of R. The autocorrelation in HMDs and methylated regions were calculated using the average nucleosome dyad score (Fig. 1c, middle) at position x = 0, …, 1000 and x = −1000, …, −100, respectively, where x = 0 is the position of boundary DNase I-seq summit.
SVM for nucleosome linker and HMD prediction
We used the previously described method  for k-mer SVM. For training of SVMDNaseI we first selected DNase I-seq peak summits within HMDs as the center of accessible nucleosome linkers. Then, we selected the center of two adjacent DNase I-seq peak summits as the nucleosome core position if the distance between the two summits was longer than 150 bp. From the linker (positive) and the core (negative) regions, 100-bp sequences were extracted. The sequences not on chromosome 8 were used for training, and those on chromosome 8 were used as test data to draw ROC and precision–recall curve. To test the performance of the prediction of DNase I pattern, we calculated the SVM score for each of the HMDs in chromosome 8 with sliding window of 100 bp with a step of 20 bp. Then, at each step, the average of overlapping windows was calculated. The correlation between the average SVM score and DNase I signal level was calculated for each HMDs.
For the positive data set of SVMDNA, all HMD sequences below 3 kb were used. For the negative data set, ten copies of original HMD genome-coordinate set were randomly distributed on methylated regions using bedtools. HMD sequences and methylated sequences not on chromosome 8 were used for training, and those on chromosome 8 were used as test data (for Fig. 4b, c).
TOMTOM  was used to search motifs similar to 6-mers. JASPAR Vertebrates and UniPROBE Mouse databases were used as target motifs.
RN performed the experiments, analyzed data, and drafted the manuscript. HT and SM supervised the research and carried out revisions of the manuscript for important intellectual content. AU calculated SNP rate between Hd-rR and HNI strains. MK conducted sequencing of DNase I-seq. All authors read and approved the final manuscript.
We thank Andrew Fire for critical reading of the manuscript.
The authors declare that they have no competing interests.
Availability of data and materials
All sequence data are deposited at the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) (Accession Number SRP058469).
Consent for publication
All authors have consented to publication.
Ethics approval and consent to participate
All experimental procedures and animal care were carried out according to the animal ethics committee of the University of Tokyo (Approval No. 14-05).
This research was supported by the Core Research for Evolutional Science and Technology (CREST) program of the Japan Science and Technology Agency (JST).
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