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To assemble this sequence of 76 images, the experiment has been performed 76 times, and the shifting distance has been increased for each consecutive experiment. A similar procedure is also applied in all the following movies. The duration of this movie corresponds to ms in real time. Transport of atoms as above, but using the height-optimized conveyor belt described in section 3. Note that the atom-surface distance now remains constant throughout the transport.
This requires more care and robust algorithms to detect larger domains that span intermittent gaps of low mappability. Notice that this is a common problem for all signal analyses in heterochromatin. For sharp marks only a very few regions are affected by restriction site depletion, as illustrated for CTCF Supplementary Fig.
Barcoding of chromatin before any further treatment facilitates pooling of scarce samples prior to ChIP, as previously shown 2 , 3.
Such pooling results in sufficient material for immunoprecipitation and quality controlling, which is typically only possible given samples with abundant material. We found that RELACS can produce robust and reproducible profiles down to cells for histone marks and cells for transcription factors, beyond which the signal-to-noise ratio deteriorates Fig.
Simple peak calling with default parameters generates consistent regions between the traditional protocol with , cells and the RELACS protocol with only cells Supplementary Fig. For each cell number, 7 technical replicates were barcoded and pooled for ChIP-seq and computationally demultiplexed before analysis.
This figure shows two selected replicates from two individual barcodes for each cell number. After sequencing, the pooled samples were demultiplexed according to the nuclear barcodes to assign all reads to their tissues of origin.
For the histone marks, we observed high-quality enrichment profiles Fig. Our results are highly reproducible, as seen by clear replicate clustering in PCA plots for all analyzed histone marks Fig. Importantly, the observed differences between pairs of tissues correspond to biological expectations. This is particularly pronounced for changes in the elongation mark, H3K36me3, over gene bodies and there is a clear enrichment for genes in the respective tissue Fig.
As shown in Supplementary Fig. Analysis of multiple tissues and biological replicates in a single ChIP. Eight mouse organs brain, heart, lungs, liver, duodenum, pancreas, spleen, skeletal muscle were extracted from two wild-type mice. Organs were independently homogenized, fixed, and nuclei were extracted. After chromatin digestion inside intact nuclei, different hairpin nuclear barcodes were used to mark nuclei extracted from each organ. After barcoding nuclei were pooled and lysed to release chromatin.
Chromatin was split to investigate three histone modifications H3K27ac, H3K36me3, H3K27me3 plus input for normalization control. Spleen icon is licensed under the Creative Commons Attribution 4. Gwilz, Source: To generate each track 25, cells have been used. Cases where only one replicate is visible indicate perfect overlap within the limits of resolution. Differential analysis of histone marks in mouse tissues. Red tracks denote H3K27ac signal and green tracks are for the elongation mark H3K36me3.
Higher scores lower p -values are mapped to A control sample input is prepared for each ChIP experiment, which not only accounts for the usual biases in the protocol, but also faithfully conveys the differences in initial sample amount and barcoding efficiency. ChIP signals of each multiplexed sample can, therefore, be normalized against their respective input controls and signals between samples can be quantitatively compared. This same procedure is then applied to multiplexed tissues, to allow proper normalization and quantitative comparisons between them Supplementary Fig.
Notice that this is an alternative to the spike-in of chromatin from other species chromatin to starting chromatin as proposed by In some cases e. We have introduced an ultra-parallel and highly standardized approach to the generation and analysis of ChIP-seq data. It can be established easily in any molecular biology lab without specific specialized equipment.
Compared to MNase-based protocols e. Unlike Mint-ChIP, it can also be applied to fixed samples, allowing profiling of transcription factors and co-factors easily lost by native ChIP approaches. The ability to label and pool large number of samples opens up the possibility to conduct controlled ChIP-seq experiments with very small cell numbers. We have obtained reliable and reproducible histone profiles for as few as cells and transcription factor profiles from cells. We do not exclude the possibility that ChIP using even lower cell numbers can be performed, by merging a higher number of barcoded small cell populations, or by adding un-barcoded carrier chromatin prior to immunoprecipitation to reduce the noise associated with low input samples 10 , This eliminates the need for an additional ChIP step just to purify chromatin prior to barcode ligation.
As a result, RELACS provides a simple and highly standardized workflow for all cell types and a wide range of sample and cell numbers. We have carefully investigated the potential limitations and biases due to the restriction site based RELACS methodology.
Overall, the genome coverage at a given sequencing depth is comparable to a traditional approach, with slightly reduced coverage of the heterochromatic region and repetitive regions due to reduced cutability and accessibility and concomitantly increased coverage of many types of open regions.
As with all other ChIP-seq protocols, we also observe a bias towards open chromatin 33 , where most of the studied marks are located active histone marks, CTCF, p These biases are accounted for by using input controls, which is already done in standard algorithms for peak calling. Importantly, for sharp marks, we achieved the same resolution as with sonication-based methods.
In this work, we have aggressively filtered and removed all duplicate alignments, or utilized UMI to distinguish technical PCR duplicates from biological duplicates derived by restriction digestion.
Given the broad applicability of RELACS universality across tissues, cell numbers, histone or transcription factor ChIP-seq , we propose that it can be used as a reference protocol for the ultra-parallel handling of limited clinical samples and large-scale comparative studies. Although we have applied RELACS to multiple mouse tissues, the protocol is also compatible with more stringent purification techniques e.
Moreover, the protocol could also be integrated into other assays, such as DNA methylation analysis or chromatin conformation studies. The intra-nuclei chromatin barcoding strategy paves the way for combinatorial barcoding strategies, similarly to recent developments 20 , 21 , 22 , used for single cell ChIP-seq analyses.
Mice were euthanized using carbon dioxide CO 2 before organ extraction. Dissected organs have been placed in room temperature D-MEM prior to fixation. For tissues, a small portion of each organ was finely chopped. Cell pellets were washed twice in PBS supplemented with a protease inhibitor cocktail Roche, and aliquoted. For all cell types, parameters for nuclei extraction were the following: The following treatment times was used: After nuclei extraction, a small aliquot of nuclei was set aside to estimate DNA concentration and cell number from tissue samples: Note that the restriction endonucleases used in RELACS lack exonuclease activity and are easier to titrate upon variation of the input material.
Barcoding efficiency is consistent between and , nuclei using an unmodified protocol. Ligase was inhibited by adding 4. This barcoded chromatin was subsequently used for ChIP. Samples were purified using Qiagen PCR purification kit columns.
Cell number for tissue samples was estimated from the total DNA amount, taking into account that each mouse diploid cell contains approximately 6. Transcription factors antibodies: For transcription factor ChIP, an additional 2.
Amplified libraries were purified twice using 0.
Library pools were denatured and prepared for instrument loading following Illumina guidelines. Using an in-house written script the sequences were demultiplexed. Sequences without barcode or having more than one mismatch between barcodes on each paired-end mate were discarded from further analysis. HepG2 reads were mapped to the hs37d5 reference human genome and mouse reads were mapped to mm10 reference genome. Next, duplicate reads and insert size distributions were determined using picard Additional quality metrics were generated using estimateReadsFiltering from deepTools 35 v3.
Coverage and normalization to the input was obtained using deepTools The human blacklist http: In all downstream analyses, duplicates and blacklisted regions were removed, and all results were computed using fragments parameter --extendReads.
All heatmaps and profiles were generated using deepTools. Sharp marks CTCF, p, H3K4me3, H3K27ac were aligned around the center of the peak computeMatrix reference-point , while other marks were considered broad and scaled to the region computeMatrix scale-regions.
In each case, flanking regions were added to show the signal away from enriched regions.
Principal component analysis was performed on the log2 ratio of the ChIP to the input bigWig. Restriction sites were identified using the Bio. In total, 44,, sites and 39,, sites were identified, respectively. The number of restriction sites per kbp was then computed using the sum of all observed overlaps divided by the sum of the respective peak length in kbp.
The parameter --extsize was given as the median fragment length computed using Picard. Peaks in blacklisted regions were removed and overlapping regions were merged. Peak annotations for 18 different mouse cell types were obtained from the group of Bing Ren We used the liftOver tool to convert this data from mm9 to mm10 and merged peaks of the same type e.
Finally, we only used merged peaks that were present in at least 2 cell types. This motif was converted into a position-specific score matrix and a position-specific energy matrix, as described in The same software was used to predict also binary motif instances using a pre-calculated balanced score threshold of 6.
The latter was used to calculate the fraction of CTCF peaks harboring a motif, while the logarithm of the predicted affinity is used for visualization of binding strength in heatmaps Fig. For the analysis of differential histone maps in mouse tissues we used a list of all protein-coding genes from Ensembl GRCm38 release 91 and counted the reads of histone marks over those gene bodies, using bedtools multicov The corresponding count matrix was used as input for DESeq2 version 1.
At the same time, we have used Input-control data to generate another count matrix from which we estimate the appropriate size factors to be used for further DESeq analysis of histone marks. Those sets were subjected to a systematic analysis of tissue enrichment, using TissueEnrich Chromatin states were obtained from the UCSC table browser Chromatin state 15 was not used, as it mostly contained human blacklisted regions.
The basic mapping and QC were done using v0. The workflows are freely available at https: For customized downstream analysis we used deepTools 35 v 2. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Dahl, J. How low can you go? Pushing the limits of low-input ChIP-seq. Lara-Astiaso, D. Chromatin state dynamics during blood formation.
Science , A Multiplexed system for quantitative comparisons of chromatin landscapes. Cell 61 , — Schmidl, C. Methods 12 , — Arrigoni, L. Standardizing chromatin research: Nucleic Acids Res. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Adli, M. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Shankaranarayanan, P. Single-tube linear DNA amplification for genome-wide studies using a few thousand cells.
Cao, Z. A microfluidic device for epigenomic profiling using cells. Rotem, A. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Gasper, W. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Aldridge, S. Genome Biol. Chabbert, C. A high-throughput ChIP-Seq for large-scale chromatin studies.
Weiner, A. Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution. Sadeh, R. Elucidating combinatorial chromatin states at single-nucleosome resolution. Cell 63 , — Garber, M. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.
Cell 47 , — Gutin, J. Fine-resolution mapping of tf binding and chromatin interactions.
Cell Rep. Mieczkowski, J. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Clark, D. Nucleosome positioning, nucleosome spacing and the nucleosome code.
Rosenberg, A. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science , — Ramani, V. Massively multiplex single-cell Hi-C. Methods 14 , — Cusanovich, D. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Rao, S. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Cell , — Kennedy-Darling, J. Measuring the formaldehyde protein—DNA cross-link reversal rate. Feng, J. Heinig, M. Differential analysis of histone modifications with broad genomic footprints. Abstract Background ChIP-Seq, which combines chromatin immunoprecipitation ChIP with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites.
Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.
Chromatin immunoprecipitation coupled with genome tiling microarrays ChIP-chip [ 1 , 2 ] and sequencing ChIP-Seq [ 3 - 6 ] have become important tools to systematically identify protein-DNA interactions. Particularly ChIP-Seq, which combines ChIP with massively parallel sequencing, offers a new genome-wide approach to extensively determine chromosome binding sites of DNA-associated proteins.
However the massive amounts of data generated from the high-throughput sequencing pose great challenges for the identification of protein binding sites. Several statistical approaches have been developed for analyzing ChIP-Seq data generated by single-end sequencing to find genomic regions that are enriched in a pool of specifically precipitated DNA fragments.
An estimation of the fragment size is used, typically by extending the read lengths of their 3'ends to identify binding motifs in these algorithms [ 16 ]. However, uncertain prediction of the precise DNA-protein binding sites still occurs, thus ChIP-Seq analysis is recognized as a relatively immature technology which requires development [ 16 ].
The Paired-end Illumina sequencing platform is a recently emerging technology, which has been developed based on the single-end sequencing system. The paired-end sequencing system generates double-end sequencing reads using the Paired-End Module, which directs regeneration and amplification operations to prepare the templates for a second round of sequencing [ 17 ]. The double-end reads can be used for more precise identification of each corresponding DNA fragment; therefore the paired-end sequencing data has the potential to increase the accuracy of identification of chromosome binding sites of DNA-associated proteins because the fragment length as well as the effective genome length can be computed accurately.
Here we describe a novel algorithm, SIPeS Site Identification from Paired-end Sequencing , which can be used to effectively mine the paired-end sequencing reads for genome-wide identification of binding sites by calculating fragment pileup values number of overlapping DNA fragments at each nucleotide position.
Then a dynamic baseline, a background model and other user-set thresholds are used to find the binding sites. AMS belongs to a basic helix-loop-helix bHLH transcription factor, which is required for tapetal cell development and the post-meiotic microspore formation in Arabidopsis thaliana [ 18 ].