Journal articles: 'Chromatin sequencing'

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Soleimani, Vahab D., Gareth A. Palidwor, Parameswaran Ramachandran, Theodore J. Perkins, and Michael A. Rudnicki. "Chromatin tandem affinity purification sequencing." Nature Protocols 8, no. 8 (July 11, 2013): 1525–34. http://dx.doi.org/10.1038/nprot.2013.088.

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Jukam, David, Charles Limouse, Owen K. Smith, Viviana I. Risca, Jason C. Bell, and Aaron F. Straight. "Chromatin‐Associated RNA Sequencing (ChAR‐seq)." Current Protocols in Molecular Biology 126, no. 1 (February 20, 2019): e87. http://dx.doi.org/10.1002/cpmb.87.

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Stergachis, Andrew B., Brian M. Debo, Eric Haugen, L. Stirling Churchman, and John A. Stamatoyannopoulos. "Single-molecule regulatory architectures captured by chromatin fiber sequencing." Science 368, no. 6498 (June 25, 2020): 1449–54. http://dx.doi.org/10.1126/science.aaz1646.

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Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.

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Xie, Wenhui, Yilang Ke, Qinyi You, Jing Li, Lu Chen, Dang Li, Jun Fang, et al. "Single-Cell RNA Sequencing and Assay for Transposase-Accessible Chromatin Using Sequencing Reveals Cellular and Molecular Dynamics of Aortic Aging in Mice." Arteriosclerosis, Thrombosis, and Vascular Biology 42, no. 2 (February 2022): 156–71. http://dx.doi.org/10.1161/atvbaha.121.316883.

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Objective: The impact of vascular aging on cardiovascular diseases has been extensively studied; however, little is known regarding the cellular and molecular mechanisms underlying age-related vascular aging in aortic cellular subpopulations. Approach and Results: Transcriptomes and transposase-accessible chromatin profiles from the aortas of 4-, 26-, and 86-week-old C57/BL6J mice were analyzed using single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing. By integrating the heterogeneous transcriptome and chromatin accessibility data, we identified cell-specific TF (transcription factor) regulatory networks and open chromatin states. We also determined that aortic aging affects cell interactions, inflammation, cell type composition, dysregulation of transcriptional control, and chromatin accessibility. Endothelial cells 1 have higher gene set activity related to cellular senescence and aging than do endothelial cells 2. Moreover, construction of senescence trajectories shows that endothelial cell 1 and fibroblast senescence is associated with distinct TF open chromatin states and an mRNA expression model. Conclusions: Our data provide a system-wide model for transcriptional and epigenetic regulation during aortic aging at single-cell resolution.

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Wu, Weixin, Zhangming Yan, Tri C. Nguyen, Zhen Bouman Chen, Shu Chien, and Sheng Zhong. "Mapping RNA–chromatin interactions by sequencing with iMARGI." Nature Protocols 14, no. 11 (October 16, 2019): 3243–72. http://dx.doi.org/10.1038/s41596-019-0229-4.

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Gorkin, David U., Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, et al. "An atlas of dynamic chromatin landscapes in mouse fetal development." Nature 583, no. 7818 (July 29, 2020): 744–51. http://dx.doi.org/10.1038/s41586-020-2093-3.

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AbstractThe Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

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Jahan, Sanzida, Tasnim H. Beacon, Wayne Xu, and James R. Davie. "Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes." Biochemistry and Cell Biology 98, no. 2 (April 2020): 171–77. http://dx.doi.org/10.1139/bcb-2019-0107.

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The major biological role of red blood cells is to carry oxygen to the tissues in the body. However, another role of the erythroid cell is to participate in the immune response. Mature erythrocytes from chickens express Toll-like receptors and several cytokines in response to stimulation of the immune system. We previously reported the application of a biochemical fractionation protocol to isolate highly enriched transcribed DNA from polychromatic erythrocytes from chickens. In conjunction with next-generation DNA, RNA sequencing, chromatin immunoprecipitation-DNA sequencing, and formaldehyde-assisted isolation of regulatory elements (FAIRE) sequencing, we identified the active chromosomal compartments and determined their structural signatures in relation to expression levels. Here, we present the detailed chromatin characteristics of erythroid genes participating in the innate immune response. Our studies revealed an atypical chromatin structure for several genes coding for Toll-like receptors, interleukins, and interferon regulatory factors. The body of these genes had nucleosome-free regions intermingled with nucleosomes modified with H3K4me3 and H3K27ac, suggesting a dynamic unstable chromatin structure. We further show that human genes involved in cell identity have gene bodies with the same chromatin-instability features as the chicken polychromatic erythrocyte genes participating in the innate immune response.

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Guo, Ziwei, Xinhong Liu, and Mo Chen. "Defining pervasive transcription units using chromatin RNA-sequencing data." STAR Protocols 3, no. 2 (June 2022): 101442. http://dx.doi.org/10.1016/j.xpro.2022.101442.

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Vega, Vinsensius B., Edwin Cheung, Nallasivam Palanisamy, and Wing-Kin Sung. "Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries." PLoS ONE 4, no. 4 (April 15, 2009): e5241. http://dx.doi.org/10.1371/journal.pone.0005241.

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Bright, Ann Rose, and Gert Jan C. Veenstra. "Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos." Cold Spring Harbor Protocols 2019, no. 1 (July 24, 2018): pdb.prot098327. http://dx.doi.org/10.1101/pdb.prot098327.

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Romanowska, Julia, and Anagha Joshi. "From Genotype to Phenotype: Through Chromatin." Genes 10, no. 2 (January 23, 2019): 76. http://dx.doi.org/10.3390/genes10020076.

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Advances in sequencing technologies have enabled the exploration of the genetic basis for several clinical disorders by allowing identification of causal mutations in rare genetic diseases. Sequencing technology has also facilitated genome-wide association studies to gather single nucleotide polymorphisms in common diseases including cancer and diabetes. Sequencing has therefore become common in the clinic for both prognostics and diagnostics. The success in follow-up steps, i.e., mapping mutations to causal genes and therapeutic targets to further the development of novel therapies, has nevertheless been very limited. This is because most mutations associated with diseases lie in inter-genic regions including the so-called regulatory genome. Additionally, no genetic causes are apparent for many diseases including neurodegenerative disorders. A complementary approach is therefore gaining interest, namely to focus on epigenetic control of the disease to generate more complete functional genomic maps. To this end, several recent studies have generated large-scale epigenetic datasets in a disease context to form a link between genotype and phenotype. We focus DNA methylation and important histone marks, where recent advances have been made thanks to technology improvements, cost effectiveness, and large meta-scale epigenome consortia efforts. We summarize recent studies unravelling the mechanistic understanding of epigenetic processes in disease development and progression. Moreover, we show how methodology advancements enable causal relationships to be established, and we pinpoint the most important issues to be addressed by future research.

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Marr, Luke T., Prasoon Jaya, Laxmi N. Mishra, and Jeffrey J. Hayes. "Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin." Biochemical Society Transactions 50, no. 1 (February 15, 2022): 199–212. http://dx.doi.org/10.1042/bst20210959.

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Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.

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Li, Niannian, Kairang Jin, Yanmin Bai, Haifeng Fu, Lin Liu, and Bin Liu. "Tn5 Transposase Applied in Genomics Research." International Journal of Molecular Sciences 21, no. 21 (November 6, 2020): 8329. http://dx.doi.org/10.3390/ijms21218329.

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The development of high-throughput sequencing (next-generation sequencing technology (NGS)) and the continuous increase in experimental throughput require the upstream sample processing steps of NGS to be as simple as possible to improve the efficiency of the entire NGS process. The transposition system has fast “cut and paste” and “copy and paste” functions, and has been innovatively applied to the NGS field. For example, the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) uses high-throughput sequencing to detect chromatin regions accessible by Tn5 transposase. Linear Amplification via Transposon Insertion (LIANTI) uses Tn5 transposase for linear amplification, haploid typing, and structural variation detection. Not only is it efficient and simple, it effectively shortens the time for NGS sample library construction, realizes large-scale and rapid sequencing, improves sequencing resolution, and can be flexibly modified for more technological innovation.

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Fittipaldi, Raffaella, and Giuseppina Caretti. "Tackling Skeletal Muscle Cells Epigenome in the Next-Generation Sequencing Era." Comparative and Functional Genomics 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/979168.

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Recent advances in high-throughput technologies have transformed methodologies employed to study cell-specific epigenomes and the approaches to investigate complex cellular phenotypes. Application of next-generation sequencing technology in the skeletal muscle differentiation field is rapidly extending our knowledge on how chromatin modifications, transcription factors and chromatin regulators orchestrate gene expression pathways guiding myogenesis. Here, we review recent biological insights gained by the application of next-generation sequencing techniques to decode the epigenetic profile and gene regulatory networks underlying skeletal muscle differentiation.

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Murdoch, Brenda M., Kimberly M. Davenport, Shangqian Xie, Mazdak Salavati, Emily Clark, Alan Archibald, Stephen N. White, et al. "378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome." Journal of Animal Science 100, Supplement_3 (September 21, 2022): 185. http://dx.doi.org/10.1093/jas/skac247.340.

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Abstract Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation of Animal Genomes (FAANG) Project aims to characterize transcriptional regulatory elements across the sheep genome to facilitate a better understanding of the biological mechanisms influencing phenotypic traits in sheep. Assays including sequencing of messenger RNA (mRNA-seq), cap analysis of gene expression (CAGE), chromatin immunoprecipitation of histones (ChIP-seq), assay for transposase-accessible chromatin (ATAC-seq), whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) were performed on tissues collected from the Rambouillet ewe used to assemble the reference genome ARS-UI_Ramb_v2.0. Histone modifications were used to define nine chromatin states for tissues across the genome depicting promoters and enhancers (active, poised, and repressed) using ChromHMM. Chromatin states were overlayed with RNA-seq, ATAC-seq and DNA methylation. These data suggest that active promoter and enhancer states reside in open chromatin regions with a greater transcriptional activity and hypomethylated regions than other states. Further, poised and repressed enhancers did not primarily reside in open chromatin and had less transcriptional activity and more hypermethylated sites compared with active states. Collectively these data define transcriptional regulatory regions throughout the ovine genome which provides a valuable resource to better understand regulatory regions in the genome and how these influence economically important traits in sheep and other livestock species.

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Buisine, Nicolas, Xiaoan Ruan, Yijun Ruan, and Laurent M. Sachs. "Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues." Cold Spring Harbor Protocols 2018, no. 8 (June 12, 2018): pdb.prot097725. http://dx.doi.org/10.1101/pdb.prot097725.

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Soyer, Jessica L., Mareike Möller, Klaas Schotanus, Lanelle R. Connolly, Jonathan M. Galazka, Michael Freitag, and Eva H. Stukenbrock. "Chromatin analyses of Zymoseptoria tritici : Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq)." Fungal Genetics and Biology 79 (June 2015): 63–70. http://dx.doi.org/10.1016/j.fgb.2015.03.006.

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Eagen, Kyle P., Erez Lieberman Aiden, and Roger D. Kornberg. "Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map." Proceedings of the National Academy of Sciences 114, no. 33 (August 1, 2017): 8764–69. http://dx.doi.org/10.1073/pnas.1701291114.

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The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or “anchors” are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of polycomb repressive complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer–promoter communication, our results indicate that loops are also associated with gene repression.

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Baumgarten, Sebastian, and Jessica Bryant. "Chromatin structure can introduce systematic biases in genome-wide analyses of Plasmodium falciparum." Open Research Europe 2 (September 15, 2022): 75. http://dx.doi.org/10.12688/openreseurope.14836.2.

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Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing of key developmental regulators. The advent of genome-wide analyses such as chromatin-immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental in understanding chromatin composition; however, even in model organisms, ChIP-seq experiments are susceptible to intrinsic experimental biases arising from underlying chromatin structure. Methods: We performed a control ChIP-seq experiment, re-analyzed previously published ChIP-seq datasets and compared different analysis approaches to characterize biases of genome-wide analyses in P. falciparum. Results: We found that heterochromatic regions in input control samples used for ChIP-seq normalization are systematically underrepresented in regard to sequencing coverage across the P. falciparum genome. This underrepresentation, in combination with a non-specific or inefficient immunoprecipitation, can lead to the identification of false enrichment and peaks across these regions. We observed that such biases can also be seen at background levels in specific and efficient ChIP-seq experiments. We further report on how different read mapping approaches can also skew sequencing coverage within highly similar subtelomeric regions and virulence gene families. To ameliorate these issues, we discuss orthogonal methods that can be used to characterize bona fide chromatin-associated proteins. Conclusions: Our results highlight the impact of chromatin structure on genome-wide analyses in the parasite and the need for caution when characterizing chromatin-associated proteins and features.

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Baumgarten, Sebastian, and Jessica Bryant. "Chromatin structure can introduce systematic biases in genome-wide analyses of Plasmodium falciparum." Open Research Europe 2 (June 10, 2022): 75. http://dx.doi.org/10.12688/openreseurope.14836.1.

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Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing of key developmental regulators. The advent of genome-wide analyses such as chromatin-immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental in understanding chromatin composition; however, even in model organisms, ChIP-seq experiments are susceptible to intrinsic experimental biases arising from underlying chromatin structure. Methods: We performed a control ChIP-seq experiment, re-analyzed previously published ChIP-seq datasets and compared different analysis approaches to characterize biases of genome-wide analyses in P. falciparum. Results: We found that heterochromatic regions in input control samples used for ChIP-seq normalization are systematically underrepresented in regard to sequencing coverage across the P. falciparum genome. This underrepresentation, in combination with a non-specific or inefficient immunoprecipitation, can lead to the identification of false enrichment and peaks across these regions. We observed that such biases can also be seen at background levels in specific and efficient ChIP-seq experiments. We further report on how different read mapping approaches can also skew sequencing coverage within highly similar subtelomeric regions and virulence gene families. To ameliorate these issues, we discuss orthogonal methods that can be used to characterize bona fide chromatin-associated proteins. Conclusions: Our results highlight the impact of chromatin structure on genome-wide analyses in the parasite and the need for caution when characterizing chromatin-associated proteins and features.

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Li, Wangchun, U. Tim Wu, Yu Cheng, Yanhao Huang, Lipeng Mao, Menghan Sun, Congling Qiu, Lin Zhou, and Lijuan Gao. "Epigenetic Application of ATAC-Seq Based on Tn5 Transposase Purification Technology." Genetics Research 2022 (August 11, 2022): 1–9. http://dx.doi.org/10.1155/2022/8429207.

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Background. Assays of transposase accessible chromatin sequencing (ATAC-seq) is an efficient assay to investigate chromatin accessibility, which depends on the activity of a robust Tn5 transposase to fragment the genome while cutting in the sequencing adapters. Methods. We propose reliable approaches for purifying hyperactive Tn5 transposase by chitin magnetic bead sorting. Double-stranded DNA of J76 cells and 293T cells were digested and subjected to tagmentation as test samples with Tn5 transposase, and libraries were established and sequenced. Sequencing data was then analyzed for peak calling, GO enrichment, and motif analysis. Results. We report a set of rapid, efficient, and low-cost methods for ATAC-seq library construction and data analysis, through large-scale and rapid sequencing. These methods can provide a reference for the study of epigenetic regulation of gene expression.

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Shah, Anjali. "Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system." Nature Methods 6, no. 4 (April 2009): ii—iii. http://dx.doi.org/10.1038/nmeth.f.247.

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Goren, Alon, Fatih Ozsolak, Noam Shoresh, Manching Ku, Mazhar Adli, Chris Hart, Melissa Gymrek, et al. "Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA." Nature Methods 7, no. 1 (November 29, 2009): 47–49. http://dx.doi.org/10.1038/nmeth.1404.

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Xing, Qiao Rui, Chadi A. El Farran, Ying Ying Zeng, Yao Yi, Tushar Warrier, Pradeep Gautam, James J. Collins, et al. "Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility." Genome Research 30, no. 7 (July 2020): 1027–39. http://dx.doi.org/10.1101/gr.257840.119.

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Mittal, Chitvan, Melissa J. Blacketer, and Michael A. Shogren-Knaak. "Nucleosome acetylation sequencing to study the establishment of chromatin acetylation." Analytical Biochemistry 457 (July 2014): 51–58. http://dx.doi.org/10.1016/j.ab.2014.04.024.

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Molitor, Jana, Jan-Philipp Mallm, Karsten Rippe, and Fabian Erdel. "Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions." Biophysical Journal 112, no. 3 (February 2017): 473–90. http://dx.doi.org/10.1016/j.bpj.2017.01.001.

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Eapen, Amy A., Sreeja Parameswaran, Carmy Forney, Lee E. Edsall, Daniel Miller, Omer Donmez, Katelyn Dunn, et al. "Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis." PLOS Genetics 18, no. 5 (May 16, 2022): e1009973. http://dx.doi.org/10.1371/journal.pgen.1009973.

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Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched and non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.

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Oh, Kyu Seon, Jisu Ha, Songjoon Baek, and Myong-Hee Sung. "XL-DNase-seq: Improved footprinting of dynamic transcription factors." Journal of Immunology 202, no. 1_Supplement (May 1, 2019): 125.17. http://dx.doi.org/10.4049/jimmunol.202.supp.125.17.

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Abstract As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data accumulating at an unprecedented rate. However, accurate inference of protein occupancy requires higher resolution footprinting analysis where major hurdles exist, including the sequence bias of nucleases and the short-lived chromatin binding of many transcription factors (TFs) with consequent lack of footprints. Here we introduce an assay termed crosslink (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. Mild crosslinking improved the detection of DNase-based footprints of dynamic TFs but interfered with ATAC-based footprinting of the same TFs. XL-DNase-seq may help extract novel gene regulatory circuits involving previously undetectable TFs. The DNase-seq and ATAC-seq data generated in our systematic comparison of various crosslinking conditions also represent an unprecedented-scale resource derived from activated mouse macrophage-like cells which share many features of inflammatory macrophages.

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Das, Akash Chandra, Aidin Foroutan, Brian Qian, Nader Hosseini Naghavi, Kayvan Shabani, and Parisa Shooshtari. "Single-Cell Chromatin Accessibility Data Combined with GWAS Improves Detection of Relevant Cell Types in 59 Complex Phenotypes." International Journal of Molecular Sciences 23, no. 19 (September 28, 2022): 11456. http://dx.doi.org/10.3390/ijms231911456.

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Several disease risk variants reside on non-coding regions of DNA, particularly in open chromatin regions of specific cell types. Identifying the cell types relevant to complex traits through the integration of chromatin accessibility data and genome-wide association studies (GWAS) data can help to elucidate the mechanisms of these traits. In this study, we created a collection of associations between the combinations of chromatin accessibility data (bulk and single-cell) with an array of 201 complex phenotypes. We integrated the GWAS data of these 201 phenotypes with bulk chromatin accessibility data from 137 cell types measured by DNase-I hypersensitive sequencing and found significant results (FDR adjusted p-value ≤ 0.05) for at least one cell type in 21 complex phenotypes, such as atopic dermatitis, Graves’ disease, and body mass index. With the integration of single-cell chromatin accessibility data measured by an assay for transposase-accessible chromatin with high-throughput sequencing (scATAC-seq), taken from 111 adult and 111 fetal cell types, the resolution of association was magnified, enabling the identification of further cell types. This resulted in the identification of significant correlations (FDR adjusted p-value ≤ 0.05) between 15 categories of single-cell subtypes and 59 phenotypes ranging from autoimmune diseases like Graves’ disease to cardiovascular traits like diastolic/systolic blood pressure.

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Miao, Feng, Zhuo Chen, Lingxiao Zhang, Jinhui Wang, Harry Gao, Xiwei Wu, and Rama Natarajan. "RNA-sequencing analysis of high glucose-treated monocytes reveals novel transcriptome signatures and associated epigenetic profiles." Physiological Genomics 45, no. 7 (April 1, 2013): 287–99. http://dx.doi.org/10.1152/physiolgenomics.00001.2013.

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We performed high throughput transcriptomic profiling with RNA sequencing (RNA-Seq) to uncover network responses in human THP-1 monocytes treated with high glucose (HG). Our data analyses revealed that interferon (IFN) signaling, pattern recognition receptors, and activated interferon regulatory factors (IRFs) were enriched among the HG-upregulated genes. Motif analysis identified an HG-responsive IRF-mediated network in which interferon-stimulated genes (ISGs) were enriched. Notably, this network showed strong overlap with a recently discovered IRF7-driven network relevant to Type 1 diabetes. We next examined if the HG-regulated genes possessed any characteristic chromatin features in the basal state by profiling 15 active and repressive chromatin marks under normal glucose conditions using chromatin immunoprecipitation linked to promoter microarrays. Composite profiles revealed higher histone H3 lysine-9-acetylation levels around the promoters of HG-upregulated genes compared with all RefSeq promoters. Interestingly, within the HG-upregulated genes, active chromatin marks were enriched not only at high CpG content promoters, but surprisingly also at low CpG content promoters. Similar results were obtained with peripheral blood monocytes exposed to HG. These new results reveal a novel mechanism by which HG can exercise IFN-α-like effects in monocytes by upregulating a set of ISGs poised for activation with multiple chromatin marks.

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Ambrosini, Giovanna, René Dreos, and Philipp Bucher. "Principles of ChIP-seq Data Analysis Illustrated with Examples." Genomics and Computational Biology 1, no. 1 (September 18, 2015): 22. http://dx.doi.org/10.18547/gcb.2015.vol1.iss1.e22.

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Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single ChIPseq experiment produces large amounts of highly reproducible data. The challenge is to extract knowledge from the data by thoughtful application of appropriate bioinformatics tools. Here we present a concise introduction into ChIP-seq data analysis in the form of a tutorial based on tools developed by our group. We expose biological questions, explain methods and provide guidelines for the interpretation of the results. While this article focuses on ChIP-seq, most of the algorithms and tools we present are applicable to other chromatin profiling assays based on next generation sequencing (NGS) technology as well.

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Tang, Lili, Meng Wang, Changbing Shen, Leilei Wen, Mengqing Li, Dan Wang, Xiaodong Zheng, et al. "Assay for Transposase-Accessible Chromatin Using Sequencing Analysis Reveals a Widespread Increase in Chromatin Accessibility in Psoriasis." Journal of Investigative Dermatology 141, no. 7 (July 2021): 1745–53. http://dx.doi.org/10.1016/j.jid.2020.12.031.

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Buisine, Nicolas, Xiaoan Ruan, Yijun Ruan, and Laurent M. Sachs. "Corrigendum: Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues." Cold Spring Harbor Protocols 2020, no. 1 (January 2020): pdb.corr106765. http://dx.doi.org/10.1101/pdb.corr106765.

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Ranawaka, Buddhini, Milos Tanurdzic, Peter Waterhouse, and Fatima Naim. "An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant." Molecular Biology Reports 47, no. 12 (November 25, 2020): 9499–509. http://dx.doi.org/10.1007/s11033-020-06013-1.

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AbstractAll flowering plants have evolved through multiple rounds of polyploidy throughout the evolutionary process. Intergenomic interactions between subgenomes in polyploid plants are predicted to induce chromatin modifications such as histone modifications to regulate expression of gene homoeologs. Nicotiana benthamiana is an ancient allotetraploid plant with ecotypes collected from climatically diverse regions of Australia. Studying the chromatin landscape of this unique collection will likely shed light on the importance of chromatin modifications in gene regulation in polyploids as well its implications in adaptation of plants in environmentally diverse conditions. Generally, chromatin immunoprecipitation and high throughput DNA sequencing (ChIP-seq) is used to study chromatin modifications. However, due to the starchy nature of mature N. benthamiana leaves, previously published protocols were unsuitable. The higher amounts of starch in leaves that co-precipitated with nuclei hindered downstream processing of DNA. Here we present an optimised ChIP protocol for N. benthamiana leaves to facilitate comparison of chromatin modifications in two closely related ecotypes. Several steps of ChIP were optimised including tissue harvesting, nuclei isolation, nuclei storage, DNA shearing and DNA recovery. Commonly available antibodies targeting histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 9 dimethylation (H3K9me2) histone modifications were used and success of ChIP was confirmed by PCR and next generation sequencing. Collectively, our optimised method is the first comprehensive ChIP method for mature starchy leaves of N. benthamiana to enable studies of chromatin landscape at the genome-wide scale.

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Beacon, Tasnim H., and James R. Davie. "Transcriptionally Active Chromatin—Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation." Cells 10, no. 6 (May 30, 2021): 1354. http://dx.doi.org/10.3390/cells10061354.

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The chicken erythrocyte model system has been valuable to the study of chromatin structure and function, specifically for genes involved in oxygen transport and the innate immune response. Several seminal features of transcriptionally active chromatin were discovered in this system. Davie and colleagues capitalized on the unique features of the chicken erythrocyte to separate and isolate transcriptionally active chromatin and silenced chromatin, using a powerful native fractionation procedure. Histone modifications, histone variants, atypical nucleosomes (U-shaped nucleosomes) and other chromatin structural features (open chromatin) were identified in these studies. More recently, the transcriptionally active chromosomal domains in the chicken erythrocyte genome were mapped by combining this chromatin fractionation method with next-generation DNA and RNA sequencing. The landscape of histone modifications relative to chromatin structural features in the chicken erythrocyte genome was reported in detail, including the first ever mapping of histone H4 asymmetrically dimethylated at Arg 3 (H4R3me2a) and histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s), which are products of protein arginine methyltransferases (PRMTs) 1 and 5, respectively. PRMT1 is important in the establishment and maintenance of chicken erythrocyte transcriptionally active chromatin.

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Loh, Christopher, Sung-ho Park, Angela Lee, Ruoxi Yuan, Lionel B. Ivashkiv, and George D. Kalliolias. "TNF-induced inflammatory genes escape repression in fibroblast-like synoviocytes: transcriptomic and epigenomic analysis." Annals of the Rheumatic Diseases 78, no. 9 (May 16, 2019): 1205–14. http://dx.doi.org/10.1136/annrheumdis-2018-214783.

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ObjectiveWe investigated genome-wide changes in gene expression and chromatin remodelling induced by tumour necrosis factor (TNF) in fibroblast-like synoviocytes (FLS) and macrophages to better understand the contribution of FLS to the pathogenesis of rheumatoid arthritis (RA).MethodsFLS were purified from patients with RA and CD14+ human monocyte-derived macrophages were obtained from healthy donors. RNA-sequencing, histone 3 lysine 27 acetylation (H3K27ac), chromatin immunoprecipitation-sequencing (ChIP-seq) and assay for transposable accessible chromatin by high throughput sequencing (ATAC-seq) were performed in control and TNF-stimulated cells.ResultsWe discovered 280 TNF-inducible arthritogenic genes which are transiently expressed and subsequently repressed in macrophages, but in RA, FLS are expressed with prolonged kinetics that parallel the unremitting kinetics of RA synovitis. 80 out of these 280 fibroblast-sustained genes (FSGs) that escape repression in FLS relative to macrophages were desensitised (tolerised) in macrophages. Epigenomic analysis revealed persistent H3K27 acetylation and increased chromatin accessibility in regulatory elements associated with FSGs in TNF-stimulated FLS. The accessible regulatory elements of FSGs were enriched in binding motifs for nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), interferon-regulatory factors (IRFs) and activating protein-1 (AP-1). Inhibition of bromodomain and extra-terminal motif (BET) proteins, which interact with histone acetylation, suppressed sustained induction of FSGs by TNF.ConclusionOur genome-wide analysis has identified the escape of genes from transcriptional repression in FLS as a novel mechanism potentially contributing to the chronic unremitting synovitis observed in RA. Our finding that TNF induces sustained chromatin activation in regulatory elements of the genes that escape repression in RA FLS suggests that altering or targeting chromatin states in FLS (eg, with inhibitors of BET proteins) is an attractive therapeutic strategy.

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Jia, Lin, Yichen Wang, Cong Wang, Zhonghua Du, Shilin Zhang, Xue Wen, Lei Zhou, et al. "Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation." Nucleic Acids Research 48, no. 7 (February 14, 2020): 3935–48. http://dx.doi.org/10.1093/nar/gkaa097.

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Abstract Formation of a pluripotency-specific chromatin network is a critical event in reprogramming somatic cells into pluripotent status. To characterize the regulatory components in this process, we used ‘chromatin RNA in situ reverse transcription sequencing’ (CRIST-seq) to profile RNA components that interact with the pluripotency master gene Oct4. Using this approach, we identified a novel nuclear lncRNA Oplr16 that was closely involved in the initiation of reprogramming. Oplr16 not only interacted with the Oct4 promoter and regulated its activity, but it was also specifically activated during reprogramming to pluripotency. Active expression of Oplr16 was required for optimal maintenance of pluripotency in embryonic stem cells. Oplr16 was also able to enhance reprogramming of fibroblasts into pluripotent cells. RNA reverse transcription-associated trap sequencing (RAT-seq) indicated that Oplr16 interacted with multiple target genes related to stem cell self-renewal. Of note, Oplr16 utilized its 3′-fragment to recruit the chromatin factor SMC1 to orchestrate pluripotency-specific intrachromosomal looping. After binding to the Oct4 promoter, Oplr16 recruited TET2 to induce DNA demethylation and activate Oct4 in fibroblasts, leading to enhanced reprogramming. These data suggest that Oplr16 may act as a pivotal chromatin factor to control stem cell fate by modulating chromatin architecture and DNA demethylation.

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Koenning, Matthias, Xianlong Wang, Menuka Karki, Rahul Kumar Jangid, Sarah Kearns, Durga Nand Tripathi, Michael Cianfrocco, et al. "Neuronal SETD2 activity links microtubule methylation to an anxiety-like phenotype in mice." Brain 144, no. 8 (May 20, 2021): 2527–40. http://dx.doi.org/10.1093/brain/awab200.

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Abstract Gene discovery efforts in autism spectrum disorder have identified heterozygous defects in chromatin remodeller genes, the ‘readers, writers and erasers’ of methyl marks on chromatin, as major contributors to this disease. Despite this advance, a convergent aetiology between these defects and aberrant chromatin architecture or gene expression has remained elusive. Recently, data have begun to emerge that chromatin remodellers also function directly on the cytoskeleton. Strongly associated with autism spectrum disorder, the SETD2 histone methyltransferase for example, has now been shown to directly methylate microtubules of the mitotic spindle. However, whether microtubule methylation occurs in post-mitotic cells, for example on the neuronal cytoskeleton, is not known. We found the SETD2 α-tubulin lysine 40 trimethyl mark occurs on microtubules in the brain and in primary neurons in culture, and that the SETD2 C-terminal SRI domain is required for binding and methylation of α-tubulin. A CRISPR knock-in of a pathogenic SRI domain mutation (Setd2SRI) that disables microtubule methylation revealed at least one wild-type allele was required in mice for survival, and while viable, heterozygous Setd2SRI/wtmice exhibited an anxiety-like phenotype. Finally, whereas RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) showed no concomitant changes in chromatin methylation or gene expression in Setd2SRI/wtmice, primary neurons exhibited structural deficits in axon length and dendritic arborization. These data provide the first demonstration that microtubules of neurons are methylated, and reveals a heterozygous chromatin remodeller defect that specifically disables microtubule methylation is sufficient to drive an autism-associated phenotype.

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Fernandes, Sunjay Jude, Matilda Ericsson, Mohsen Khademi, Maja Jagodic, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum, and Jesper Tegnér. "Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients." Epigenomics 13, no. 20 (October 2021): 1607–18. http://dx.doi.org/10.2217/epi-2021-0205.

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Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-sequencing profiles from sorted blood immune CD4+ and CD8+ T cells, CD14+ monocytes and CD19+ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS patients and HCs, primarily in CD4+ and CD19+. CD4+ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4+ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4+ and CD19+ cells in MS.

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Ott, Christopher J., Raphael Szalat, Matthew Lawlor, Mehmet Kemal Samur, Yan Xu, Charles B. Epstein, Charles Y. Lin, et al. "Chromatin Accessibility Profiling Reveals Cis-Regulatory Heterogeneity and Novel Transcription Factor Dependencies in Multiple Myeloma." Blood 132, Supplement 1 (November 29, 2018): 1313. http://dx.doi.org/10.1182/blood-2018-99-119941.

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Abstract Multiple myeloma (MM) is a plasma cell malignancy characterized by clinical and genomic heterogeneity. Recurrent IgH translocations, copy number abnormalities and somatic mutations have been reported to participate in myelomagenesis; however no universal driver of the disease has been identified. Here, we hypothesize that transcriptional deregulation is critical for MM pathogenesis and the maintenance of the MM cell state. In order to capture signatures of transcription factor engagement with the myeloma epigenome, we performed the assay for transposase-accessible chromatin sequencing (ATAC sequencing), deep RNA sequencing in 23 primary myeloma samples and 5 normal plasma cell samples (NPC) from healthy donors along with whole genome sequencing and H3K27ac ChIP-seq in a cohort of these primary MM samples. We identified 22,603 variable accessible loci between MM and NPC and correlated impact of these on expression of associated genes using RNA-seq data. Together with robust differential analysis of open chromatin regions and nuclease-accessibility footprints to identify discrete transcription factor binding events, we have discerned the myeloma-specific open chromatin landscape, identified transcription factor dependencies and potential new myeloma drivers. In our dataset we observe a vast number of loci with heterogeneous chromatin states across the sample cohort, and the majority of the open chromatin sites identified are unique to a single sample. However, distinct variable chromatin accessibility signatures indicative of the MM chromatin state when compared to normal plasma cells were observed. Remarkably, we observed more frequent recurrent loss of variable accessible loci compared to gains. In addition, specific open chromatin profiles evident in hyperdiploid and non-hyperdiploid MM were also identified. Accessibility footprinting revealed MM-specific enrichment for transcription factors known to be essential for MM cell survival including Interferon Regulatory Factors (IRFs), Nuclear Factor Kappa B (NFkB), Ikaros, and Sp1. Interestingly, we also identify the myocyte enhancer factor 2 (MEF2) family of transcription factors as being specifically enriched in open chromatin regions in MM cells. Using a CRISPR-Cas9 knockout system, we identify the MEF2 family member MEF2C as essential for MM cell proliferation and survival. MEF2C is significantly overexpressed at the RNA level in our study as well as in several independent cohorts and is a central enhancer-localized transcription factor in MM core regulatory circuitry as determined by H3K27ac ChIP-sequencing profiles of primary MM samples. In order to evaluate MEF2C as a therapeutic target, we used small molecule inhibitors targeting MEF2C activity via inhibition of MEF2C phosphorylation using inhibitors of salt-induced kinases (SIK) and microtubule-associated protein/microtubule affinity regulating kinases (MARK). SIK/MARK have been described to specifically activate MEF2C. SIK and MARK inhibition resulted in both dose- and time-dependent inhibition of MM cell growth and survival in a panel of 12 MM cell lines with various genotypic and phenotypic characteristics, revealing a potential approach to targeting the dysregulated gene regulatory state of myeloma. To conclude, here we identify here an altered chromatin accessibility landscape in multiple myeloma that likely contributes to oncogenic transcription states through the activity of transcription factors such as MEF2C, representing a new MM dependency and potential therapeutic target. Disclosures Anderson: Millennium Takeda: Consultancy; C4 Therapeutics: Equity Ownership, Other: Scientific founder; Bristol Myers Squibb: Consultancy; Gilead: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy; OncoPep: Equity Ownership, Other: Scientific founder. Young:Camp4 Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Syros Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Omega Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Munshi:OncoPep: Other: Board of director.

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Tolstorukov, Michael Y., Peter V. Kharchenko, and Peter J. Park. "Analysis of the primary structure of chromatin with next-generation sequencing." Epigenomics 2, no. 2 (April 2010): 187–97. http://dx.doi.org/10.2217/epi.09.48.

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Yang, Chia-Chun, Michael J. Buck, Min-Hsuan Chen, Yun-Fan Chen, Hsin-Chi Lan, Jeremy JW Chen, Chao Cheng, and Chun-Chi Liu. "Discovering chromatin motifs using FAIRE sequencing and the human diploid genome." BMC Genomics 14, no. 1 (2013): 310. http://dx.doi.org/10.1186/1471-2164-14-310.

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Ku, Wai Lim, Kosuke Nakamura, Weiwu Gao, Kairong Cui, Gangqing Hu, Qingsong Tang, Bing Ni, and Keji Zhao. "Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification." Nature Methods 16, no. 4 (March 28, 2019): 323–25. http://dx.doi.org/10.1038/s41592-019-0361-7.

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Fanelli, Mirco, Stefano Amatori, Iros Barozzi, and Saverio Minucci. "Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue." Nature Protocols 6, no. 12 (November 10, 2011): 1905–19. http://dx.doi.org/10.1038/nprot.2011.406.

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Wills, Andrea E., Rakhi Gupta, Edward Chuong, and Julie C. Baker. "Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis." Methods 66, no. 3 (April 2014): 410–21. http://dx.doi.org/10.1016/j.ymeth.2013.09.010.

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Zhu, Mingda, Jingyang Zhang, Guangyu Li, and Zhenzhen Liu. "ELOVL2-AS1 inhibits migration of triple negative breast cancer." PeerJ 10 (April 14, 2022): e13264. http://dx.doi.org/10.7717/peerj.13264.

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In this study, we identified a key enhancer RNA (eRNA) region in breast cancer (BRCA) by applying an integrated analysis method. Reported eRNA region and genes affected by them were selected as presumed target pairs. Kaplan–Meier (KM) survival and correlation analyses were performed to screen valuable eRNA region. Based on the KM value and its correlation with the paired target genes, we carefully selected ELOVL2-AS1 as a potential key eRNA region in BRCA. Subsequently, we analyzed the expression of ELOVL2-AS1 and ELOVL2 in four BRCA subtypes and in different BRCA cell lines. The expression of ELOVL2-AS1 and ELOVL2 in triple negative breast cancer (TNBC) was significantly lower than those in Luminal A. After that, we analyzed the function of genes that are positively correlated with ELOVL2-AS1. We found that the co-expression gene mainly related to cilia and cilia characteristics of TNBC is significantly weaker than that of Luminal A. Considering the stronger invasion and metastasis of TNBC (compared with Luminal A) and the close relationship between decreased cilia and metastasis, we overexpressed ELOVL2-AS1 in TNBC and observed its effect on cell migration. The results show that it can inhibit the migration of TNBC. Finally, we analyzed the assay for transposase-accessible chromatin sequencing data, chromatin interaction analysis with paired-end tag sequencing data, and chromatin immunoprecipitation sequencing data and identified the chromatin interaction between ELOVL2-AS1 and ELOVL2, suggesting a direct regulatory interaction.

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Kraus, Lindsay, and Brianna Beavens. "The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure." Biomedicines 11, no. 2 (February 16, 2023): 579. http://dx.doi.org/10.3390/biomedicines11020579.

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Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.

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Quan, Cheng, Jie Ping, Hao Lu, Gangqiao Zhou, and Yiming Lu. "3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database." Nucleic Acids Research 50, no. D1 (November 1, 2021): D950—D955. http://dx.doi.org/10.1093/nar/gkab1008.

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Abstract The rapid development of single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) technologies presents both challenges and opportunities for the annotation of noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variant annotation, to expand its applications to structural variation (SV) and to implement variant annotation down to single-cell resolution. The updates of 3DSNP include (i) annotation of 108 317 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures, (ii) evaluation of the accessible chromatin peaks flanking the variants across 126 cell types/subtypes in 15 human fetal tissues and 54 cell types/subtypes in 25 human adult tissues by integrating scATAC-seq data and (iii) expansion of Hi-C data to 49 human cell types. In summary, this version is a significant and comprehensive improvement over the previous version. The 3DSNP v2.0 database is freely available at https://omic.tech/3dsnpv2/.

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Kubalová, Ivona, Amanda Souza Câmara, Petr Cápal, Tomáš Beseda, Jean-Marie Rouillard, Gina Marie Krause, Kateřina Holušová, et al. "Helical coiling of metaphase chromatids." Nucleic Acids Research, March 2, 2023. http://dx.doi.org/10.1093/nar/gkad028.

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Abstract Chromatids of mitotic chromosomes were suggested to coil into a helix in early cytological studies and this assumption was recently supported by chromosome conformation capture (3C) sequencing. Still, direct differential visualization of a condensed chromatin fibre confirming the helical model was lacking. Here, we combined Hi-C analysis of purified metaphase chromosomes, biopolymer modelling and spatial structured illumination microscopy of large fluorescently labeled chromosome segments to reveal the chromonema - a helically-wound, 400 nm thick chromatin thread forming barley mitotic chromatids. Chromatin from adjacent turns of the helix intermingles due to the stochastic positioning of chromatin loops inside the chromonema. Helical turn size varies along chromosome length, correlating with chromatin density. Constraints on the observable dimensions of sister chromatid exchanges further supports the helical chromonema model.

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Ma, Shaoqian, and Yongyou Zhang. "Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq." Molecular Biomedicine 1, no. 1 (October 10, 2020). http://dx.doi.org/10.1186/s43556-020-00009-w.

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Abstract Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.

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Journal articles on the topic 'Chromatin sequencing'

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