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Journal articles on the topic 'Chromatin sequencing'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Gather, Fabian. "Chromatin Immunoprecipitation Sequencing (ChIPseq)." Annals of Anatomy - Anatomischer Anzeiger 260 (June 2025): 152421. https://doi.org/10.1016/j.aanat.2025.152421.

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2

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 (2013): 1525–34. http://dx.doi.org/10.1038/nprot.2013.088.

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3

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 (2019): e87. http://dx.doi.org/10.1002/cpmb.87.

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4

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 (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 expose

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Xie, Wenhui, Yilang Ke, Qinyi You, 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 (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 T

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Gorkin, David U., Iros Barozzi, Yuan Zhao, et al. "An atlas of dynamic chromatin landscapes in mouse fetal development." Nature 583, no. 7818 (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

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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 (2019): 3243–72. http://dx.doi.org/10.1038/s41596-019-0229-4.

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8

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 (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-

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9

Haghani, Viktoria, Aditi Goyal, Alan Zhang, et al. "Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip." F1000Research 14 (June 25, 2025): 625. https://doi.org/10.12688/f1000research.164319.1.

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Background As genome sequencing technologies advance, the growing accumulation of sequencing data in public databases highlights the need for more robust and adaptable analysis workflows for chromatin immunoprecipitation assays. These workflows must promote reproducibility and replicability of results while effectively leveraging publicly available data to enhance biological insights. Methods Here, we present Rocketchip, a Python-based command-line tool that integrates existing software through Snakemake, enabling efficient, automated, and reproducible analysis of both newly generated chromati

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10

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 (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 (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 trans

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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

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13

Murdoch, Brenda M., Kimberly M. Davenport, Shangqian Xie, et al. "378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome." Journal of Animal Science 100, Supplement_3 (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 h

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Vasilev, V. A., D. M. Ryabov, A. K. Shaytan, and G. A. Armeev. "Updating nucleosome positions within individual genes using molecular modeling methods and mnase sequencing data." Биофизика 68, no. 5 (2023): 911–19. http://dx.doi.org/10.31857/s0006302923050101.

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Organization of chromatin plays an important role in regulating the genetic machinery of the cell. The basic unit of chromatin packaging is a nucleosome, which harbors DNA of about 145 base pairs in length. The packaging of genetic material and its accessibility to transcription enzymes and other regulatory chromatin proteins depends on the positions of nucleosomes. MNase sequencing is used to examine nucleosome positions in a genome. MNase sequencing data are sufficient for detecting the presence of nucleosomes on the sequence, but a determination of the precise locations of nucleosomes can b

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Romanowska, Julia, and Anagha Joshi. "From Genotype to Phenotype: Through Chromatin." Genes 10, no. 2 (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 never

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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 (2022): 101442. http://dx.doi.org/10.1016/j.xpro.2022.101442.

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17

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 (2009): e5241. http://dx.doi.org/10.1371/journal.pone.0005241.

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18

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

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19

Wang, Xilin. "ATAC-seq: A powerful tool for investigating chromatin accessibility and transcription factor binding." Theoretical and Natural Science 6, no. 1 (2023): 316–22. http://dx.doi.org/10.54254/2753-8818/6/20230267.

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Chromatin Transposase Accessibility Sequencing is a new high-throughput sequencing technique developed by Professor William Greenleaf in 2013 which uses DNA transposase to probe chromatin accessibility with Tn5 transposase. This technique, which is simpler and more sensitive than DNase-seq, MNase-seq and FAIRE-seq and requires fewer cells, has been used to study chromatin accessibility using Tn5 transposase. ATAC-seq is important for the study of epigenetic molecular mechanisms because it can map chromatin accessibility on a genome-wide scale, compare open chromatin regions in different tumour

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20

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

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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

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22

Stevens, Claire, Leonardo Gonzalez-Smith, Huan Cao, and Suhn K. Rhie. "Abstract 7013: Methyl-Micro-C: simultaneous high-resolution characterization of three-dimensional chromatin structure and the DNA methylome." Cancer Research 84, no. 6_Supplement (2024): 7013. http://dx.doi.org/10.1158/1538-7445.am2024-7013.

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Abstract Understanding cancer biology allows for the determination of patient prognosis through biomarkers and predicting treatment sensitivity. For many cancer types, genetic changes have been largely characterized, but the contributions of epigenetic changes, which are also implicated in tumorigenesis, are not yet well understood. Three-dimensional chromatin architecture changes occur throughout tumor development, changing the states and interactions between cis-regulatory elements, overall inducing gene dysregulation. Chromatin structure changes have previously been interrogated using Hi-C,

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Reeves, G. Adam, Param Priya Singh, and Anne Brunet. "Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq inNothobranchius furzeri." Cold Spring Harbor Protocols 2024, no. 3 (2023): pdb.prot107747. http://dx.doi.org/10.1101/pdb.prot107747.

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The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei an

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24

Eapen, Amy A., Sreeja Parameswaran, Carmy Forney, et al. "Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis." PLOS Genetics 18, no. 5 (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 ka

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Li, Wangchun, U. Tim Wu, Yu Cheng, et al. "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 call

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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 (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

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Venters, Bryan J., Paul W. Hook, Vishnu S. Kumary, et al. "Abstract 7026: Multi-omic genomic mapping with long read sequencing." Cancer Research 84, no. 6_Supplement (2024): 7026. http://dx.doi.org/10.1158/1538-7445.am2024-7026.

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Abstract Gene transcription is regulated by the complex interplay between histone post-translational modifications (PTMs), chromatin associated proteins (CAPs), and DNA methylation (DNAme). Mapping their genomic locations and examining the relationships between these chromatin elements is a powerful approach to decipher mechanisms of disease, thereby enabling discovery of novel biomarkers and therapeutics. Leading epigenomic mapping technologies (e.g., ChIP-seq, CUT&RUN) rely upon DNA fragmentation to isolate regions of interest for sequencing on short read platforms (e.g., Illumina). This

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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 (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 accessibil

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Kubalová, Ivona, Amanda Souza Câmara, Petr Cápal, 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 mitoti

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Ma, Kai, Kaili Yin, Jiong Li, et al. "The Hypothalamic Epigenetic Landscape in Dietary Obesity." Advanced Science, December 20, 2023. http://dx.doi.org/10.1002/advs.202306379.

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AbstractThe hypothalamus in the brain plays a pivotal role in controlling energy balance in vertebrates. Nutritional excess through high‐fat diet (HFD) feeding can dysregulate hypothalamic signaling at multiple levels. Yet, it remains largely unknown in what magnitude HFD feeding may impact epigenetics in this brain region. Here, it is shown that HFD feeding can significantly alter hypothalamic epigenetic events, including posttranslational histone modifications, DNA methylation, and chromatin accessibility. The authors comprehensively analyze the chromatin immunoprecipitation‐sequencing (ChIP

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Elise, van Bree, Haring Nina, and Jacobs Frank. "Snakemake pipeline for Chromatin Immunoprecipitation sequencing." March 1, 2019. https://doi.org/10.5281/zenodo.2581325.

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32

Subramanian, Vijayalakshmi V. "Preprint Highlight: Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms." Molecular Biology of the Cell 34, no. 5 (2023). http://dx.doi.org/10.1091/mbc.p23-03-0010.

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Cohesins organize chromatin within the nucleus by promoting loop extrusion via cis contacts on chromatin and sister chromatid cohesion via trans contacts between chromatids. Whether cohesins employ a distinct mechanism for these two functions is not known. The authors use a carefully designed conditional expression of cohesin, mutated at its hinge domain, and assess its function with a variety of in vitro and in vivo experiments including live TIRF imaging, loop extrusion assay, Hi-C, and calibrated ChIP sequencing. A mutation in the hinge domain separates the two functions of cohesin, as the

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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 (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 ep

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Lee, Isac, Roham Razaghi, Timothy Gilpatrick, et al. "Methylation and accessibility profiling of GM12878, MCF-10A, MCF-7, and MDA-MB-231 using nanopore sequencing." August 5, 2020. https://doi.org/10.5281/zenodo.3969567.

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Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic feat

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Ren, Zongna, Wanqing Zhao, Dandan Li, et al. "INO80-Dependent Remodeling of Transcriptional Regulatory Network Underlies the Progression of Heart Failure." Circulation, December 28, 2023. http://dx.doi.org/10.1161/circulationaha.123.065440.

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BACKGROUND: Progressive remodeling of cardiac gene expression underlies decline in cardiac function, eventually leading to heart failure. However, the major determinants of transcriptional network switching from normal to failed hearts remain to be determined. METHODS: In this study, we integrated human samples, genetic mouse models, and genomic approaches, including bulk RNA sequencing, single-cell RNA sequencing, chromatin immunoprecipitation followed by high-throughput sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing, to identify the role of chromat

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Lee, Beoung Hun, Zexun Wu, and Suhn K. Rhie. "Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C." Epigenetics & Chromatin 15, no. 1 (2022). http://dx.doi.org/10.1186/s13072-022-00473-4.

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Abstract Background Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed. Here, we generated and analyzed Hi-C, Micro-C, and promoter capture Micro-C datasets with different sequencing depths to study chromatin interactions of regulatory elements and nucleosome positions in human prostate cancer cells. Results Compared to Hi-C, Micro-C identifies more high-resolution loops, including ones around structural variants.

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Holzmann, Johann, Antonio Z. Politi, Kota Nagasaka, et al. "Absolute quantification of cohesin, CTCF and their regulators in human cells." eLife 8 (June 17, 2019). http://dx.doi.org/10.7554/elife.46269.

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The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrom

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Bell, Jason C., David Jukam, Nicole A. Teran, et al. "Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts." eLife 7 (April 12, 2018). http://dx.doi.org/10.7554/elife.27024.

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RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-

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Li, Mengyao, Zhenhuan Jiang, Xueqiang Xu, et al. "Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2." Science 387, no. 6741 (2025). https://doi.org/10.1126/science.adp4319.

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In mammals, fertilized eggs undergo genome-wide epigenetic reprogramming to generate the organism. However, our understanding of epigenetic dynamics during preimplantation development at single-cell resolution remains incomplete. Here, we developed scNanoATAC-seq2, a single-cell assay for transposase-accessible chromatin using long-read sequencing for scarce samples. We present a detailed chromatin accessibility landscape of mouse preimplantation development, revealing distinct chromatin signatures in the epiblast, primitive endoderm, and trophectoderm during lineage segregation. Differences b

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Kumar, Banushree, Carmen Navarro, Philip Yuk Kwong Yung, et al. "Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors." Nature Protocols, October 3, 2024. http://dx.doi.org/10.1038/s41596-024-01058-z.

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Xi, Xiao-Li, Yi-Dong Yang, Hui-Ling Liu, Jie Jiang, and Bin Wu. "Chromatin accessibility module identified by single-cell sequencing underlies the diagnosis and prognosis of hepatocellular carcinoma." World Journal of Hepatology 17, no. 6 (2025). https://doi.org/10.4254/wjh.v17.i6.107329.

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BACKGROUND Hepatocellular carcinoma (HCC) is notorious for its aggressive progression and dismal prognosis, with chromatin accessibility dynamics emerging as pivotal yet poorly understood drivers. AIM To dissect how multilayered chromatin regulation sustains oncogenic transcription and tumor-stroma crosstalk in HCC, we combined multiomics single cell analysis. METHODS We integrated single-cell RNA sequencing and paired single-cell assay for transposase-accessible chromatin with sequencing data of HCC samples, complemented by bulk RNA sequencing validation across The Cancer Genome Atlas, Liver

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Leduque, Basile, Alejandro Edera, Clémentine Vitte, and Leandro Quadrana. "Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing." Nucleic Acids Research, April 27, 2024. http://dx.doi.org/10.1093/nar/gkae306.

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Abstract Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibilit

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Zhang, Haowen, Li Song, Xiaotao Wang, et al. "Fast alignment and preprocessing of chromatin profiles with Chromap." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-26865-w.

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AbstractAs sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.

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Nakamura, Kosuke, Kosuke Nakamura, Keji Zhao, et al. "A single-cell chromatin immunocleavage sequencing (scChIC-seq)." Protocol Exchange, February 5, 2019. http://dx.doi.org/10.1038/protex.2019.011.

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Fullwood, Melissa J., Yuyuan Han, Chia‐Lin Wei, Xiaoan Ruan, and Yijun Ruan. "Chromatin Interaction Analysis Using Paired‐End Tag Sequencing." Current Protocols in Molecular Biology 89, no. 1 (2010). http://dx.doi.org/10.1002/0471142727.mb2115s89.

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Bai, Gali, Namrita Dhillon, Colette Felton, et al. "SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing." Nucleic Acids Research 53, no. 14 (2025). https://doi.org/10.1093/nar/gkaf671.

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Abstract Studies of in vivo chromatin organization have relied on the accessibility of the underlying DNA to nucleases or methyltransferases, which is limited by their requirement for purified nuclei and enzymatic treatment. Here, we introduce a nanopore-based sequencing technique called small-molecule adduct sequencing (SMAdd-seq), where we profile chromatin accessibility by treating nuclei or intact cells with a small molecule, angelicin. Angelicin preferentially forms photoadducts with thymine bases in linker DNA, thereby labeling accessible DNA regions. By applying SMAdd-seq in Saccharomyc

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Long, Keren, Duo Su, Xiaokai Li, et al. "Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle." BMC Genomics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12864-022-08737-9.

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Abstract Background Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regulation of Myh genes transcription depends on three-dimensional chromatin conformation interaction, but the mechanistic details remain to be determined. Results In this study, we characterized the interaction profiles of Myh genes using 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing). The interaction profile of Myh genes changed b

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Zhang, Qiqi, Fengli Zhao, Zhe Wu, and Danling Zhu. "A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis." Plant Methods 18, no. 1 (2022). http://dx.doi.org/10.1186/s13007-022-00967-y.

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Abstract Background Chromatin-bound RNAs are the primary product of transcription that undergo on-chromatin processing such as capping, splicing, and polyadenylation. These processing steps then determine the fate of RNAs. Albeit its vital importance, a simple and robust method for isolating different fractions of chromatin-bound RNAs is missing in plants. Result Here, we describe our updated method and the associated step-by-step protocol for chromatin-bound RNAs isolation in A. thaliana. The chromatin-bound RNAs isolation is based on the 1 M UREA wash that removes the majority of non-chromat

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Shin, Hyun Mu, Gwanghun Kim, Sangjib Kim, et al. "Chromatin accessibility of circulating CD8+ T cells predicts treatment response to PD-1 blockade in patients with gastric cancer." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-21299-w.

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AbstractAlthough tumor genomic profiling has identified small subsets of gastric cancer (GC) patients with clinical benefit from anti-PD-1 treatment, not all responses can be explained by tumor sequencing alone. We investigate epigenetic elements responsible for the differential response to anti-PD-1 therapy by quantitatively assessing the genome-wide chromatin accessibility of circulating CD8+ T cells in patients’ peripheral blood. Using an assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify unique open regions of chromatin that significantly distinguish anti-P

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Song, Yi, Jieqiang He, Junxing Guo, et al. "The chromatin remodeller MdRAD5B enhances drought tolerance by coupling MdLHP1‐mediated H3K27me3 in apple." Plant Biotechnology Journal, October 24, 2023. http://dx.doi.org/10.1111/pbi.14210.

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SummaryRAD5B belongs to the Rad5/16‐like group of the SNF2 family, which often functions in chromatin remodelling. However, whether RAD5B is involved in chromatin remodelling, histone modification, and drought stress tolerance is largely unclear. We identified a drought‐inducible chromatin remodeler, MdRAD5B, which positively regulates apple drought tolerance. Transposase‐accessible chromatin with high‐throughput sequencing (ATAC‐seq) analysis showed that MdRAD5B affects the expression of 466 drought‐responsive genes through its chromatin remodelling function in response to drought stress. In

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