Relevant bibliographies by topics / Chromatin sequencing

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Chromatin sequencing'

Author: Grafiati
Published: 9 March 2023
Last updated: 31 July 2025

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Journal articles on the topic "Chromatin sequencing"

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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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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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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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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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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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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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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Dissertations / Theses on the topic "Chromatin sequencing"

1

Cook, David. "SNF2H-Mediated Chromatin Remodelling and Its Regulation of the Pluripotent State." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35097.

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In embryonic stem cells (ESCs), the SWI/SNF, CHD, and INO80 families of ATP-dependent chromatin remodellers have been implicated in maintaining pluripotency-associated gene expression, however the involvement of ISWI family remodellers has yet to be defined. Here, we explore the importance of the mammalian ISWI homologue SNF2H (Smarca5) by deriving a conditional knockout mouse ESC line and observing the consequences of SNF2H depletion on the pluripotent state. Cre-mediated deletion of Snf2h disrupts hallmark characteristics of pluripotency, resulting in distinct morphological changes; reduced
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Josserand, Manon. "Exploring chromatin states in the Drosophila intestinal lineage." Electronic Thesis or Diss., Université Paris sciences et lettres, 2022. http://www.theses.fr/2022UPSLS056.

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Les cellules souches adultes s'auto-renouvellent et se différencient en un ou plusieurs types cellulaires, assurant ainsi l'homéostasie d’un tissu. Comprendre leur régulation est crucial pour mieux appréhender les mécanismes de prolifération incontrôlée et de défauts de différenciation observés lors de la tumorigenèse et du déclin fonctionnel des tissus pendant le vieillissement. Ma thèse avait pour but de mieux comprendre les états chromatiniens associés à l'activité des cellules souches adultes in vivo, dans un tissu homéostatique en utilisant l'intestin adulte de la drosophile comme modèle.
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LUCINI, FEDERICA. "Unconventional nuclear architecture in CD4+ T lymphocytes uncouples chromatin solubility from function." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2020. http://hdl.handle.net/10281/262913.

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Nei nuclei delle cellule eucarioti, l'informazione genetica codificata nel DNA è concentrata nel microscopico volume nucleare in forma di cromatina, un complesso di DNA e proteine. I meccanismi molecolari che gestiscono la compattazione e il ripiegamento della cromatina e che consentono l'espressione mirata delle porzioni di genoma necessarie alle attività della cellula sono noti come ‘epigenoma’. L’azione dell’epigenoma determina un avvolgimento e un posizionamento nucleare della cromatina specifico per ogni tipo cellulare, con aree dense e trascrizionalmente inattive (eterocromatina) ed aree
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Aitken, Sarah Jane. "The pathological and genomic impact of CTCF depletion in mammalian model systems." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284403.

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CCCTC-binding factor (CTCF) binds DNA, thereby helping to partition the mammalian genome into discrete structural and regulatory domains. In doing so, it insulates chromatin and fine-tunes gene activation, repression, and silencing. Complete removal of CTCF from mammalian cells causes catastrophic genomic dysregulation, most likely due to widespread collapse of 3D chromatin looping within the nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction in CTCF expression are viable but have an increased incidence of spontaneous multi-lineage malignancies. In addition, CTCF is mutated in
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Deng, Chengyu. "Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience." Diss., Virginia Tech, 2021. http://hdl.handle.net/10919/101765.

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The epigenome carries dynamic information that controls gene expression and maintains cell identity during both disease and normal development. The inherent plasticity of the epigenome paves new avenues for developing diagnostic and therapeutic tools for human diseases. Microfluidic technology has improved the sensitivity and resolution of epigenomic analysis due to its outstanding ability to manipulate nanoliter-scale liquid volumes. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms
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Hunt, Spencer Philip. "Whole-Genome Assembly of Atriplex hortensis L. Using OxfordNanopore Technology with Chromatin-Contact Mapping." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8580.

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Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise h
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Kremsky, Isaac Jacob 1983. "Assessing the relationship between chromatin and splicing factors in alternative splicing." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/316790.

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Proteins that bind to DNA or RNA are both known to influence alternative splicing. However, there has not been so far a systematic experimental exploration of the relationship between these factors in their effect on splicing. In this thesis, we make use of the large amounts of publicly available high throughput sequencing data that now make it possible to explore this question on a genome-wide scale. We made exhaustive use of a method known as profiling to address this question. As most profiling methods in common use are merely qualitative, the first task of the thesis was to generate
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Sarma, Mimosa. "Microfluidic platforms for Transcriptomics and Epigenomics." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90294.

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A cell, the building block of all life, stores a plethora of information in its genome, epigenome, and transcriptome which needs to be analyzed via various Omic studies. The heterogeneity in a seemingly similar group of cells is an important factor to consider and it could lead us to better understand processes such as cancer development and resistance to treatment, fetal development, and immune response. There is an ever growing demand to be able to develop more sensitive, accurate and robust ways to study Omic information and to analyze subtle biological variation between samples even with l
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Tavernari, Daniele. "Statistical and network-based methods for the analysis of chromatin accessibility maps in single cells." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/12297/.

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In questo lavoro, metodi provenienti dalla Fisica, dalla Statistica e dalla Teoria dei Grafi sono stati impiegati per caratterizzare ed analizzare profili di apertura e accessibilità della cromatina ottenuti con la tecnica ATAC-seq in singole cellule, nella fattispecie linfociti B provenienti da tre pazienti affetti da Leucemia Linfocitica Cronica. Una pipeline bioinformatica è stata sviluppata per processare i dati di sequencing ed ottenere le posizioni accessibili del genoma per ciascuna cellula. La quantità di regioni aperte e la loro distribuzione spaziale lungo il DNA sono state caratter
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Ma, Sai. "Microfluidics for Genetic and Epigenetic Analysis." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/78187.

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Microfluidics has revolutionized how molecular biology studies are conducted. It permits profiling of genomic and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this thesis, we focus on three projects (diffusion-based PCR, MID-RRBS, and SurfaceChIP-seq), which improved the sensitivities of conventional assays by coupling with microfluidic technology. MID-RRBS and SurfaceChI
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Books on the topic "Chromatin sequencing"

1

Liang, Xiaoshan. Studies of rainbow trout Ki-ras gene: Sequencing, aflatoxin B1 binding, and chromatin structure. 1993.

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Mifsud, Borbala, and Anais Bardet. Practical Guide to Chip-Seq Data Analysis. Taylor & Francis Group, 2018.

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Mifsud, Borbala, Kathi Zarnack, and Anaïs F. Bardet. Practical Guide to ChIP-Seq Data Analysis. Taylor & Francis Group, 2018.

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Mifsud, Borbala, Kathi Zarnack, and Anais Bardet. Practical Guide to Chip-Seq Data Analysis. Taylor & Francis Group, 2021.

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Mifsud, Borbala, Kathi Zarnack, and Anaïs F. Bardet. Practical Guide to ChIP-Seq Data Analysis. Taylor & Francis Group, 2018.

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Practical Guide to ChIP-Seq Data Analysis. Taylor & Francis Group, 2018.

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Book chapters on the topic "Chromatin sequencing"

1

Ismail, Hamid D. "Chromatin Immunoprecipitation Sequencing." In Bioinformatics. Chapman and Hall/CRC, 2023. http://dx.doi.org/10.1201/9781003355205-6.

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Ribarska, Teodora, and Gregor D. Gilfillan. "Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers." In Chromatin Immunoprecipitation. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7380-4_14.

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Hoeijmakers, Wieteke Anna Maria, and Richárd Bártfai. "Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq)." In Chromatin Immunoprecipitation. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7380-4_8.

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Ludwig, Leif S., and Caleb A. Lareau. "Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq." In Chromatin Accessibility. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2899-7_14.

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Stewart-Morgan, Kathleen R., and Anja Groth. "Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq." In Chromatin Accessibility. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2899-7_6.

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AbstractOpen or accessible chromatin typifies euchromatic regions and helps define cell type-specific transcription programs. DNA replication massively disorders chromatin composition and structure, and how accessible regions are affected by and recover from this disruption has been unclear. Here, we present repli-ATAC-seq, a protocol to profile accessible chromatin genome-wide on replicated DNA starting from 100,000 cells. In this method, replicated DNA is labeled with a short 5-ethynyl-2′-deoxyuridine (EdU) pulse in cultured cells and isolated from a population of tagmented fragments for amp
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Soares, Mário A. F., and Diogo S. Castro. "Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing." In Chromatin Immunoprecipitation. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7380-4_5.

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Diaz, Roxanne E., Aurore Sanchez, Véronique Anton Le Berre, and Jean-Yves Bouet. "High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing." In The Bacterial Nucleoid. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_6.

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Brahma, Sandipan, and Steven Henikoff. "CUT&RUN Profiling of the Budding Yeast Epigenome." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2257-5_9.

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AbstractMapping the epigenome is key to describe the relationship between chromatin landscapes and the control of DNA-based cellular processes such as transcription. Cleavage under targets and release using nuclease (CUT&RUN) is an in situ chromatin profiling strategy in which controlled cleavage by antibody-targeted Micrococcal Nuclease solubilizes specific protein-DNA complexes for paired-end DNA sequencing. When applied to budding yeast, CUT&RUN profiling yields precise genome-wide maps of histone modifications, histone variants, transcription factors, and ATP-dependent chromatin re
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Sridhar, Divya, and Aziz Aboobaker. "Monitoring Chromatin Regulation in Planarians Using Chromatin Immunoprecipitation Followed by Sequencing (ChIP-seq)." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_28.

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AbstractPlanarians are an accessible model system to study animal regeneration and stem cells. Over the last two decades, new molecular techniques have provided us with powerful tools to understand whole-body regeneration and pluripotent adult stem cells specifically. We describe a method for performing Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) on planarian cells that relies on FACS to isolate different cell populations followed by immunoprecipitation and library preparation for next-generation sequencing. Whole-genome profiling of histone modifications enables a greater
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Lopez-Rubio, Jose-Juan, T. Nicolai Siegel, and Artur Scherf. "Genome-wide Chromatin Immunoprecipitation-Sequencing in Plasmodium." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-026-7_23.

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Conference papers on the topic "Chromatin sequencing"

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Sun, Jialiang, Zhihan Ruan, Chaoyang Yan, and Jian Liu. "AREDCI: Assessing Reproducibility and Differential Chromatin Interactions for ChIA-PET Sequencing Data." In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2024. https://doi.org/10.1109/bibm62325.2024.10822709.

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Qiao, Yi, Xiaomeng Huang, and Gabor Marth. "Abstract 40: scBayes: A computational method to study tumor subclone-specific gene expression and chromatin accessibility using single-cell RNA sequencing and single-cell ATAC sequencing in combination of bulk DNA sequencing." In Abstracts: AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; January 9-12, 2020; San Diego, CA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.advprecmed20-40.

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Дергилев, А. И., О. Б. Добровольская, Н. Г. Орлова, and Ю. Л. Орлов. "STUDY OF TRANSCRIPTIONAL REGULATORY CIRCUITS AND CLUSTERS OF TRANSCRIPTION FACTOR BINDING SITES IN PLANT GENOMES ACCORDING TO CHIP-SEQ DATA." In Биотехнология в растениеводстве, животноводстве и сельскохозяйственной микробиологии. Crossref, 2021. http://dx.doi.org/10.48397/arriab.2021.21.xxi.005.

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С развитием технологий высокопроизводительного геномного секвенирования, в том числе иммунопреципитации хроматина с последующим секвенированием ChIP-seq, появляется возможность исследовать сайты связывания транскрипционных факторов в масштабе генома для многих модельных организмов, включая растения, имеющие биотехнологическое значение. Объёмы данных об экспериментально определенных сайтах связывания продолжают расти, и это приводит к появлению всё новых и новых качественных задач биоинформатики, среди которых: определение параметров регуляции экспрессии генов транскрипционными факторами, опред
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Reports on the topic "Chromatin sequencing"

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule se
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