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  1. Artikel ; Online: Genomic Analysis of Foxp3 Function in Regulatory T Cells.

    Dolsten, Gabriel A / Pritykin, Yuri

    Journal of immunology (Baltimore, Md. : 1950)

    2023  Band 210, Heft 7, Seite(n) 880–887

    Abstract: Regulatory T (Treg) cells are critical for tolerance to self-antigens and for preventing autoimmunity. Foxp3 has been identified as a Treg cell lineage-defining transcription factor controlling Treg cell differentiation and function. In this article, we ... ...

    Abstract Regulatory T (Treg) cells are critical for tolerance to self-antigens and for preventing autoimmunity. Foxp3 has been identified as a Treg cell lineage-defining transcription factor controlling Treg cell differentiation and function. In this article, we review the current mechanistic and systemic understanding of Foxp3 function enabled by experimental and computational advances in high-throughput genomics.
    Mesh-Begriff(e) T-Lymphocytes, Regulatory ; Cell Differentiation/genetics ; Gene Expression Regulation ; Transcription Factors/genetics ; Genomics ; Forkhead Transcription Factors/metabolism
    Chemische Substanzen Transcription Factors ; Forkhead Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2023-03-22
    Erscheinungsland United States
    Dokumenttyp Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.2200864
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.

    Mitra, Sneha / Malik, Rohan / Wong, Wilfred / Rahman, Afsana / Hartemink, Alexander J / Pritykin, Yuri / Dey, Kushal K / Leslie, Christina S

    Nature genetics

    2024  Band 56, Heft 4, Seite(n) 627–636

    Abstract: We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses ... ...

    Abstract We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene-peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
    Mesh-Begriff(e) Chromatin/genetics ; Genome-Wide Association Study ; Regulatory Sequences, Nucleic Acid ; Gene Expression Regulation ; Promoter Regions, Genetic/genetics ; RNA ; Single-Cell Analysis/methods
    Chemische Substanzen Chromatin ; RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2024-03-21
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-024-01689-8
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  3. Artikel ; Online: Author Correction: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.

    Mitra, Sneha / Malik, Rohan / Wong, Wilfred / Rahman, Afsana / Hartemink, Alexander J / Pritykin, Yuri / Dey, Kushal K / Leslie, Christina S

    Nature genetics

    2024  

    Sprache Englisch
    Erscheinungsdatum 2024-05-23
    Erscheinungsland United States
    Dokumenttyp Published Erratum
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-024-01805-8
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  4. Artikel: Universal recording of cell-cell contacts

    Nakandakari-Higa, Sandra / Canesso, Maria C C / Walker, Sarah / Chudnovskiy, Aleksey / Jacobsen, Johanne T / Bilanovic, Jana / Parigi, S Martina / Fiedorczuk, Karol / Fuchs, Elaine / Bilate, Angelina M / Pasqual, Giulia / Mucida, Daniel / Pritykin, Yuri / Victora, Gabriel D

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study ... ...

    Abstract Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study these "kiss-and-run" interactions directly
    Sprache Englisch
    Erscheinungsdatum 2023-04-18
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.03.16.533003
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Simple topological features reflect dynamics and modularity in protein interaction networks.

    Pritykin, Yuri / Singh, Mona

    PLoS computational biology

    2013  Band 9, Heft 10, Seite(n) e1003243

    Abstract: The availability of large-scale protein-protein interaction networks for numerous organisms provides an opportunity to comprehensively analyze whether simple properties of proteins are predictive of the roles they play in the functional organization of ... ...

    Abstract The availability of large-scale protein-protein interaction networks for numerous organisms provides an opportunity to comprehensively analyze whether simple properties of proteins are predictive of the roles they play in the functional organization of the cell. We begin by re-examining an influential but controversial characterization of the dynamic modularity of the S. cerevisiae interactome that incorporated gene expression data into network analysis. We analyse the protein-protein interaction networks of five organisms, S. cerevisiae, H. sapiens, D. melanogaster, A. thaliana, and E. coli, and confirm significant and consistent functional and structural differences between hub proteins that are co-expressed with their interacting partners and those that are not, and support the view that the former tend to be intramodular whereas the latter tend to be intermodular. However, we also demonstrate that in each of these organisms, simple topological measures are significantly correlated with the average co-expression of a hub with its partners, independent of any classification, and therefore also reflect protein intra- and inter- modularity. Further, cross-interactomic analysis demonstrates that these simple topological characteristics of hub proteins tend to be conserved across organisms. Overall, we give evidence that purely topological features of static interaction networks reflect aspects of the dynamics and modularity of interactomes as well as previous measures incorporating expression data, and are a powerful means for understanding the dynamic roles of hubs in interactomes.
    Mesh-Begriff(e) Animals ; Cluster Analysis ; Computational Biology/methods ; Databases, Protein ; Drosophila melanogaster ; Escherichia coli ; Humans ; Protein Interaction Mapping/methods ; Protein Interaction Maps/physiology ; Proteins/chemistry ; Proteins/metabolism ; Saccharomyces cerevisiae ; Statistics, Nonparametric
    Chemische Substanzen Proteins
    Sprache Englisch
    Erscheinungsdatum 2013-10-10
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1003243
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families.

    Zhong, Yi / Walker, Sarah K / Pritykin, Yuri / Leslie, Christina S / Rudensky, Alexander Y / van der Veeken, Joris

    Nature immunology

    2021  Band 23, Heft 1, Seite(n) 122–134

    Abstract: T cell activation, a key early event in the adaptive immune response, is subject to elaborate transcriptional control. In the present study, we examined how the activities of eight major transcription factor (TF) families are integrated to shape the ... ...

    Abstract T cell activation, a key early event in the adaptive immune response, is subject to elaborate transcriptional control. In the present study, we examined how the activities of eight major transcription factor (TF) families are integrated to shape the epigenome of naive and activated CD4 and CD8 T cells. By leveraging extensive polymorphisms in evolutionarily divergent mice, we identified the 'heavy lifters' positively influencing chromatin accessibility. Members of Ets, Runx and TCF/Lef TF families occupied the vast majority of accessible chromatin regions, acting as 'housekeepers', 'universal amplifiers' and 'placeholders', respectively, at sites that maintained or gained accessibility upon T cell activation. In addition, a small subset of strongly induced immune response genes displayed a noncanonical TF recruitment pattern. Our study provides a key resource and foundation for the understanding of transcriptional and epigenetic regulation in T cells and offers a new perspective on the hierarchical interactions between critical TFs.
    Mesh-Begriff(e) Adaptive Immunity/immunology ; Animals ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Chromatin/immunology ; Epigenesis, Genetic/immunology ; Epigenome/immunology ; Gene Expression Regulation/immunology ; Lymphocyte Activation/immunology ; Male ; Mice ; Transcription Factors/immunology
    Chemische Substanzen Chromatin ; Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2021-12-22
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-021-01086-x
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel: A unified atlas of CD8 T cell dysfunctional states in cancer and infection

    Pritykin, Yuri / van der Veeken, Joris / Pine, Allison R / Zhong, Yi / Sahin, Merve / Mazutis, Linas / Pe’er, Dana / Rudensky, Alexander Y / Leslie, Christina S

    Molecular cell. 2021 June 03, v. 81, no. 11

    2021  

    Abstract: CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across experimental and ... ...

    Abstract CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across experimental and clinical settings. By carrying out a unified analysis of over 300 assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) experiments from 12 studies of CD8 T cells in cancer and infection, we defined a shared differentiation trajectory toward dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infection using single-cell ATAC (scATAC)-seq and allele-specific single-cell RNA (scRNA)-seq identified state-specific drivers and captured the emergence of similar TCF1⁺ progenitor-like populations at an early branch point, at which functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.
    Schlagwörter CD8-positive T-lymphocytes ; RNA ; chromatin ; dissection ; immunity ; neoplasms ; sequence analysis ; transcription (genetics)
    Sprache Englisch
    Erscheinungsverlauf 2021-0603
    Umfang p. 2477-2493.e10.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.03.045
    Datenquelle NAL Katalog (AGRICOLA)

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  8. Artikel ; Online: Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function.

    Konopacki, Catherine / Pritykin, Yuri / Rubtsov, Yury / Leslie, Christina S / Rudensky, Alexander Y

    Nature immunology

    2019  Band 20, Heft 2, Seite(n) 232–242

    Abstract: Regulatory T cells ( ... ...

    Abstract Regulatory T cells (T
    Mesh-Begriff(e) Animals ; Cells, Cultured ; Chromatin/metabolism ; Female ; Forkhead Transcription Factors/genetics ; Forkhead Transcription Factors/immunology ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation/immunology ; Interleukin-2/immunology ; Interleukin-2/metabolism ; Male ; Mice ; Mice, Transgenic ; Primary Cell Culture ; Repressor Proteins/genetics ; Repressor Proteins/immunology ; Repressor Proteins/metabolism ; Signal Transduction/genetics ; Signal Transduction/immunology ; T-Lymphocytes, Regulatory/immunology ; T-Lymphocytes, Regulatory/metabolism
    Chemische Substanzen Chromatin ; Forkhead Transcription Factors ; Foxp1 protein, mouse ; Foxp3 protein, mouse ; Interleukin-2 ; Repressor Proteins
    Sprache Englisch
    Erscheinungsdatum 2019-01-14
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-018-0291-z
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Universal recording of immune cell interactions in vivo.

    Nakandakari-Higa, Sandra / Walker, Sarah / Canesso, Maria C C / van der Heide, Verena / Chudnovskiy, Aleksey / Kim, Dong-Yoon / Jacobsen, Johanne T / Parsa, Roham / Bilanovic, Jana / Parigi, S Martina / Fiedorczuk, Karol / Fuchs, Elaine / Bilate, Angelina M / Pasqual, Giulia / Mucida, Daniel / Kamphorst, Alice O / Pritykin, Yuri / Victora, Gabriel D

    Nature

    2024  Band 627, Heft 8003, Seite(n) 399–406

    Abstract: Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their ... ...

    Abstract Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function
    Mesh-Begriff(e) CD8-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/immunology ; Cell Communication/immunology ; Dendritic Cells/cytology ; Dendritic Cells/immunology ; Ligands ; T-Lymphocytes, Regulatory/cytology ; T-Lymphocytes, Regulatory/immunology ; T Follicular Helper Cells/cytology ; T Follicular Helper Cells/immunology ; B-Lymphocytes/cytology ; B-Lymphocytes/immunology ; Germinal Center/cytology ; Single-Cell Gene Expression Analysis ; Epithelial Cells/cytology ; Epithelial Cells/immunology ; Intestinal Mucosa/cytology ; Intestinal Mucosa/immunology ; Lymphocytic choriomeningitis virus/immunology ; Lymphocytic Choriomeningitis/immunology ; Lymphocytic Choriomeningitis/virology ; Organ Specificity
    Chemische Substanzen Ligands
    Sprache Englisch
    Erscheinungsdatum 2024-03-06
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-024-07134-4
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Buch ; Online: On Almost Periodicity Criteria for Morphic Sequences in Some Particular Cases

    Pritykin, Yuri

    2007  

    Abstract: In some particular cases we give criteria for morphic sequences to be almost periodic (=uniformly recurrent). Namely, we deal with fixed points of non-erasing morphisms and with automatic sequences. In both cases a polynomial-time algorithm solving the ... ...

    Abstract In some particular cases we give criteria for morphic sequences to be almost periodic (=uniformly recurrent). Namely, we deal with fixed points of non-erasing morphisms and with automatic sequences. In both cases a polynomial-time algorithm solving the problem is found. A result more or less supporting the conjecture of decidability of the general problem is given.

    Comment: 9 pages. To be presented on 11th International Conference on Developments in Language Theory (DLT'2007), Turku, Finland, July 2007.
    Schlagwörter Computer Science - Discrete Mathematics ; Computer Science - Logic in Computer Science ; G.2.1 ; F.2.2 ; F.4.3
    Erscheinungsdatum 2007-04-02
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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