Affinage

XCL1

Lymphotactin · UniProt P47992

Length
114 aa
Mass
12.5 kDa
Annotated
2026-06-11
100 papers in source corpus 16 papers cited in narrative 15 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 4/5 claims corpus-supported (80%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

XCL1 is a metamorphic chemokine that reversibly interconverts between a canonical α-β chemokine fold, which engages its GPCR XCR1 to drive directed cell migration, and an alternate β-sheet dimer fold that binds glycosaminoglycans and remodels microbial membranes, a behavior enabled by its lack of a disulfide bond conserved in other chemokines (PMID:32243126, PMID:39840812). In the chemokine fold, the extreme N-terminal residues Val1-Glu4 contribute the bulk of XCR1 binding energy, with Glu4 of XCL1 contacting Tyr117/Arg273 of XCR1 to trigger IP3 accumulation, calcium release, and chemotaxis (PMID:31481523). The β-sheet dimer binds heparan sulfate via basic residues Arg23 and Arg43 in a length- and sulfation-dependent manner, and selectively induces negative Gaussian curvature in bacterial and fungal membranes to confer antimicrobial activity (PMID:32243126, PMID:26836755). Functionally, XCL1 selectively recruits XCR1+ cDC1 dendritic cells: it is produced by CD8+ T cells, γδ T cells, and other sources to drive cDC1-dependent CTL priming, tissue-resident memory T cell formation and positioning, and tolerogenic DC migration that establishes oral tolerance (PMID:31666238, PMID:30755656, PMID:31578268, PMID:39841133, PMID:38346928). Beyond immune cell positioning, XCL1-XCR1 signaling promotes trophoblast invasion and epithelial-mesenchymal transition through PI3K/AKT, MEK/ERK, and HIF-1α pathways (PMID:29856101, PMID:33374849), drives osteoclastogenesis (PMID:32849609), and acts in the spinal cord—via both XCR1 and a second receptor, ITGA9—to enhance nociceptive transmission in neuropathic pain (PMID:27387353, PMID:36618360).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1996 Medium

    Establishing that XCL1 (SCM-1alpha/lymphotactin) is an inducible, immune-expressed gene defined the molecular identity and chromosomal context of the chemokine before its receptor and mechanism were known.

    Evidence Gene cloning, sequencing, chromosomal mapping, and mitogenic induction in PBMCs

    PMID:8849694

    Open questions at the time
    • No receptor or signaling mechanism defined
    • Functional role of the L7a pseudogene in intron 1 unresolved
  2. 2016 High

    Identifying that the XCL1 dimer binds glycosaminoglycans through Arg23/Arg43 distinguished a GAG-binding surface separable from receptor activation and linked it to gp120/HIV-1 inhibition.

    Evidence Site-directed mutagenesis of XCL1 dimer variant, heparin chromatography, SPR, and fluorescence polarization with HS oligosaccharides

    PMID:26836755

    Open questions at the time
    • In vivo relevance of GAG binding to immune positioning not tested
    • Relationship between GAG binding and the metamorphic fold equilibrium not directly resolved here
  3. 2016 Medium

    Demonstrating that spinal XCL1/XCR1 are upregulated and that XCL1 enhances nociception extended XCL1 function beyond classical immune chemotaxis into pain neurotransmission.

    Evidence Streptozotocin diabetic neuropathy model, intrathecal recombinant XCL1 and neutralizing antibody, behavioral testing, and primary microglial cultures

    PMID:27387353

    Open questions at the time
    • Whether the neuronal effect is direct via XCR1 on neurons was not fully resolved
    • A second receptor was not yet considered
  4. 2018 Medium

    Placing XCL1-XCR1 upstream of MMP activity and PI3K/AKT, MEK, and JNK signaling showed the axis can drive cellular invasion in a non-immune (trophoblast) context.

    Evidence Transwell invasion and wound healing with recombinant XCL1, gelatin zymography, and pathway inhibitor experiments

    PMID:29856101

    Open questions at the time
    • Direct receptor dependence not tested by XCR1 knockdown
    • In vivo placental requirement unestablished
  5. 2019 High

    Mapping the XCL1 N-terminus (Val1-Glu4) as the major XCR1 binding determinant and defining Glu4–Tyr117/Arg273 contacts resolved how the chemokine fold activates its GPCR at residue resolution.

    Evidence Rosetta homology modeling with ligand and receptor mutagenesis, IP3, calcium, and migration assays

    PMID:31481523

    Open questions at the time
    • No experimental high-resolution XCL1-XCR1 complex structure
    • Conformational state of XCL1 during receptor engagement not directly visualized
  6. 2019 Medium

    Showing that XCL1 fusion vaccines and γδ T cell-derived XCL1 selectively target XCR1+ cDC1s established the axis as a tunable route for CTL priming and tolerogenic DC migration.

    Evidence In vitro DC chemoattraction and IL-12 assays, in vivo fusion vaccine immunization, TCRδ−/− knockout, DC depletion, and EAE/influenza functional readouts

    PMID:30755656 PMID:31578268 PMID:31666238

    Open questions at the time
    • Molecular basis of cDC1 selectivity beyond XCR1 expression not dissected
    • Quantitative contribution of different XCL1 cellular sources unresolved
  7. 2020 High

    Defining XCL1 as a metamorphic protein whose β-sheet and unfolded forms induce negative Gaussian curvature revealed a structurally distinct, receptor-independent antimicrobial function.

    Evidence SAXS of XCL1 structural variants against defined membranes and in vitro anti-Candida assay

    PMID:32243126

    Open questions at the time
    • In vivo antimicrobial relevance not demonstrated
    • Regulation of the fold equilibrium in tissue not defined
  8. 2020 Medium

    Placing XCL1-XCR1 on the ERK/HIF-1α/EMT axis and showing osteoclastogenic activity broadened the signaling outputs of the chemokine into tumor cell migration and bone resorption.

    Evidence XCR1 siRNA knockdown and MEK1/2 inhibition in breast cancer lines; in vitro and in vivo osteoclast/calvarial models with neutralizing antibody

    PMID:32849609 PMID:33374849

    Open questions at the time
    • Direct versus indirect cellular targets in bone not fully separated
    • Tumor-intrinsic XCR1 signaling not validated in vivo
  9. 2022 Medium

    Identifying ITGA9 as a second functional XCL1 receptor in the spinal cord, more effective than XCR1 in driving hypersensitivity, redefined XCL1 nociceptive signaling as a two-receptor system.

    Evidence CCI neuropathic pain model with XCR1 antagonist (vMIP-II) and ITGA9-neutralizing antibody (YA4), behavioral tests, and analgesic potentiation experiments

    PMID:36618360

    Open questions at the time
    • Direct XCL1-ITGA9 binding interface not mapped
    • Whether ITGA9 signaling operates outside the nervous system unknown
  10. 2025 High

    Genetic loss- and gain-of-function established XCL1 as a non-cell-autonomous cue that, via cDC1s, controls tissue-resident memory T cell formation and spatial positioning during infection and in tumors.

    Evidence Xcl1-deficient mice, targeted spatial transcriptomics, adoptive transfer with enforced Xcl1, and tumor survival experiments

    PMID:39841133

    Open questions at the time
    • Spatial cues integrating XCL1 with other positioning signals not fully defined
    • Human translation of TRM positioning role untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the metamorphic fold equilibrium is regulated in vivo to partition XCL1 between XCR1/ITGA9 receptor signaling, GAG binding, and antimicrobial membrane activity remains unresolved.
  • No in vivo measurement of fold state coupled to function
  • Triggers and tissue determinants of fold switching unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0048018 receptor ligand activity 3 GO:0008289 lipid binding 2 GO:0060089 molecular transducer activity 2 GO:0090729 toxin activity 1
Localization
GO:0005576 extracellular region 4
Pathway
R-HSA-168256 Immune System 4 R-HSA-162582 Signal Transduction 3 R-HSA-1500931 Cell-Cell communication 2
Partners
ITGA9XCR1

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2019 The extreme N-terminal residues of XCL1 (Val1, Gly2, Ser3, Glu4) contribute a large fraction of binding energy to XCR1, while residues near the disulfide-bond-forming Cys11 modulate XCR1 activation. Alterations in the XCL1 N-terminus changed XCR1 activation as measured by IP3 accumulation, intracellular calcium release, and directed cell migration. Computational modeling combined with mutagenesis identified Glu4 of XCL1 and Tyr117/Arg273 of XCR1 as key functional contacts; mutation of Tyr117 and Arg273 diminished XCR1 binding and activation. Structure-function mutagenesis combined with Rosetta homology modeling; IP3 accumulation assay, intracellular calcium release assay, directed cell migration assay, receptor mutagenesis Science signaling High 31481523
2020 XCL1 is a metamorphic protein that interconverts between its canonical α-β chemokine fold (which binds GPCR XCR1 and controls cell migration) and a β-sheet dimer fold. Only the β-sheet and unfolded XCL1 structures induce negative Gaussian curvature (NGC) in membranes—the topology required for membrane permeation—as determined by SAXS. The β-sheet structure selectively remodels bacterial and fungal (but not mammalian) model membranes, and XCL1 exhibits anti-Candida activity in vitro. Small angle X-ray scattering (SAXS) of XCL1 structural variants with defined membrane compositions; in vitro anti-Candida activity assay ACS infectious diseases High 32243126
2016 The XCL1 dimer (XCL1dim) binds glycosaminoglycans (GAGs) via basic residues Arg23 and Arg43; mutation of these residues greatly diminished heparin binding in heparin Sepharose chromatography and surface plasmon resonance. The GAG binding affinity correlates with the length and sulfation level of heparan sulfate oligosaccharides. This GAG-binding surface on XCL1dim also includes residues important for HIV-1 inhibition through gp120 interaction. Site-directed mutagenesis of XCL1 dimer variant (W55D); heparin Sepharose chromatography; surface plasmon resonance; solution fluorescence polarization assay with heparan sulfate oligosaccharides of varying length/sulfation Biochemistry High 26836755
1996 There are two highly homologous SCM-1/lymphotactin (XCL1) genes, designated SCM-1alpha (XCL1) and SCM-1beta (XCL2), both with three exons and two introns, both mapped to human chromosome 1q23. Both genes are similarly induced in peripheral blood mononuclear cells by mitogenic stimulation. The two mature proteins differ at amino acid positions 7 and 8. SCM-1alpha's first intron contains a pseudogene of ribosomal large subunit L7a; SCM-1beta has a 1.5-kb deletion in that intron. Gene cloning and sequencing; chromosomal mapping; primer extension and RNase protection for transcription start sites; mitogenic stimulation of PBMCs FEBS letters Medium 8849694
2019 XCL1 fusion vaccines specifically target XCR1+ cDC1s (CD8α+ DCs in mice; CD141+ DCs in humans) and promote their IL-12 production. After subcutaneous injection, XCL1-fused antigen (GPC3) was predominantly detected in CD8α+ DCs of draining lymph nodes. XCL1-GPC3 targeted DCs enhanced antigen-specific CD8+ T cell proliferation and induced de novo GPC3-specific CD8+ T cells. Intradermal but not intramuscular delivery of Xcl1-HA fusion vaccine maintained Th1-polarized responses and induced higher IFNγ-secreting T cells compared to Ccl3-HA; Xcl1-HA conferred superior protection against influenza infection after intradermal immunization. In vitro DC chemoattraction assay; IL-12 production assay; in vivo plasmid immunization; flow cytometry for DC and T cell phenotyping; in vivo cytotoxicity assay; viral challenge protection assay Cancer immunology research / Scientific reports Medium 30755656 31666238
2019 XCL1 secreted by small intestine lamina propria γδ T cells (upon oral anti-CD3 administration) induces tolerogenic XCR1+ DC migration to the mesenteric lymph node, where Treg cells are induced and oral tolerance is established. TCRδ−/− mice failed to develop oral tolerance upon oral anti-CD3, and this tolerance mechanism is distinct from that induced by fed antigens. Genetic knockout models (TCRδ−/− mice); DC depletion experiments; in vivo oral anti-CD3 administration; flow cytometry for Treg cell quantification; EAE model for functional validation Journal of immunology Medium 31578268
2018 The XCL1-XCR1 pathway promotes trophoblast invasion by increasing MMP-9 and MMP-2 activity (including the MMP-2/TIMP-2 complex) via the PI3K/AKT, MEK, and JNK signaling pathways. XCL1 and XCR1 are expressed at higher levels in first-trimester than in term placenta. Wound healing assay; Transwell invasion assay with recombinant XCL1; qRT-PCR; gelatin zymography for MMP activity; PI3K, MEK, and JNK pathway inhibitor experiments American journal of reproductive immunology Medium 29856101
2020 XCL1 treatment of MDA-MB-231 and SK-BR-3 breast cancer cells enhanced cell migration and EMT (E-cadherin downregulation, N-cadherin and vimentin upregulation, β-catenin nuclear translocation) via XCR1-mediated activation of the ERK/HIF-1α pathway. Knockdown of XCR1 by siRNA negated XCL1 effects. MEK1/2 inhibitor U0126 blocked XCL1-induced HIF-1α accumulation and cell migration. Cell migration assay; Western blot for EMT markers and signaling proteins; siRNA knockdown of XCR1; pharmacological inhibition of MEK1/2 with U0126 International journal of molecular sciences Medium 33374849
2020 XCL1 promotes osteoclastogenesis and bone-resorbing activity: recombinant XCL1 added to RANKL-stimulated human monocytes promoted osteoclast differentiation and resorbing activity. XCL1 also promoted expression of inflammatory and osteoclastogenic factors (IL-6, IL-8, RANKL) in human osteoblasts. In vivo, injection of recombinant XCL1 onto murine calvaria worsened osteolytic lesions, while XCL1-neutralizing antibody significantly reduced bone erosion and osteoclast numbers induced by UHMWPE particles. In vitro osteoclast differentiation assay from human monocytes + RANKL; in vivo murine calvarial osteolysis model with XCL1 injection and neutralizing antibody; Western blot; ELISA for cytokines Frontiers in immunology Medium 32849609
2016 In a mouse model of streptozotocin-induced diabetic neuropathy, spinal XCL1 and XCR1 levels are upregulated. Intrathecal injection of XCL1 in naïve mice enhanced nociceptive transmission; injection of XCL1-neutralizing antibody diminished allodynia/hyperalgesia in diabetic mice. XCR1 is co-expressed with spinal neurons. Microglia activation in primary cultures led to enhanced XCL1 release and XCR1 expression. Streptozotocin mouse model; intrathecal injection of recombinant XCL1 and neutralizing antibody; von Frey and cold plate behavioral tests; Western blot; immunofluorescence; primary microglial cell cultures Anesthesiology Medium 27387353
2022 In neuropathic pain (CCI model), XCL1 is released by spinal cord astroglial cells despite neural localization of its two receptors, XCR1 and ITGA9. Blockade/neutralization of both XCR1 (with vMIP-II) and ITGA9 (with YA4 antibody) reversed hypersensitivity after intrathecal XCL1 in naïve mice, with ITGA9 neutralization more effective. Neutralization of ITGA9 enhanced both buprenorphine and morphine analgesia; XCR1 blockade improved buprenorphine effectiveness. CCI neuropathic pain mouse model; intrathecal injection of antagonists (vMIP-II for XCR1) and neutralizing antibodies (YA4 for ITGA9); von Frey and cold plate tests; RT-qPCR; Western blot; ELISA; immunofluorescence Frontiers in immunology Medium 36618360
2025 The CD8+ T cell-derived chemokine XCL1 is critical for tissue-resident memory T cell (TRM) formation and supports positioning of intestinal CD8+ T cells during acute viral infection via XCR1+ cDC1s. In tumors, enforced Xcl1 expression by antigen-specific CD8+ T cells promoted intratumoral cDC1 accumulation and T cell persistence, improving overall survival. XCL1 acts non-cell autonomously to guide intestinal CD8+ TRM spatial differentiation. Murine genetic models (Xcl1-deficient); targeted spatial transcriptomics; adoptive transfer with enforced Xcl1 expression; tumor survival experiments The Journal of experimental medicine High 39841133
2024 Intratumoral delivery of a highly active locked-disulfide form of XCL1 (mXCL1-V21C/A59C) via hydrophilic gel patch increased cDC1 accumulation in tumor masses and promoted their migration to regional lymph nodes, resulting in enhanced tumor-specific CTL induction. Tumor-infiltrating cDC1s produced CXCL9 (a CXCR3 ligand for CTLs/NK cells), and anti-CXCL9 treatment decreased CTL tumor infiltration. The approach reduced tumor growth and prolonged survival in two murine tumor models and was enhanced by anti-PD-1 combination. In vivo tumor models (E.G7-OVA, B16-F10); hydrophilic gel patch delivery of engineered XCL1; flow cytometry for immune cell phenotyping; anti-CXCL9 depletion experiment; tumor growth and survival measurement International journal of cancer Medium 38346928
2025 XCL1 interconverts between two distinct native structures: a chemokine fold with high affinity for GPCR XCR1 (mediating cell migration and immune signaling) and an alternate fold that binds GAGs and exhibits antimicrobial activity. This metamorphic behavior is enabled by the absence of a conserved disulfide bond present in all other chemokines. Review of structure-function data (citing prior NMR, SAXS, mutagenesis, and functional studies) Protein science Medium 39840812
2021 XCL1 overexpression in high-glucose-treated human renal glomerular endothelial cells promoted apoptosis and inflammatory response (IL-1β, TNF-α upregulation), and these effects were associated with upregulation of p53 and NF-κB pathway changes. p53 silencing (with pifithrin-α) blocked apoptosis and inflammation in XCL1-overexpressed HG-treated cells; pifithrin-α also reversed XCL1-induced NF-κB downregulation. Cell viability assay (CCK-8); flow cytometry for apoptosis; ELISA and Western blot for inflammatory cytokines and p53/NF-κB; XCL1 overexpression vector; p53 inhibitor pifithrin-α; in vivo db/db diabetic mouse model Nephron Low 34518457

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Current protocols in molecular biology 2528 25559105
2017 An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 1884 28846090
2022 Chromatin accessibility profiling by ATAC-seq. Nature protocols 394 35478247
2020 From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. Genome biology 319 32014034
2021 Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature communications 304 33637727
2020 Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell stem cell 242 33352111
2018 Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement. Nature communications 171 30451828
2011 XCL1 and XCR1 in the immune system. Microbes and infection 153 22100876
2019 SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature communications 145 31594952
2012 ATAC-king the complexity of SAGA during evolution. Genes & development 145 22426530
2020 ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Science advances 141 32440553
2022 scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning. Nature biotechnology 112 35058621
2018 Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine 111 29686426
2020 Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. Computational and structural biotechnology journal 108 32637041
2021 Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nature communications 95 34489465
2022 A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data. Genome biology 68 35022082
2020 Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq. Molecular biomedicine 63 34765994
2020 ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions. Molecular cell 60 31999955
2019 Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas 58 31427911
1996 Structure and expression of two highly related genes encoding SCM-1/human lymphotactin. FEBS letters 57 8849694
2021 Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs. Frontiers in nutrition 53 34660666
2023 Modeling fragment counts improves single-cell ATAC-seq analysis. Nature methods 52 38049697
2022 Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads. eLife 52 35195064
2021 Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nature biotechnology 52 34675424
2023 Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nature protocols 51 36792778
2021 A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. Nature protocols 51 34282334
2022 ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Genome research 49 35858748
2019 Classifying cells with Scasat, a single-cell ATAC-seq analysis tool. Nucleic acids research 45 30335168
2023 Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. Genome biology 44 37875977
2018 Genome-wide analysis of chromatin accessibility using ATAC-seq. Methods in cell biology 43 30948010
2016 Microglial Inhibition Influences XCL1/XCR1 Expression and Causes Analgesic Effects in a Mouse Model of Diabetic Neuropathy. Anesthesiology 43 27387353
2023 Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC biology 40 36726129
2023 Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature biotechnology 38 37537502
2019 XCL1/Glypican-3 Fusion Gene Immunization Generates Potent Antitumor Cellular Immunity and Enhances Anti-PD-1 Efficacy. Cancer immunology research 37 31666238
2017 Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Scientific reports 37 28550296
2020 Single-cell ATAC-seq signal extraction and enhancement with SCATE. Genome biology 36 32620137
2023 Cellcano: supervised cell type identification for single cell ATAC-seq data. Nature communications 35 37012226
2022 Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs. Frontiers in nutrition 35 36276837
2021 CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis. Genomics, proteomics & bioinformatics 32 34284136
2019 methyl-ATAC-seq measures DNA methylation at accessible chromatin. Genome research 31 31160376
2019 Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic acids research 31 31584093
2023 ATAC-clock: An aging clock based on chromatin accessibility. GeroScience 29 37924441
2019 Dendritic cell targeted Ccl3- and Xcl1-fusion DNA vaccines differ in induced immune responses and optimal delivery site. Scientific reports 27 30755656
2023 maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 26 36719906
2023 Integrated analysis of ATAC-seq and RNA-seq unveils the role of ferroptosis in PM2.5-induced asthma exacerbation. International immunopharmacology 25 37976599
2023 scBridge embraces cell heterogeneity in single-cell RNA-seq and ATAC-seq data integration. Nature communications 24 37770437
2020 Involvement of the ERK/HIF-1α/EMT Pathway in XCL1-Induced Migration of MDA-MB-231 and SK-BR-3 Breast Cancer Cells. International journal of molecular sciences 24 33374849
2023 Integrated ATAC-Seq and RNA-Seq Data Analysis to Reveal OsbZIP14 Function in Rice in Response to Heat Stress. International journal of molecular sciences 23 36982696
2024 Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data. Briefings in bioinformatics 22 38493343
2024 scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome biology 22 38589969
2020 Blockade of XCL1/Lymphotactin Ameliorates Severity of Periprosthetic Osteolysis Triggered by Polyethylene-Particles. Frontiers in immunology 22 32849609
2019 ATAC-pipe: general analysis of genome-wide chromatin accessibility. Briefings in bioinformatics 22 29982337
2024 Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit. Plant communications 21 38794796
2023 ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Cell reports 21 37682711
2022 Single-Cell RNA and ATAC Sequencing Reveal Hemodialysis-Related Immune Dysregulation of Circulating Immune Cell Subpopulations. Frontiers in immunology 21 35720370
2021 Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages. Blood advances 21 34170284
2019 Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1. Science signaling 21 31481523
2019 γδ T Cell-Secreted XCL1 Mediates Anti-CD3-Induced Oral Tolerance. Journal of immunology (Baltimore, Md. : 1950) 21 31578268
2025 Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature protocols 20 40119005
2024 Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nature genetics 20 38361031
2020 Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq. ACS synthetic biology 20 32786350
2018 XCL1-XCR1 pathway promotes trophoblast invasion at maternal-fetal interface by inducing MMP-2/MMP-9 activity. American journal of reproductive immunology (New York, N.Y. : 1989) 20 29856101
2018 Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity. Methods in cell biology 20 30948003
2022 New insights into the analgesic properties of the XCL1/XCR1 and XCL1/ITGA9 axes modulation under neuropathic pain conditions - evidence from animal studies. Frontiers in immunology 19 36618360
2024 Inflammatory response in traumatic brain and spinal cord injury: The role of XCL1-XCR1 axis and T cells. CNS neuroscience & therapeutics 18 38887195
2020 A functional variant near XCL1 gene improves breast cancer survival via promoting cancer immunity. International journal of cancer 18 31904872
2016 Examination of Glycosaminoglycan Binding Sites on the XCL1 Dimer. Biochemistry 18 26836755
2024 txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. Genome biology 17 38519979
2021 Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. Nature protocols 17 34663963
2023 Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data. Oncogenesis 16 37217468
2020 Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1. ACS infectious diseases 15 32243126
2020 Traumatic brain injury in mice induces changes in the expression of the XCL1/XCR1 and XCL1/ITGA9 axes. Pharmacological reports : PR 15 33185818
2024 Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace. Nature methods 14 38724693
2022 Application of ATAC-seq in tumor-specific T cell exhaustion. Cancer gene therapy 14 35794339
2020 Analytical Approaches for ATAC-seq Data Analysis. Current protocols in human genetics 14 32543102
2023 Integration of ATAC-Seq and RNA-Seq identifies key genes and pathways involved in the neuroprotection of S-adenosylmethionine against perioperative neurocognitive disorder. Computational and structural biotechnology journal 13 36942104
2020 Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq. Journal of visualized experiments : JoVE 13 32925882
2025 The XCL1-XCR1 axis supports intestinal tissue residency and antitumor immunity. The Journal of experimental medicine 12 39841133
2023 ATAC-seq and RNA-seq analysis unravel the mechanism of sex differentiation and infertility in sex reversal chicken. Epigenetics & chromatin 12 36617567
2023 Integrated analysis of ATAC-seq and RNA-seq reveals the transcriptional regulation network in SLE. International immunopharmacology 12 36738683
2023 Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit. Frontiers in plant science 12 36968400
2023 An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs. International journal of molecular sciences 12 37834260
2022 Mapping open chromatin by ATAC-seq in bread wheat. Frontiers in plant science 12 36466281
2021 Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing. Biology 12 34198745
2024 Intratumoral delivery of a highly active form of XCL1 enhances antitumor CTL responses through recruitment of CXCL9-expressing conventional type-1 dendritic cells. International journal of cancer 11 38346928
2023 Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors. BMC genomics 11 37173651
2022 Fundamental and practical approaches for single-cell ATAC-seq analysis. aBIOTECH 11 36313930
2021 Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq. Nucleic acids research 11 34313779
2024 Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls. Nature communications 10 38697975
2024 Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. Briefings in bioinformatics 10 39082647
2024 KAT tales: Functions of Gcn5 and PCAF lysine acetyltransferases in SAGA and ATAC. The Journal of biological chemistry 10 39222683
2023 Integrative single-cell RNA and ATAC sequencing reveals that the FOXO1-PRDX2-TNF axis regulates tendinopathy. Frontiers in immunology 10 37223090
2023 ATACAmp: a tool for detecting ecDNA/HSRs from bulk and single-cell ATAC-seq data. BMC genomics 10 37950200
2021 XCL1 Aggravates Diabetic Nephropathy-Mediated Renal Glomerular Endothelial Cell Apoptosis and Inflammatory Response via Regulating p53/Nuclear Factor-Kappa B Pathway. Nephron 10 34518457
2025 The multifaceted role of XCL1 in health and disease. Protein science : a publication of the Protein Society 9 39840812
2023 Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. Methods in molecular biology (Clifton, N.J.) 9 36807060
2023 RNA- and ATAC-sequencing Reveals a Unique CD83+ Microglial Population Focally Depleted in Parkinson's Disease. bioRxiv : the preprint server for biology 9 37292857
2022 Immunogenicity of the Xcl1-SARS-CoV-2 Spike Fusion DNA Vaccine for COVID-19. Vaccines 9 35335039
2025 STAT3 Facilitates Super Enhancer Formation to Promote Fibroblast-To-Myofibroblast Differentiation by the Analysis of ATAC-Seq, RNA-Seq and ChIP-Seq. Journal of cellular and molecular medicine 8 40464702
2022 RNA-seq and ATAC-seq analysis of CD163+ macrophage-induced progestin-insensitive endometrial cancer cells. Cancer medicine 8 36373483

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