Explanipedia

Foxp3 M370I mutation allows the activation of T effector programs in regulatory T cells 3759 Open

Kole Tison, Joseph Gillen, Xi Chen, Yaqiang Cao, Aleksandra Nita‐Lazar , et al. · 2025

Description The transcription factor Foxp3 in mice dictates the development and function of regulatory T cells (Tregs) to maintain self-tolerance. The mutation of amino acid 370 (M to I) of FOXP3 protein was identified in IPEX patients wit…

Optimal CXCR5 expression during Tfh maturation involves the Bhlhe40-Pou2af1 axis Open

Xiaoliang Zhu, Xi Chen, Yaqiang Cao, Chengyu Liu, Zoey J Kline , et al. · 2025

The pair of transcription factors Bcl6-Blimp1 is well known for follicular T helper (Tfh) early cell fate determination; however, the mechanism(s) for late regulation of CXCR5 during Tfh migration into germinal centers (GCs) is still uncle…

CBFβ-SMMHC–driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice Open

Tao Zhen, Yaqiang Cao, Tongyi Dou, Yun Chen, Guadalupe Lopez , et al. · 2025

The leukemia fusion gene CBFB-MYH11 requires RUNX1 for leukemogenesis, but the underlying mechanism is unclear. By in vitro studies, we found that CBFβ-SMMHC, the chimeric protein encoded by CBFB-MYH11, could enhance the binding affinity b…

BLIMP1 negatively regulates IL-2 signaling in T cells Open

Suyasha Roy, Min Ren, Peng Li, Kairong Cui, Yaqiang Cao , et al. · 2025

Interleukin-2 (IL-2) regulates immune homeostasis by fine-tuning the balance between effector and regulatory T (T reg ) cells. To identify regulators of IL-2 signaling, we performed genome-wide CRISPR-knockout screening in IL-2–dependent c…

Rapid enrichment of progenitor exhausted neoantigen-specific CD8 T cells from peripheral blood Open

Mamduh Khateb, Roland Jung, Stav Leibou, Philip B. Hadley, Zhiya Yu , et al. · 2025

Neoantigen-reactive peripheral blood lymphocytes (NeoPBL) are tumor-specific T cells found at ultra-low frequencies in the blood. Unlike tumor-infiltrating lymphocytes (TIL), NeoPBL exist in a favorable less dysfunctional phenotypic state …

Three-dimensional chromatin reorganization regulates B cell development during ageing Open

Fei Ma, Yaqiang Cao, Hansen Du, Fatima Zohra Braikia, Le Zong , et al. · 2024

Optimal CXCR5 Expression during Tfh Maturation Involves the Bhlhe40-Pou2af1 Axis Open

Xiaoliang Zhu, Xi Chen, Yaqiang Cao, Chengyu Liu, Gangqing Hu , et al. · 2024

The pair of transcription factors Bcl6-Blimp1 is well-known for follicular T helper (Tfh) cell fate determination, however, the mechanism(s) for Bcl6-independent regulation of CXCR5 during Tfh migration into germinal center (GC) is still u…

Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction Open

Shuai Liu, Yaqiang Cao, Kairong Cui, Gang Ren, Tingting Zhao , et al. · 2024

Hi-TrAC detects active sub-TADs and reveals internal organizations of super-enhancers Open

Yaqiang Cao, Shuai Liu, Kairong Cui, Qingsong Tang, Keji Zhao · 2023

The spatial folding of eukaryotic genome plays a key role in genome function. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among accessible genomic regions, can detect active su…

Restraint of IFN-γ expression through a distal silencer CNS–28 for tissue homeostasis Open

Kairong Cui, Zuojia Chen, Yaqiang Cao, Shuai Liu, Gangqing Hu , et al. · 2023

Interferon-g (IFN-g) is a key cytokine in response to viral or intracellular bacterial infection in mammals. While a number of enhancers are described to promote IFN-g responses, no silencers for the Ifng gene have been identified. By exam…

Restraint of IFN-γ expression through a distal silencer CNS–28 for tissue homeostasis Open

Kairong Cui, Zuojia Chen, Yaqiang Cao, Shuai Liu, Gang Ren , et al. · 2023

Enhancer-promoter interactions are reconfigured through the formation of long-range multiway chromatin hubs as mouse ES cells exit pluripotency Open

David Lando, Xiaoyan Ma, Yaqiang Cao, Aleksandra Jartseva, Tim J. Stevens , et al. · 2023

Summary Enhancers are genomic DNA sequences that bind transcription factors, chromatin regulators and non-coding transcripts to modulate the expression of target genes. They have been found to act from different locations relative to a gen…

Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops Open

Shuai Liu, Yaqiang Cao, Kairong Cui, Qingsong Tang, Keji Zhao · 2022

Personal airborne chemical exposure and epigenetic ageing biomarkers in healthy Chinese elderly individuals: Evidence from mixture approaches Open

Wanying Shi, Xu Gao, Yaqiang Cao, Yuanyuan Chen, Qian Cui , et al. · 2022

Experimental and numerical simulation of solute transport in non-penetrating fractured clay Open

Jun Liu, Yue Su, Huan Shen, Yaqiang Cao, Wenjie Yang , et al. · 2022

A set of one-dimensional experimental device for solute transport in non-penetrating fractured clay are developed, which can study the laws of groundwater flow and solute transport under different hydraulic heads, fractured aperture, and t…

Nested epistasis enhancer networks for robust genome regulation Open

Xueqiu Lin, Yanxia Liu, Shuai Liu, Xiang Zhu, Lingling Wu , et al. · 2022

Mammalian genomes have multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, but it is unclear how these enhancers coordinate to achieve this task. We combine multiplexed CRISPRi screening with machine…

Transcription factors TCF-1 and GATA3 are key factors for the epigenetic priming of early innate lymphoid progenitors toward distinct cell fates Open

Gang Ren, Binbin Lai, Christelle Harly, Songjoon Baek, Yi Ding , et al. · 2022

Hi-TrAC reveals fractal nesting of super-enhancers Open

Yaqiang Cao, Shuai Liu, Kairong Cui, Qingsong Tang, Keji Zhao · 2022

Eukaryotic genome spatial folding plays a key role in genome function. Decoding the principles and dynamics of 3D genome organization depends on improving technologies to achieve higher resolution. Chromatin domains have been suggested as …

scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells Open

Lixia Pan, Wai Lim Ku, Qingsong Tang, Yaqiang Cao, Keji Zhao · 2022

Cell-to-cell variation in gene expression is a widespread phenomenon, which may play important roles in cellular differentiation, function, and disease development 1–9 . Chromatin is implicated in contributing to the cellular heterogeneity…

Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors Open

Shuai Liu, Yaqiang Cao, Kairong Cui, Qingsong Tang, Keji Zhao · 2022

The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory e…

Differential regulation of transcription factor T-bet induction during NK cell development and T helper-1 cell differentiation Open

Difeng Fang, Kairong Cui, Yaqiang Cao, Mingzhu Zheng, Takeshi Kawabe , et al. · 2022

cLoops2: a full-stack comprehensive analytical tool for chromatin interactions Open

Yaqiang Cao, Shuai Liu, Gang Ren, Qingsong Tang, Keji Zhao · 2021

Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for understanding the regulation of gene expression. Compared to Hi-C and its variants, the emerging 3D mapping technologies fo…

Integrated high-throughput small RNA and transcriptome sequencing unveil the shape-dependent toxicity of nano-alumina in rat astrocytes Open

Yuanyuan Chen, Dong Li, Fuchang Deng, Yaqiang Cao, Yuanzheng Fu , et al. · 2021

Background The large-scale applications of alumina nanoparticles (Al 2 O 3 -NPs), one of the most important NPs in the global market, are causing severe damages to the environment and human health. Our previous research has revealed a crit…

Integrated High-Throughput Small RNA and Transcriptome Sequencing Unveil The Shape-Dependent Toxicity of Nano-Alumina in Rat Astrocytes Open

Yuanyuan Chen, Dong Li, Fuchang Deng, Yaqiang Cao, Yuanzheng Fu , et al. · 2021

Background The large-scale applications of alumina nanoparticles (Al₂O₃-NPs), one of the most important NPs in the global market, is causing severe damages to the environment and human health. Our previous research ha…

PNMA5 Promotes Bone Metastasis of Non-small-Cell Lung Cancer as a Target of BMP2 Signaling Open

Fei Huang, Yaqiang Cao, Caihong Wang, Ruilong Lan, Bing Wu , et al. · 2021

Bone metastases frequently occur in NSCLC patients at the late stage, indicating poor survival. However, mechanisms about the initiation of NSCLC bone metastases remain largely unclear. In our previous reports, BMP2 signaling activation ha…

Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing Open

Wai Lim Ku, Lixia Pan, Yaqiang Cao, Weiwu Gao, Keji Zhao · 2021

Recently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these prob…

Differential Regulation of Transcription Factor T-Bet Induction During NK Cell Development and Th1 Cell Differentiation Open

Difeng Fang, Kairong Cui, Yaqiang Cao, Mingzhu Zheng, Takeshi Kawabe , et al. · 2021

A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association Open

Mengmeng Han, Jialun Li, Yaqiang Cao, Yuanyong Huang, Wen Li , et al. · 2020

LSH, a SNF2 family DNA helicase, is a key regulator of DNA methylation in mammals. How LSH facilitates DNA methylation is not well defined. While previous studies with mouse embryonic stem cells (mESc) and fibroblasts (MEFs) derived from L…

RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development Open

Tao Zhen, Yaqiang Cao, Gang Ren, Ling Zhao, R. Katherine Hyde , et al. · 2020

Inversion of chromosome 16 is a consistent finding in patients with acute myeloid leukemia subtype M4 with eosinophilia, which generates a CBFB-MYH11 fusion gene. It is generally considered that CBFβ-SMMHC, the fusion protein encoded by CB…

Altered 3D chromatin structure permits inversional recombination at the <i>IgH</i> locus Open

Xiang Qiu, Fei Ma, Mingming Zhao, Yaqiang Cao, Lillian Shipp , et al. · 2020

Different mechanisms govern the first and second steps of IgH gene recombination.

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