Article
Biochemical Research Methods
Alberto Zenere, Olof Rundquist, Mika Gustafsson, Claudio Altafini
Summary: This article explores novel aspects of using paired RNA-seq and ATAC-seq data to investigate causal relationships between transcription factors, chromatin, and target genes. Results show a strong connection between selected regulatory motifs and structural balance in sample correlation graphs, suggesting that internal consistency is a necessary condition for satisfying causality rules in 3-node regulatory motifs.
Article
Immunology
Chenshen Huang, Na Zhang, Hao Xiong, Ning Wang, Zhizhong Chen, Zhizhan Ni, Xiaohong Liu, Boxu Lin, Bujun Ge, Bing Du, Qi Huang
Summary: This study aims to explore a novel method for transcriptional regulation and proposes a new pipeline for analyzing the role of GPRC5B in COAD. By using RNA-seq, ATAC-seq, and ChIP-seq, researchers found the correlation between GPRC5B and macrophages and identified TF GATA4 as a key upstream factor.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Polymer Science
Kuixia Xie, Jingrun Yang, Qianqian Yao, Yang Xu, Yonglin Peng, Xinhua Liu
Summary: This study investigated the dynamic changes of chromatin accessibility and the transcriptome in dermal fibroblasts (DFs) during keloid formation. The results showed extensive alterations in chromatin accessibility and transcriptome in keloid DFs compared to normal samples. In addition, the downregulation of BRCA1 in keloid DFs was found to be closely associated with changes in gene expression, which may contribute to the formation of keloids.
Article
Biotechnology & Applied Microbiology
Aileen R. Ferraro, Abigail J. Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Summary: Regulation of chromatin accessibility and transcription are coordinated processes. This study characterizes accessible chromatin regions in Neurospora crassa, revealing molecular features and histone modifications associated with accessibility and inaccessibility. H3K27 acetylation is the most predictive histone modification for open chromatin in N. crassa, while H3K36 methylation is a key marker of inaccessible chromatin.
Article
Biochemistry & Molecular Biology
Zhilong Zhang, Yongfeng Zhang, Qi Bao, Yarong Gu, Chunnian Liang, Min Chu, Xian Guo, Pengjia Bao, Ping Yan
Summary: This study investigated the dynamic changes in chromatin accessibility during yak adipocyte differentiation using ATAC-seq. The results revealed the unique characteristics of open chromatin and identified the involvement of key pathways and transcription factors in regulating adipogenesis. This study provides valuable insights into the transcriptional regulatory mechanisms of adipogenesis and the adaptation of plateau species to high-altitude environments through fat metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Hao Zhang, Michael E. Rice, Joseph W. Alvin, Dominique Farrera-Gaffney, James J. Galligan, Michael D. L. Johnson, Darren A. Cusanovich
Summary: In this study, the effects of different protocol choices on ATAC-seq data quality were evaluated. Several different ATAC-seq components were tested, including reaction buffers, reaction temperatures, enzyme sources, and the use of native or fixed nuclei. The results showed that temperature and fixation had a major impact on data quality metrics. Additionally, the choice of protocol components could bias the functional class of profiled elements. The study recommends evaluating multiple metrics and formulations in new experiments.
Article
Biotechnology & Applied Microbiology
Trevor F. Freeman, Qiuxia Zhao, Agustian Surya, Reed Rothe, Elif Sarinay Cenik
Summary: This study investigates the impact of depleting the ribosome biogenesis components RPOA-2 and GRWD-1 on chromatin accessibility using ATAC-seq. The results show similar changes in chromatin accessibility for both perturbations, but a weak correlation with gene expression.
Article
Nutrition & Dietetics
Zhong Xu, Junjing Wu, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Nanqi Chen, Favour Oluwapelumi Oyelami, Xianwen Peng, Shuqi Mei
Summary: This study used ATAC-seq and RNA-seq analysis to examine the accessible chromatin and gene expression in Xidu black pigs, identifying key genes and regulatory pathways associated with meat quality and fat deposition.
FRONTIERS IN NUTRITION
(2022)
Article
Multidisciplinary Sciences
Parashar Dhapola, Johan Rodhe, Rasmus Olofzon, Thomas Bonald, Eva Erlandsson, Shamit Soneji, Goran Karlsson
Summary: Scarf is a modularly designed Python package that enables memory-efficient single-cell analysis and can run on low-cost devices. It provides efficient implementations for memory and computation and supports accurate reference-anchored mapping and subsampling of large single-cell datasets.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang, Jia-Wei Wang
Summary: In this study, we introduce FindIT2, a software package that can process and analyze multi-omics data to infer influential transcription factors using ChIP-seq/ATAC-seq datasets. The package annotates ChIP-seq/ATAC-seq peaks, identifies transcription factor targets by combining ChIP-seq and RNA-seq data, and supports inference of influential transcription factors based on different types of data input. Moreover, FindIT2 is compatible with any species with genomic annotations, making it particularly useful for less well-studied non-model species.
Article
Endocrinology & Metabolism
Sangyong Lee, Myoung Jun Kim, Seor I. Ahn, Sung Kyung Choi, Keun Young Min, Wahn Soo Choi, Jueng Soo You
Summary: Recently improved techniques were used to analyze the genome-wide chromatin accessibility during the differentiation of murine osteoclasts (OCs). The study found that global chromatin accessibility decreased, especially early in OC differentiation, and restoration of reduced accessibility through acetate treatment suppressed OC differentiation.
Article
Biochemistry & Molecular Biology
Shicong Wang, Jieqiang He, Mengting Deng, Caixia Wang, Ruifeng Wang, Jinjiao Yan, Minrong Luo, Fengwang Ma, Qingmei Guan, Jidi Xu
Summary: Drought resistance in plants is influenced by multiple signaling pathways and epigenetic modifications, with changes in chromatin accessibility playing an important role in abiotic stress. Analysis in apples under drought conditions revealed 23,466 upregulated peaks and 2447 downregulated peaks in chromatin accessibility. Drought-induced chromatin accessibility changes genes enriched in metabolism, stimulus, and binding pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Sitong Liu, Rui Wei, Hongyang Liu, Ruiqi Liu, Pengxiao Li, Xiaoyu Zhang, Wei Wei, Xiaodong Zhao, Xiaomeng Li, Yang Yang, Xueqi Fu, Kang Zou
Summary: This study demonstrates the connection between p53 and pluripotency-associated factors in the transformation of SSCs, with SMAD3 identified as a key factor. However, an unknown event is required to activate SMAD3, serving as a prerequisite for SSCs reprogramming in long-term culture.
CELL PROLIFERATION
(2022)
Article
Developmental Biology
Jennifer Shannon, Aishwarya Sundaresan, Orhan Bukulmez, Zexu Jiao, Kaitlin Doody, Sarah Capelouto, Bruce Carr, Laura A. Banaszynski
Summary: Understanding how gene regulatory elements influence ovarian follicle development is crucial for addressing issues such as decreased fertility with age and short-term graft function after ovarian tissue cryopreservation. The ATAC-seq technique can identify regulatory elements important for gene regulation and fertility, but challenges remain in obtaining data from frozen samples.
MOLECULAR HUMAN REPRODUCTION
(2022)
Article
Oncology
Yin-Cheng Huang, Joseph Chieh-Yu Lai, Pei-Hua Peng, Kuo-Chen Wei, Kou-Juey Wu
Summary: This study identified GSTM1 as a significant prognostic marker for predicting survival in GBM patients using ATAC-seq and RNA-seq methods. Knockdown of GSTM1 led to decreased cell viability, cell cycle arrest, and reduced levels of phosphorylated NF-kB p65 and STAT3. Analysis of chromatin accessibility in patient samples could provide an independent biomarker for predicting patient survival.
CLINICAL EPIGENETICS
(2021)
Article
Biochemistry & Molecular Biology
Hyung Joo Lee, Yiran Hou, Ju Heon Maeng, Nakul M. Shah, Yujie Chen, Heather A. Lawson, Hongbo Yang, Feng Yue, Ting Wang
Summary: This study systematically investigates the epigenomic and transcriptomic profile of transposable elements (TEs) in zebrafish tissues. The results show that TEs significantly contribute to gene regulation in zebrafish, with a portion of TEs being in active regulatory states. Specific TE subfamilies are found to be enriched in different tissues, and TE-derived transcriptional units are expressed across tissues.
Article
Immunology
Vincent Peng, Xiaoyun Xing, Jennifer K. Bando, Tihana Trsan, Blanda Di Luccia, Patrick L. Collins, Daofeng Li, Wei-Le Wang, Hyung Joo Lee, Eugene M. Oltz, Ting Wang, Marco Colonna
Summary: This study characterizes the whole-genome distribution of DNA methylation and hydroxymethylation in innate lymphocytes. It identifies differentially methylated and hydroxymethylated regions between NK cells, ILC2s, and ILC3s and correlates them with transcriptional signatures. The study also reveals unique patterns of DNA methylation/hydroxymethylation in relation to open chromatin regions, histone modifications, and TF-binding sites.
Article
Biochemistry & Molecular Biology
Daofeng Li, Deepak Purushotham, Jessica K. Harrison, Silas Hsu, Xiaoyu Zhuo, Changxu Fan, Shane Liu, Vincent Xu, Samuel Chen, Jason Xu, Shinyi Ouyang, Angela S. Wu, Ting Wang
Summary: WashU Epigenome Browser is a web-based tool for exploring, visualizing, and analyzing genomic data. It has a renovated user interface and functions that allow users to interact with data of different dimensions in a single web page. The browser supports displaying three-dimensional chromatin structures and animated time-series data, as well as viewing imaging data from microscopy experiments. In addition to software development, the browser serves and expands data hubs for large consortia.
NUCLEIC ACIDS RESEARCH
(2022)
Letter
Biochemical Research Methods
Daofeng Li, Jessica K. Harrison, Deepak Purushotham, Ting Wang
Article
Cell Biology
Mithila Sawant, Kiran Mahajan, Arun Renganathan, Cody Weimholt, Jingqin Luo, Vandna Kukshal, Joseph M. Jez, Myung Sik Jeon, Bo Zhang, Tiandao Li, Bin Fang, Yunting Luo, Nicholas J. Lawrence, Harshani R. Lawrence, Felix Y. Feng, Nupam P. Mahajan
Summary: Resistance to enzalutamide in castration-resistant prostate cancer (CRPC) is a common issue without effective therapeutic options. This study reveals that acetylation at Lys(609) in the DNA binding domain of androgen receptor (AR) allows AR translocation and confers enzalutamide insensitivity. The acetylation is mediated by ACK1 kinase-mediated AR Y267 phosphorylation, which leads to positive feedback loops at both transcriptional and posttranslational levels. Inhibiting ACK1 kinase with a small-molecule inhibitor compromises enzalutamide-resistant CRPC xenograft tumor growth.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Alan Y. Du, Xiaoyu Zhuo, Vasavi Sundaram, Nicholas O. Jensen, Hemangi G. Chaudhari, Nancy L. Saccone, Barak A. Cohen, Ting Wang
Summary: Transposable elements (TEs) containing transcription factor binding sites have potential regulatory activity. Our study systematically tested the regulatory activity of the human LTR18A subfamily and identified AP-1 and CEBP motifs as drivers of enhancer activity. Through evolutionary analysis, we found that LTR18A elements have lost regulatory activity over time through sequence changes, with mutations in the AP-1 and CEBP motifs having the largest effects. We also discovered that these motifs are more conserved than expected. Our findings provide insights into the origin, evolution, and utilization of TE-derived regulatory elements.
Review
Cell Biology
Andrew J. Modzelewski, Johnny Gan Chong, Ting Wang, Lin He
Summary: This review discusses how sequences introduced by transposon activities contribute to genome innovation and document the evolutionary path of each species.
NATURE CELL BIOLOGY
(2022)
Editorial Material
Genetics & Heredity
Surag Nair, Arjun Barrett, Daofeng Li, Brian J. Raney, Brian T. Lee, Peter Kerpedjiev, Vivekanandan Ramalingam, Anusri Pampari, Fritz Lekschas, Ting Wang, Maximilian Haeussler, Anshul Kundaje
Summary: High-throughput experimental platforms revolutionize the analysis of the biochemical and functional properties of biological sequences. However, existing genome browser tracks are not suitable for visualizing high-resolution DNA sequence features.
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Haocheng Qin, Cuicui Wang, Yonghua He, Aiwu Lu, Tiandao Li, Bo Zhang, Jie Shen
Summary: Osteoarthritis (OA) is a prevalent joint disease and a leading cause of disability, but its underlying pathogenesis is poorly understood. Inflammation is known to disturb joint homeostasis in OA, and microRNA-146a-5p (miR-146a-5p) has been identified as a key regulator of inflammation in this study. Increased expression of miR-146a-5p was found in human OA cartilage, and experimental results showed that miR-146a-5p can regulate inflammatory responses and catabolism in chondrocytes. Silencing miR-146a-5p alleviated cartilage destruction and reduced OA-induced pain in a mouse model.
Article
Biochemistry & Molecular Biology
Xiaoyu Zhuo, Silas Hsu, Deepak Purushotham, Prashant Kumar Kuntala, Jessica K. Harrison, Alan Y. Du, Samuel Chen, Daofeng Li, Ting Wang
Summary: Genome browsers are important tools to visualize and analyze genomic features and data, and there is a growing need for a comparative epigenome browser that can display and compare genomic and epigenomic data sets across different species. The WashU Comparative Epigenome Browser allows users to load functional genomic data sets mapped to different genomes and display them over syntenic regions simultaneously, while also visualizing genetic differences between the genomes. This browser expands on the widely used WashU Epigenome Browser infrastructure and supports multiple species, facilitating comparative genomic/epigenomic research and comparison of different genome assemblies.
Review
Genetics & Heredity
Heather A. Lawson, Yonghao Liang, Ting Wang
Summary: Transposable elements (TEs) are mobile DNA elements that can replicate and integrate into new positions in host genomes. They regulate gene expression by maintaining and shaping 3D genome structure, contributing to mammalian genome evolution and gene regulation.
NATURE REVIEWS GENETICS
(2023)
Article
Oncology
Christine R. Zhang, Elizabeth L. Ostrander, Ostap Kukhar, Cates Mallaney, Jiameng Sun, Emily Haussler, Hamza Celik, Won Kyun Koh, Katherine Y. King, Paul Gontarz, Grant A. Challen
Summary: Clonal hematopoiesis (CH) is the age-related expansion of specific clones in the blood system, often associated with mutations in the gene DNMT3A. Despite the prevalence of DNMT3A mutations in CH, a unified molecular mechanism explaining the competitive advantage of DNMT3A-mutant HSCs is currently lacking.
BLOOD CANCER DISCOVERY
(2022)