Article
Genetics & Heredity
Siqi Zhao, Clarice K. Y. Hong, Connie A. Myers, David M. Granas, Michael A. White, Joseph C. Corbo, Barak A. Cohen
Summary: Massively parallel reporter gene assays are essential for regulatory genomics but lack the ability to identify cell-type-specific regulatory elements without sequential assays. To overcome this, a single-cell massively parallel reporter assay (scMPRA) was developed to simultaneously measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell types. The scMPRA was shown to be reproducible and capable of detecting cell-type-specific cis-regulatory activity using a library of core promoters in HEK293 and K562 cells. Furthermore, scMPRA was used to measure promoter variants in live mouse retinas, revealing that subtle genetic variations can result in cell-type-specific effects on cis-regulatory activity. The scMPRA is expected to have wide applications in studying CRSs in different cell types.
Article
Oncology
Min-Kyung Yeo, Yoonjoo Kim, Da Hye Lee, Chaeuk Chung, Go Eun Bae
Summary: This study found that the expression of NF-kappa B and AICDA increased in EGFR-TKI-resistant LAC, and the suppression of NF-kappa B and AICDA had a significant therapeutic effect in overcoming EGFR-TKI resistance.
Article
Plant Sciences
John Pablo Mendieta, Ankush Sangra, Haidong Yan, Mark A. A. Minow, Robert J. Schmitz
Summary: Cis-regulatory elements (CREs) are crucial for gene expression and various plant biological processes. However, studying CREs in plant genomes has been challenging due to the totipotent nature of plant cells and technical difficulties caused by the cell wall. Recent advances in single-cell epigenomics offer tremendous potential to enhance our understanding of plant CRE biology and diverse plant phenomena. Despite the potential benefits, analyzing single-cell epigenomic datasets comes with significant biological and computational challenges. This review discusses the historical background of plant single-cell research, challenges in analyzing plant single-cell epigenomic data, and the transformative impact of single-cell epigenomics on our understanding of CRE importance in plant genomes.
Article
Biochemistry & Molecular Biology
David A. Gallegos, Melyssa Minto, Fang Liu, Mariah F. Hazlett, S. Aryana Yousefzadeh, Luke C. Bartelt, Anne E. West
Summary: This study found that amphetamine regulates the transcription of PV+ interneurons in the NAc and the regulation program is distinct from that of other GABAergic neurons in the NAc. Chromatin accessibility at enhancers predicts cell-type specific gene regulation, providing insight into transcriptional mechanisms. The functional importance of this transcriptional program was explored through expression assessment in a mouse strain with heightened behavioral sensitivity.
MOLECULAR PSYCHIATRY
(2023)
Review
Immunology
Charlotte Bruzeau, Jeanne Cook-Moreau, Eric Pinaud, Sandrine Le Noir
Summary: This study provides an overview of the regulation of B cell immunoglobulin gene rearrangement. Tight regulation of IgH rearrangement is crucial to prevent mutations or translocations in oncogenes. The study highlights the importance of Ig gene regulatory elements in nuclear positioning and chromatin modifications.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Tianjiao Zhang, Liangyu Li, Hailong Sun, Dali Xu, Guohua Wang
Summary: This article introduces a deep learning framework called DeepICSH for identifying silencers in specific cells. DeepICSH leverages multiple biological data sources and a convolutional neural network to capture biologically relevant signal combinations associated with silencers. Through extensive experiments, DeepICSH has shown superior performance in silencer identification.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Alex M. Mawla, Talitha van der Meulen, Mark O. Huising
Summary: Using ATAC-Seq, the chromatin landscape of mouse alpha, beta, and delta cells were compared, revealing that alpha and delta cells are poised, but repressed, from becoming beta cells. Differential chromatin accessibility also showed preferentially enriched distal-intergenic regions in beta cells compared to alpha or delta cells.
Review
Engineering, Biomedical
Amy Gelmi, Carolyn E. Schutt
Summary: Engineering biomaterials can recreate the microenvironmental and endogenous cues affecting stem cell fate in an ex vivo environment, providing temporal and spatial cues to stem cells through responsive to exogenous stimulation. These stimuli-responsive biomaterials have versatile applications in studying stem cell responses and cellular manipulation, with promising potential for future personalized tissue engineering and organoid models.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Biology
Alyssa J. Lawler, Easwaran Ramamurthy, Ashley R. Brown, Naomi Shin, Yeonju Kim, Noelle Toong, Irene M. Kaplow, Morgan Wirthlin, Xiaoyu Zhang, BaDoi N. Phan, Grant A. Fox, Kirsten Wade, Jing He, Bilge Esin Ozturk, Leah C. Byrne, William R. Stauffer, Kenneth N. Fish, Andreas R. Pfenning
Summary: Recent discoveries of extreme cellular diversity in the brain necessitate the development of technologies to access specific cell populations within heterogeneous tissue. This study introduces a virus-based strategy called Specific Nuclear-Anchored Independent Labeling (SNAIL) that uses machine learning to identify cell type-specific gene activation features and enables cell labeling and nuclear isolation. The SNAIL approach has been successfully validated for parvalbumin-expressing neurons and shows promise for cell type-specific observation and manipulation in different species and disease models.
Article
Medicine, Research & Experimental
Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P. Somerville, Sandhya R. Panch, Ping Jin, David F. Stroncek
Summary: The study found differences in integration patterns, insertion hotspots, and effects on gene expression between lentiviral and gamma-retroviral vectors used in CAR T-cell products, which provide a foundation for further analysis.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Shaherin Basith, Md Mehedi Hasan, Gwang Lee, Leyi Wei, Balachandran Manavalan
Summary: Enhancers are DNA fragments that enhance the transcription of related genes when bound by transcription factors. Identifying enhancers from the human genome is challenging due to their sporadic distribution and similar fractions. The proposed integrative machine learning framework, Enhancer-IF, showed excellent prediction performance in identifying cell-specific enhancers across different cell types, highlighting its superiority in enhancer identification.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
James D. Hocker, Olivier B. Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang E. Li, Yanxiao Zhang, Elie N. Farah, Allen Wang, Andrew D. McCulloch, Kyle J. Gaulton, Bing Ren, Neil C. Chi, Sebastian Preissl
Summary: This study identified cCREs in the human heart and found their associations with cardiac cell types and heart failure. It also discovered that genetic variants associated with cardiovascular diseases are enriched within these cCREs, with some potentially linked to atrial fibrillation.
Article
Medicine, General & Internal
Jared M. Andrews, Sarah C. Pyfrom, Jennifer A. Schmidt, Olivia I. Koues, Rodney A. Kowalewski, Nicholas R. Grams, Jessica J. Sun, Leigh R. Berman, Eric J. Duncavage, Yi-Shan Lee, Amanda F. Cashen, Eugene M. Oltz, Jacqueline E. Payton
Summary: This study mapped the transcriptional circuitry of the most common blood cancers, revealing that a critical subset of B-cell transcription factors and their cognate enhancers form self-regulatory transcriptional feedback loops, representing a shared mechanism underlying diverse subtypes of B-cell lymphoma.
Article
Biochemistry & Molecular Biology
Mingcong Xu, Xuefeng Bai, Bo Ai, Guorui Zhang, Chao Song, Jun Zhao, Yuezhu Wang, Ling Wei, Fengcui Qian, Yanyu Li, Xinyuan Zhou, Liwei Zhou, Yongsan Yang, Jiaxin Chen, Jiaqi Liu, Desi Shang, Xuan Wang, Yu Zhao, Xuemei Huang, Yan Zheng, Jian Zhang, Qiuyu Wang, Chunquan Li
Summary: The TF-Marker database contains 5905 entries of human TFs and related markers, covering 383 cell types and 95 tissue types, providing valuable resources for understanding the regulatory patterns of different tissues and cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Diana Avalos, Guillaume Rey, Diogo M. Ribeiro, Anna Ramisch, Emmanouil T. Dermitzakis, Olivier Delaneau
Summary: An analysis of cis-regulatory domains (CRDs) derived from ChIP-seq peaks and methylation data reveals cell-type specific regulatory mechanisms in immunity. Important biological mechanisms, such as cell-specific transcription factor binding sites and immune disease-associated loci, are discovered through this study. CRD-QTLs aid in interpreting GWAS findings and mapping functional regulatory units using population genomics allows the discovery of important mechanisms in gene expression regulation in immune cells. This study establishes a comprehensive resource for understanding cell-type specific regulatory mechanisms of immunity.
COMMUNICATIONS BIOLOGY
(2023)
Article
Immunology
Azza Al Ismail, Afzal Husain, Maki Kobayashi, Tasuku Honjo, Nasim A. Begum
INTERNATIONAL IMMUNOLOGY
(2017)
Editorial Material
Immunology
Matteo M. Guerrini, Alexis Vogelzang, Sidonia Fagarasan
Article
Immunology
Akira Nakajima, Alexis Vogelzang, Mikako Maruya, Michio Miyajima, Megumi Murata, Aoi Son, Tomomi Kuwahara, Tatsuaki Tsuruyama, Satoshi Yamada, Minoru Matsuura, Hiroshi Nakase, Daniel A. Peterson, Sidonia Fagarasan, Keiichiro Suzuki
JOURNAL OF EXPERIMENTAL MEDICINE
(2018)
Editorial Material
Multidisciplinary Sciences
Keiichiro Suzuki, Alexis Vogelzang, Sidonia Fagarasan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Ziwei Yin, Maki Kobayashi, Wenjun Hu, Koichi Higashi, Nasim A. Begum, Ken Kurokawa, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Afzal Husain, Jianliang Xu, Hodaka Fujii, Mikiyo Nakata, Maki Kobayashi, Ji-Yang Wang, Jan Rehwinkel, Tasuku Honjo, Nasim A. Begum
Review
Immunology
Edgar Rodrigo Guzman-Bautista, Keiichiro Suzuki, Shohei Asami, Sidonia Fagarasan
CURRENT OPINION IN IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Maryam Akrami, Rosemary Menzies, Kenji Chamoto, Michio Miyajima, Ryuji Suzuki, Hiroyuki Sato, Akiko Nishii, Michio Tomura, Sidonia Fagarasan, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Nasim A. Begum, Farazul Hague, Andre Stanlie, Afzal Husain, Samiran Mondal, Mikiyo Nakata, Takako Taniguchi, Hisaaki Taniguchi, Tasuku Honjo
Summary: Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement that involves multiple factors, with Phf5a identified as a novel regulator of DNA repair in this process. Through maintaining chromatin integrity, Phf5a facilitates NHEJ-dependent DNA repair during CSR.
Article
Rheumatology
Mirei Shirakashi, Mikako Maruya, Keiji Hirota, Tatsuaki Tsuruyama, Takashi Matsuo, Ryu Watanabe, Koichi Murata, Masao Tanaka, Hiromu Ito, Hajime Yoshifuji, Koichiro Ohmura, Dirk Elewaut, Shimon Sakaguchi, Sidonia Fagarasan, Tsuneyo Mimori, Motomu Hashimoto
Summary: This study reveals that defective TCR signaling alters the gut microbiota, promotes Th17 cell differentiation, and triggers systemic autoimmunity, which is a significant finding for understanding the pathogenesis of SLE.
ARTHRITIS & RHEUMATOLOGY
(2022)
Article
Biology
Afzal Husain, Nasim A. Begum, Maki Kobayashi, Tasuku Honjo
Article
Medicine, Research & Experimental
Ryusuke Hatae, Kenji Chamoto, Young Hak Kim, Kazuhiro Sonomura, Kei Taneishi, Shuji Kawaguchi, Hironori Yoshida, Hiroaki Ozasa, Yuichi Sakamori, Maryam Akrami, Sidonia Fagarasan, Izuru Masuda, Yasushi Okuno, Fumihiko Matsuda, Toyohiro Hirai, Tasuku Honjo
Meeting Abstract
Immunology
Michio Miyajima, Baihao Zhang, Matteo Guerrini, Yuki Sugiura, Sidonia Fagarasan
JOURNAL OF IMMUNOLOGY
(2019)
Article
Immunology
Masamichi Muramatsu, Kazuo Kinoshita, Sidonia Fagarasan, Shuichi Yamada, Yoichi Shinkai, Tasuku Honjo
JOURNAL OF IMMUNOLOGY
(2018)
Article
Immunology
Michio Miyajima, Baihao Zhang, Yuki Sugiura, Kazuhiro Sonomura, Matteo M. Guerrini, Yumi Tsutsui, Mikako Maruya, Alexis Vogelzang, Kenji Chamoto, Kurara Honda, Takatoshi Hikida, Satomi Ito, Hongyan Qin, Rikako Sanuki, Keiichiro Suzuki, Takahisa Furukawa, Yasushi Ishihama, Fumihiko Matsuda, Makoto Suematsu, Tasuku Honjo, Sidonia Fagarasan