Article
Biochemistry & Molecular Biology
Robin Vuilleumier, Mo Miao, Sonia Medina-Giro, Clara-Maria Ell, Stephane Flibotte, Tianshun Lian, Grant Kauwe, Annie Collins, Sophia Ly, George Pyrowolakis, A. Pejmun Haghighi, Douglas W. Allan
Summary: Retrograde BMP signaling in the Drosophila neuromuscular junction regulates a gene network involved in synaptic maturation, specifically in motor neurons.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
David Gokhman, Rachel M. Agoglia, Maia Kinnebrew, Wei Gordon, Danqiong Sun, Vivek K. Bajpai, Sahin Naqvi, Coral Chen, Anthony Chan, Chider Chen, Dmitri A. Petrov, Nadav Ahituv, Honghao Zhang, Yuji Mishina, Joanna Wysocka, Rajat Rohatgi, Hunter B. Fraser
Summary: The study of human-chimpanzee hybrid induced pluripotent stem cells reveals evidence of lineage-specific selection on the hedgehog signaling pathway, which may have contributed to the unique craniofacial morphology of humans. This approach offers a new perspective on understanding gene expression differences between species.
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
Biochemistry & Molecular Biology
Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz
Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Article
Biochemistry & Molecular Biology
Ting Wu, Danli Jiang, Meijuan Zou, Wei Sun, Di Wu, Jing Cui, Ian Huntress, Xinxia Peng, Gang Li
Summary: This study utilized Reel-seq and FREP-MS analysis techniques to systematically identify cis-regulatory elements (cis-REs) at high resolution in the human genome, revealing their role in regulating gene expression by recruiting specific proteins and transcription factors, thereby impacting cellular senescence.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jaime Alvarez-Benayas, Nikolaos Trasanidis, Alexia Katsarou, Kanagaraju Ponnusamy, Aristeidis Chaidos, Philippa C. May, Xiaolin Xiao, Marco Bua, Maria Atta, Irene A. G. Roberts, Holger W. Auner, Evdoxia Hatjiharissi, Maria Papaioannou, Valentina S. Caputo, Ian M. Sudbery, Anastasios Karadimitris
Summary: Multiple myeloma is a genetically heterogeneous cancer driven by overexpression of specific oncogenes. By analyzing chromatin accessibility and transcriptome profiles, researchers have identified distinct genetic subgroups within multiple myeloma and uncovered unique gene regulatory networks that contribute to the disease. This study highlights the importance of understanding the transcriptional landscape in driving multiple myeloma progression and identifying potential therapeutic targets.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Carly Weiss, Lana Harshman, Fumitaka Inoue, Hunter B. Fraser, Dmitri A. Petrov, Nadav Ahituv, David Gokhman
Summary: The study utilized massively parallel reporter assays to investigate the regulatory effects of modern human-specific variants, revealing that a portion of these variants drove differential gene expression between human populations, particularly in genes related to vocal tract and brain anatomy and function.
Review
Plant Sciences
Yu Ding, Jiannan Zhu, Dongsheng Zhao, Qiaoquan Liu, Qingqing Yang, Tao Zhang
Summary: Rice grain quality is a complex trait influenced by various factors, making it a major target for breeding. Genome editing technologies offer new possibilities for improving rice quality by modifying CREs to fine-tune gene expression levels. While CREs hold promise for enhancing grain quality, challenges and experimental considerations must be taken into account.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Daniel S. Kim, Viviana I. Risca, David L. Reynolds, James Chappell, Adam J. Rubin, Namyoung Jung, Laura K. H. Donohue, Vanessa Lopez-Pajares, Arwa Kathiria, Minyi Shi, Zhixin Zhao, Harsh Deep, Mahfuza Sharmin, Deepti Rao, Shin Lin, Howard Y. Chang, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Paul A. Khavari
Summary: By analyzing multiomic data and using a deep learning framework, cooperative DNA sequence rules that regulate gene modules during epidermal differentiation were identified. The temporal dynamics and cis-regulatory logic were validated through massively parallel reporter assay analysis.
Article
Biotechnology & Applied Microbiology
Yu Bai, Emmanuel Caussinus, Stefano Leo, Fritz Bosshardt, Faina Myachina, Gregor Rot, Mark D. Robinson, Christian F. Lehner
Summary: Temperature change affects cellular processes in a disruptive manner, with ectotherms exhibiting poor understanding of temperature acclimation mechanisms. Cell-type specificity in transcriptional response to cool temperature exists, with unknown cis-regulatory elements and transcription factors. Functional characterization of the CoolUp enhancer offers insights into transcriptional upregulation induced by lower temperatures.
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.
Review
Developmental Biology
Jihyun Irizarry, Angelike Stathopoulos
Summary: Morphogen concentrations in space and time during development are important for specifying cell fate. Bicoid and Dorsal are two morphogens that directly regulate target genes in Drosophila embryos, providing insights into how morphogens interact and change roles over time. In addition to these factors, there are other inputs working together to control spatiotemporal gene expression in embryos.
Review
Plant Sciences
Alan E. Yocca, Patrick P. Edger
Summary: This review covers the contribution of CRE variation to phenotypic evolution, evidence of selective pressures in non-coding regions, studies on accessible chromatin regions in plants and their insights into CREs, as well as the potential of current sequencing technologies in advancing our understanding of CRE variation.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Plant Sciences
Alexandre P. Marand, Robert J. Schmitz
Summary: Plant tissues and organs are composed of different cell types with variations in cell identity and function. Single-cell profiling has emerged as a powerful tool to study the relationship between cellular phenotypic variation and cis-regulatory mechanisms in plants.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Genetics & Heredity
Sebastian Preissl, Kyle J. Gaulton, Bing Ren
Summary: This article discusses cell type-specific gene regulation and its changes during development and disease. Single-cell epigenomic methods and data analysis tools provide a deeper understanding of gene regulatory programs and their roles in different environments and diseases.
NATURE REVIEWS GENETICS
(2022)
Article
Virology
Majid Kazemian, Min Ren, Jian-Xin Lin, Wei Liao, Rosanne Spolski, Warren J. Leonard
JOURNAL OF VIROLOGY
(2015)
Article
Biochemistry & Molecular Biology
Majid Kazemian, Min Ren, Jian-Xin Lin, Wei Liao, Rosanne Spolski, Warren J. Leonard
MOLECULAR SYSTEMS BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Charles Blatti, Majid Kazemian, Scot Wolfe, Michael Brodsky, Saurabh Sinha
NUCLEIC ACIDS RESEARCH
(2015)
Article
Oncology
Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M. Troy, Christopher Seward, Xiaochen Lu, Lisa Stubbs
Article
Multidisciplinary Sciences
Jian-Xin Lin, Ning Du, Peng Li, Majid Kazemian, Tesfay Gebregiorgis, Rosanne Spolski, Warren J. Leonard
NATURE COMMUNICATIONS
(2017)
Article
Biology
Rosanne Spolski, Erin E. West, Peng Li, Sharon Veenbergen, Sunny Yung, Majid Kazemian, Jangsuk Oh, Zu-Xi Yu, Alexandra F. Freeman, Stephen M. Holland, Philip M. Murphy, Warren J. Leonard
Article
Biology
Jonathan Martinez-Fabregas, Stephan Wilmes, Luopin Wang, Maximillian Hafer, Elizabeth Pohler, Juliane Lokau, Christoph Garbers, Adeline Cozzani, Paul K. Fyfe, Jacob Piehler, Majid Kazemian, Suman Mitra, Ignacio Moraga
Article
Multidisciplinary Sciences
Min Ren, Majid Kazemian, Ming Zheng, JianPing He, Peng Li, Jangsuk Oh, Wei Liao, Jessica Li, Jonathan Rajaseelan, Brian L. Kelsall, Gary Peltz, Warren J. Leonard
NATURE COMMUNICATIONS
(2020)
Article
Medicine, Research & Experimental
Sungtae Park, Brad Griesenauer, Hua Jiang, Djamilatou Adom, Pegah Mehrpouya-Bahrami, Srishti Chakravorty, Majid Kazemian, Tanbeena Imam, Rajneesh Srivastava, Tristan A. Hayes, Julian Pardo, Sarath Chandra Janga, Sophie Paczesny, Mark H. Kaplan, Matthew R. Olson
Article
Cell Biology
Jonathan Martinez-Fabregas, Luopin Wang, Elizabeth Pohler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Article
Biology
Risa Ebina-Shibuya, Erin E. West, Rosanne Spolski, Peng Li, Jangsuk Oh, Majid Kazemian, Daniel Gromer, Phillip Swanson, Ning Du, Dorian B. McGavern, Warren J. Leonard
Summary: TSLP plays a crucial role in the development of diseases such as asthma, atopic dermatitis, and allergic inflammation, but its role in CD8(+) T-cell primary responses and memory CD8(+) T cell responses to secondary viral infection is still controversial. Research has shown that TSLP limits the primary CD8(+) T-cell response to influenza, but has little effect on T cell function and the number of memory CD8(+) T cells generated after influenza infection, while inhibiting memory CD8(+) T-cell responses to secondary viral infections.
Article
Immunology
D. Alejandro Canaria, Bingyu Yan, Maia G. Clare, Zonghao Zhang, Grace A. Taylor, David L. Boone, Majid Kazemian, Matthew R. Olson
Summary: Th9 cells, which produce IL-9, have dual roles in immunity against parasites and cancers as well as in the pathogenesis of allergic diseases and colitis. The differentiation of Th9 cells is regulated by IL-2-induced STAT5 signaling, which is vital for chromatin accessibility within Il9 loci. In allergic disease, Th9 cells exhibit a gene repression signature associated with a Th17-like phenotype, suggesting a balance between these two T cell subsets controlled by IL-2/STAT5 signaling.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Immunology
Abu Osman, Bingyu Yan, Ying Li, Kevin D. Pavelko, Jasmine Quandt, Abdulrahman Saadalla, Mahendra Pal Singh, Majid Kazemian, Fotini Gounari, Khashayarsha Khazaie
Summary: Research shows that TCF-1 collaborates with FOXP3 to regulate suppressive activities of T-reg cells, with TCF-1 deficiency promoting inflammation and compromising T-cell cytotoxicity control. TCF-1 primarily suppresses transcription of co-bound genes by Foxp3, and deficiency in TCF-1 leads to activation and characteristics of the T(H)17 subset in T-reg cells. TCF-1 deficiency in T-reg cells can determine colorectal cancer outcome by regulating inflammation and T-cell cytotoxicity.
Article
Biochemistry & Molecular Biology
Chaohao Li, Jinpeng Liu, Daheng He, Fengyi Mao, Xiongjian Rao, Yue Zhao, Nadia A. Lanman, Majid Kazemian, Elia Farah, Jinghui Liu, Chrispus M. Ngule, Zhuangzhuang Zhang, Yanquan Zhang, Yifan Kong, Lang Li, Chi Wang, Xiaoqi Liu
Summary: This study identifies glutathione S-transferase Mu 2 (GSTM2) as an important determinant in the acquisition of resistance to second-generation androgen receptor inhibitors (SG-ARIs) in prostate cancer. Elevated GSTM2 levels are associated with cross-resistance to enzalutamide, apalutamide, and darolutamide. Mechanistically, GSTM2 antagonizes the effects of SG-ARIs by rescuing cells from oxidative stress-associated damage and activation of p38 MAPK pathway.
Article
Immunology
Behdad Afzali, Juha Gronholm, Jana Vandrovcova, Charlotte O'Brien, Hong-Wei Sun, Ine Vanderleyden, Fred P. Davis, Ahmad Khoder, Yu Zhang, Ahmed N. Hegazy, Alejandro V. Villarino, Ira W. Palmer, Joshua Kaufman, Norman R. Watts, Majid Kazemian, Olena Kamenyeva, Julia Keith, Anwar Sayed, Dalia Kasperaviciute, Michael Mueller, Jason D. Hughes, Ivan J. Fuss, Mohammed F. Sadiyah, Kim Montgomery-Recht, Joshua McElwee, Nicholas P. Restifo, Warren Strober, Michelle A. Linterman, Paul T. Wingfield, Holm H. Uhlig, Rahul Roychoudhuri, Timothy J. Aitman, Peter Kelleher, Michael J. Lenardo, John J. O'Shea, Nichola Cooper, Arian D. J. Laurence
