Editorial Material
Cell & Tissue Engineering
Piotr Konieczny, Shruti Naik
Summary: The preference of mammals to heal with scaring rather than functional tissue regeneration has been discovered. In this research, super-healermice were used to identify cis-regulatory variations that direct regenerative versus fibrotic gene expression in wound fibroblasts, and complement factor H was found to be a molecular driver of skin regeneration.
Editorial Material
Genetics & Heredity
Emily R. Miraldi, Xiaoting Chen, Matthew T. Weirauch
Summary: A new study introduces a novel deep-learning approach to decode the syntax of transcription-factor binding from high-resolution ChIP-nexus data. In silico simulations confirmed complex sequence-based predictions, including helical periodicity and directional cooperativity between transcription factors.
Review
Microbiology
Sabine Brantl, Peter Mueller
Summary: sRNAs act as abundant posttranscriptional regulators in all three kingdoms of life, with various methods being used to study chromosome-encoded sRNAs in bacteria over the past 20 years; while improved bioinformatics tools can predict potential sRNA targets, experimental confirmation remains challenging; known sRNAs in B. subtilis have defined targets and regulatory mechanisms.
Article
Cell Biology
Lauren Winkler, Maria Jimenez, Joshua T. Zimmer, Adam Williams, Matthew D. Simon, Nadya Dimitrova
Summary: The study shows that the full transcription, splicing, and accumulation of lincRNA-p21 are not crucial for gene regulation, but the production of lincRNA-p21 through specific exon regions can promote cis-activation of the gene.
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)
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.
Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
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.
Article
Biology
Tzu-Hsien Yang, Yu-Huai Yu, Sheng-Hang Wu, Fang-Yuan Zhang
Summary: In this research, the CRM Function Annotator (CFA) model was developed to provide complete CRM transcriptional role labeling based on epigenetic profiling interpretation. CFA achieves high performance and outperforms existing tools in promoter/enhancer/insulator identification. By considering the higher-order combinations of the epigenetic codes, CFA significantly reduces false-positive rates in CRM transcriptional role annotation.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Genetics & Heredity
Biswajyoti Sahu, Tuomo Hartonen, Paivi Pihlajamaa, Bei Wei, Kashyap Dave, Fangjie Zhu, Eevi Kaasinen, Katja Lidschreiber, Michael Lidschreiber, Carsten O. Daub, Patrick Cramer, Teemu Kivioja, Jussi Taipale
Summary: Analysis of massively parallel reporter assays reveals that most transcription factor activity is additive and does not rely on specific TF-TF interactions. DNA sequences can determine gene expression, but the exact sequence determinants are still unknown. Machine learning models suggest that TFs act in an additive manner with weak grammar, and most enhancers increase gene expression without involving specific TF-TF interactions.
Article
Biotechnology & Applied Microbiology
Kurtis Stefan, Artem Barski
Summary: Cis-regulatory elements (CRE) are essential for coordinating gene expression programs in specific cells. The STARR-Seq technique has been used to annotate functional CREs, but is mostly limited to cell lines. In this study, Lenti-STARR-Seq was successfully implemented in human CD4+ T cells, providing a genome-wide analysis of CRE function in primary cells. The study identified thousands of enhancers and negative regulatory elements (NREs) in CD4+ T cells, and revealed differences in nucleosome organization between enhancers and NREs. The findings also support the concept of silencer repurposing as enhancers in alternate cell types.
Article
Biochemistry & Molecular Biology
Megane Collobert, Ozvan Bocher, Anais Le Nabec, Emmanuelle Genin, Claude Ferec, Stephanie Moisan
Summary: This study investigates the regulation mechanisms of the CFTR gene, identifying two new introns with strong cooperative effects in intestinal cells. By combining chromatin immunoprecipitation analysis, a 3D structure of the CFTR gene locus in intestinal cells is proposed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Ching-Hua Shih, Justin Fay
Summary: The evolution of cis-regulatory sequences is influenced by their impact on gene expression. Studies have shown that allele-specific expression dynamics are affected by cis-acting variations within and between species, suggesting a key role of cis-regulatory sequences in tuning gene expression dynamics.
Article
Biochemistry & Molecular Biology
Katya L. Mack, Tyler A. Square, Bin Zhao, Craig T. Miller, Hunter B. Fraser
Summary: This study reveals the importance of gene regulatory evolution in the adaptation of threespine sticklebacks to freshwater habitats, especially concerning tissue-specific differences. The findings suggest that cis-regulatory changes play a significant role in gene divergence, with most of the differences occurring in specific tissues between freshwater and marine environments. The study also identified selective processes, particularly within the Wnt signaling pathway in dental tissues, indicating the role of specific genes in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(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
Oncology
Lisa Liang, Ludivine Coudiere-Morrison, Nazanin Tatari, Margaret Stromecki, Agnes Fresnoza, Christopher J. Porter, Marc R. Del Bigio, Cynthia Hawkins, Jennifer A. Chan, Timothy C. Ryken, Michael D. Taylor, Vijay Ramaswamy, Tamra E. Werbowetski-Ogilvie
Article
Biochemistry & Molecular Biology
Sisi Chen, Xiaohan Mei, Amelia Yin, Hang Yin, Xiao-Bing Cui, Shi-You Chen
Article
Medicine, Research & Experimental
Liwei Xie, Amelia Yin, Anna S. Nichenko, Aaron M. Beedle, Jarrod A. Call, Hang Yin
JOURNAL OF CLINICAL INVESTIGATION
(2018)
Article
Radiology, Nuclear Medicine & Medical Imaging
Gregory Simchick, Amelia Yin, Hang Yin, Qun Zhao
MAGNETIC RESONANCE IMAGING
(2018)
Article
Biochemistry & Molecular Biology
Wenyan Fu, Yang Liu, Christina Sun, Hang Yin
Article
Endocrinology & Metabolism
Sungjin Kim, Xiangkun Yang, Amelia Yin, Junyi Zha, Zanna Beharry, Aiping Bai, Alicja Bielawska, Michael G. Bartlett, Hang Yin, Houjian Cai
Review
Cell & Tissue Engineering
Wenyan Fu, Yang Liu, Hang Yin
STEM CELLS INTERNATIONAL
(2019)
Article
Multidisciplinary Sciences
Gregory C. Addicks, Caroline E. Brun, Marie-Claude Sincennes, John Saber, Christopher J. Porter, A. Francis Stewart, Patricia Ernst, Michael A. Rudnicki
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Shoma Matsumoto, Christopher J. Porter, Naomi Ogasawara, Chizuru Iwatani, Hideaki Tsuchiya, Yasunari Seita, Yu-Wei Chang, Ikuhiro Okamoto, Mitinori Saitou, Masatsugu Ema, Theodore J. Perkins, William L. Stanford, Satoshi Tanaka
SCIENTIFIC REPORTS
(2020)
Article
Medicine, Research & Experimental
Jose L. Vinas, Christopher J. Porter, Adrianna Douvris, Matthew Spence, Alex Gutsol, Joseph A. Zimpelmann, Karishma Tailor, Pearl A. Campbell, Kevin D. Burns
Article
Multidisciplinary Sciences
Jamie Zagozewski, Ghazaleh M. Shahriary, Ludivine Coudiere Morrison, Olivier Saulnier, Margaret Stromecki, Agnes Fresnoza, Gareth Palidwor, Christopher J. Porter, Antoine Forget, Olivier Ayrault, Cynthia Hawkins, Jennifer A. Chan, Maria C. Vladoiu, Lakshmikirupa Sundaresan, Janilyn Arsenio, Michael D. Taylor, Vijay Ramaswamy, Tamra E. Werbowetski-Ogilvie
NATURE COMMUNICATIONS
(2020)
Article
Urology & Nephrology
Jose L. Vinas, Matthew Spence, Christopher J. Porter, Adrianna Douvris, Alex Gutsol, Joseph A. Zimpelmann, Pearl A. Campbell, Kevin D. Burns
Summary: The study demonstrates the therapeutic potential of miR-486-5p in acute kidney injury (AKI) by improving kidney function, reducing injury, and decreasing apoptosis in AKI patients.
KIDNEY INTERNATIONAL
(2021)
Article
Biology
Jamie Zagozewski, Stephanie Borlase, Brent J. Guppy, Ludivine Coudiere-Morrison, Ghazaleh M. Shahriary, Victor Gordon, Lisa Liang, Stephen Cheng, Christopher J. Porter, Rhonda Kelley, Cynthia Hawkins, Jennifer A. Chan, Yan Liang, Jingjing Gong, Carolina Nor, Olivier Saulnier, Robert J. Wechsler-Reya, Vijay Ramaswamy, Tamra E. Werbowetski-Ogilvie
Summary: RNA sequencing of MEK inhibitor-treated tumors shows increased activation of the JAK/STAT3 pathway. Combinatorial therapy with JAK/STAT3 inhibitors and selumetinib reduces tumor growth and improves survival in preclinical models, pointing to a potential novel therapeutic strategy for SHH medulloblastoma.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
William M. Southern, Anna S. Nichenko, Kayvan F. Tehrani, Melissa J. McGranahan, Laxminarayanan Krishnan, Anita E. Qualls, Nathan T. Jenkins, Luke J. Mortensen, Hang Yin, Amelia Yin, Robert E. Guldberg, Sarah M. Greising, Jarrod A. Call
SCIENTIFIC REPORTS
(2019)