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.
Article
Genetics & Heredity
Steven K. Reilly, Sager J. Gosai, Alan Gutierrez, Ava Mackay-Smith, Jacob C. Ulirsch, Masahiro Kanai, Kousuke Mouri, Daniel Berenzy, Susan Kales, Gina M. Butler, Adrianne Gladden-Young, Redwan M. Bhuiyan, Michael L. Stitzel, Hilary K. Finucane, Pardis C. Sabeti, Ryan Tewhey
Summary: HCR-FlowFISH is a new approach for characterizing CRISPR-perturbed cis-regulatory elements (CREs) by accurately quantifying native transcripts and using CASA for analysis. The study found that CREs can regulate multiple genes and exhibit activating and/or silencing effects. At the FADS locus, endogenous screens combined with reporter assays successfully identified target genes for multiple genome-wide association signals.
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
Anushua Biswas, Leelavati Narlikar
Summary: cisDIVERSITY is a new statistical framework that analyzes various gene regulation activities by modeling regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves.
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
Biochemical Research Methods
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schuebeler, Michael B. Stadler
Summary: Proteins binding to specific nucleotide sequences, such as transcription factors, have significant roles in regulating gene expression. The monaLisa package, an R/Bioconductor package, provides methods to identify relevant transcription factors from experimental data. It allows seamless motif analyses without relying on software outside of R.
Article
Biochemistry & Molecular Biology
Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R. Zhang
Summary: The epigenetic control of gene expression is highly cell-type and context specific, and can be broken down into modular components by a transcription factor activating or repressing the target gene expression. A new nonparametric approach, TRIPOD, is proposed to detect and characterize the relationships between TF, target gene, and TF binding site accessibility using single-cell RNA and ATAC multiomic data.
Review
Plant Sciences
Mohsen Hajheidari, Shao-shan Carol Huang
Summary: Transcription factors play a critical role in cell fate decisions, integrating developmental and environmental signals through binding to specific cis-regulatory modules. Precise identification of TF binding sites is essential for understanding regulatory networks and genetic variations.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
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.
Article
Biochemistry & Molecular Biology
Peng Zhou, Tara A. Enders, Zachary A. Myers, Erika Magnusson, Peter A. Crisp, Jaclyn M. Noshay, Fabio Gomez-Cano, Zhikai Liang, Erich Grotewold, Kathleen Greenham, Nathan M. Springer
Summary: Changes in gene expression are crucial for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes reveals many alterations in transcript abundance. By analyzing expression responses in multiple genotypes and identifying cis- or trans-regulatory variation, predictive models of gene expression responses for thermal stress-responsive genes can be developed. Models focusing on unmethylated regions near the transcription start sites (TSSs) show improved accuracy, suggesting that different genes may have varying response dynamics to stress.
Article
Biochemistry & Molecular Biology
Baoxing Song, Edward S. Buckler, Hai Wang, Yaoyao Wu, Evan Rees, Elizabeth A. Kellogg, Daniel J. Gates, Merritt Khaipho-Burch, Peter J. Bradbury, Jeffrey Ross-Ibarra, Matthew B. Hufford, M. Cinta Romay
Summary: Thousands of species are set to be sequenced in the coming years, and understanding the functionality of their genomes requires molecular and evolutionary approaches. A study focusing on the Andropogoneae tribe, which includes multiple crop species, revealed highly conserved noncoding sequences rich in functional elements. These findings shed light on the evolution and functional significance of CNSs in maize.
Review
Plant Sciences
Alexandre P. Marand, Andrea L. Eveland, Kerstin Kaufmann, Nathan M. Springer
Summary: This article discusses the functions and identification methods of various classes of cis-regulatory elements in plant development and response to the environment. It also highlights the opportunities to exploit cis-regulatory variants for crop improvement efforts.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Cell Biology
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J. Grisdale, Emma Titmuss, Janessa Laskin, Steven J. M. Jones, Isidro Cortes-Ciriano, Marco A. Marra, Chad J. Creighton
Summary: The study found that somatic structural variants (SVs) have an impact on gene regulation in advanced tumors, leading to altered expression of hundreds of genes near SV breakpoints. Some of these SV-expression associations are correlated with patient survival rates, while a high overall SV burden is associated with treatment using specific drugs.
Article
Multidisciplinary Sciences
Ilias Georgakopoulos-Soares, Chengyu Deng, Vikram Agarwal, Candace S. Y. Chan, Jingjing Zhao, Fumitaka Inoue, Nadav Ahituv
Summary: The grammar of gene regulation is challenging to understand, which hinders our ability to connect genotype with phenotype. In this study, the researchers used massively parallel reporter assays to examine over 200,000 synthetic sequences, revealing that the order and orientation of transcription factor binding sites (TFBS) significantly impact gene regulatory activity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jennifer W. Israel, Grace A. Chappell, Jeremy M. Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, Hala S. Boulos, Wanda Bodnar, Jason D. Lieb, Gregory E. Crawford, Terrence S. Furey, Ivan Rusyn
Article
Neurosciences
Oressia Zalucki, Lachlan Harris, Tracey J. Harvey, Danyon Harkins, Jocelyn Widagdo, Sabrina Oishi, Elise Matuzelski, Xuan Ling Hilary Yong, Hannes Schmidt, Victor Anggono, Thomas H. J. Burne, Richard M. Gronostajski, Michael Piper
Article
Anatomy & Morphology
James Fraser, Alexandra Essebier, Alexander S. Brown, Raul Ayala Davila, Ameet S. Sengar, YuShan Tu, Kathleen S. Ensbey, Bryan W. Day, Matthew P. Scott, Richard M. Gronostajski, Brandon J. Wainwright, Mikael Boden, Tracey J. Harvey, Michael Piper
BRAIN STRUCTURE & FUNCTION
(2019)
Article
Medicine, General & Internal
Sabrina Oishi, Danyon Harkins, Nyoman D. Kurniawan, Maria Kasherman, Lachlan Harris, Oressia Zalucki, Richard M. Gronostajski, Thomas H. J. Burne, Michael Piper
Article
Neurosciences
Brian S. Clark, Genevieve L. Stein-O'Brien, Fion Shiau, Gabrielle H. Cannon, Emily Davis-Marcisak, Thomas Sherman, Clayton P. Santiago, Thanh V. Hoang, Fatemeh Rajaii, Rebecca E. James-Esposito, Richard M. Gronostajski, Elana J. Fertig, Loyal A. Goff, Seth Blackshaw
Article
Genetics & Heredity
Martin Zenker, Jens Bunt, Ina Schanze, Denny Schanze, Michael Piper, Manuela Priolo, Erica H. Gerkes, Richard M. Gronostajski, Linda J. Richards, Julie Vogt, Marja W. Wessels, Raoul C. Hennekam
AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS
(2019)
Article
Neurosciences
James Fraser, Alexandra Essebier, Alexander S. Brown, Raul Ayala Davila, Danyon Harkins, Oressia Zalucki, Lauren P. Shapiro, Peter Penzes, Brandon J. Wainwright, Matthew P. Scott, Richard M. Gronostajski, Mikael Boden, Michael Piper, Tracey J. Harvey
Article
Multidisciplinary Sciences
David Gokhman, Malka Nissim-Rafinia, Lily Agranat-Tamir, Genevieve Housman, Raquel Garcia-Perez, Esther Lizano, Olivia Cheronet, Swapan Mallick, Maria A. Nieves-Colon, Heng Li, Songul Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Jason M. Osinski, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Deus Mjungu, Ivanela Kondova, Ronald Bontrop, Ottmar Kullmer, Gerhard Weber, Tal Shahar, Mona Dvir-Ginzberg, Marina Faerman, Ellen E. Quillen, Alexander Meissner, Yonatan Lahav, Leonid Kandel, Meir Liebergall, Maria E. Prada, Julio M. Vidal, Richard M. Gronostajski, Anne C. Stone, Benjamin Yakir, Carles Lalueza-Fox, Ron Pinhasi, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Rene C. Adam, Hanseul Yang, Yejing Ge, Nicole R. Infarinato, Shiri Gur-Cohen, Yuxuan Miao, Ping Wang, Yilin Zhao, Catherine P. Lu, Jeong E. Kim, Joo Y. Ko, Seung S. Paik, Richard M. Gronostajski, Jaehwan Kim, James G. Krueger, Deyou Zheng, Elaine Fuchs
NATURE CELL BIOLOGY
(2020)
Article
Neurosciences
Lu Qi, Guangjuan Yin, Yongchao Zhang, Yeqi Tao, Xiaohua Wu, Richard M. Gronostajski, Mengsheng Qiu, Yang Liu
NEUROSCIENCE BULLETIN
(2020)
Article
Oncology
Kok-Siong Chen, Zorana Lynton, Jonathan W. C. Lim, Thomas Robertson, Richard M. Gronostajski, Jens Bunt, Linda J. Richards
Summary: Nuclear factor one (NFI) proteins may act as tumor suppressors in glioma. Deletion of NFI genes results in reduced survival time, increased tumor load, and a more aggressive tumor phenotype in mice. NFI genes could be a credible target for both diagnostic analyses and therapeutic strategies to combat high-grade glioma.
Article
Reproductive Biology
Raul Ayala Davila, Cassy Spiller, Danyon Harkins, Tracey Harvey, Philip W. Jordan, Richard M. Gronostajski, Michael Piper, Josephine Bowles
Summary: Members of the NFI family play essential roles in stem cell biology during development, and their expression patterns in the seminiferous tubules show distinct patterns. NFIX is found to be critical for meiotic progression during spermatogenesis. Its deletion leads to defective synaptonemal complex and unrepaired DNA double-strand breaks in spermatocytes.
BIOLOGY OF REPRODUCTION
(2022)
Article
Biology
Elise Matuzelski, Alexandra Essebier, Lachlan Harris, Richard M. Gronostajski, Tracey J. Harvey, Michael Piper
BMC RESEARCH NOTES
(2020)
Meeting Abstract
Ophthalmology
Clayton Santiago, Thanh Hoang, David F. Espinoza, Patrick Leavey, Jie Wang, Jiang Qian, Richard M. Gronostajski, Seth Blackshaw
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2020)
Meeting Abstract
Ophthalmology
Clayton Santiago, Thanh Hoang, David F. Espinoza, Jie Wang, Jiang Qian, Richard M. Gronostajski, Brian Clark, Seth Blackshaw
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2019)