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
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
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.
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.
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)
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
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
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
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.
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.
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
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
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
Biotechnology & Applied Microbiology
Zain M. Patel, Timothy R. Hughes
Summary: Models of transcription factor binding with or without spacing and orientation constraints predict that regulatory sequences should be fundamentally short, unique, and turn over rapidly. We posit that the existence of master regulators may be, in part, a consequence of evolutionary pressure to limit the complexity and increase evolvability of regulatory sites.
Article
Cell Biology
Farzan Ghanegolmohammadi, Mitsunori Yoshida, Shinsuke Ohnuki, Yuko Sukegawa, Hiroki Okada, Keisuke Obara, Akio Kihara, Kuninori Suzuki, Tetsuya Kojima, Nozomu Yachie, Dai Hirata, Yoshikazu Ohya
MOLECULAR BIOLOGY OF THE CELL
(2017)
Article
Genetics & Heredity
Reiko Tajiri, Nobuhiro Ogawa, Haruhiko Fujiwara, Tetsuya Kojima
Article
Biology
Tetsuya Kojima
CURRENT OPINION IN INSECT SCIENCE
(2017)
Article
Biotechnology & Applied Microbiology
Shun Okamoto, Ryo Futahashi, Tetsuya Kojima, Kazuei Mita, Haruhiko Fujiwara
Article
Developmental Biology
Toshiya Ando, Tetsuya Kojima, Haruhiko Fujiwara
DEVELOPMENTAL BIOLOGY
(2011)
Article
Developmental Biology
Kohei Natori, Reiko Tajiri, Shiori Furukawa, Tetsuya Kojima
DEVELOPMENTAL BIOLOGY
(2012)
Article
Genetics & Heredity
Kaoru Sato, Tomoko Matsuoka Matsunaga, Ryo Futahashi, Tetsuya Kojima, Kazuei Mita, Yutaka Banno, Haruhiko Fujiwara
Article
Developmental Biology
Takuya Tsubota, Kaoru Saigo, Tetsuya Kojima
MECHANISMS OF DEVELOPMENT
(2008)
Editorial Material
Cell Biology
Kohei Natori, Tetsuya Kojima
Article
Multidisciplinary Sciences
Hongyuan Jin, Shinichi Yoda, Liang Liu, Tetsuya Kojima
Article
Multidisciplinary Sciences
Shinichi Yoda, Kousuke Sakakura, Tasuku Kitamura, Yusuke KonDo, Kazuki Sato, Ryosuke Ohnuki, Itsuki Someya, Shinya Komata, Tetsuya Kojima, Shinya Yoshioka, Haruhiko Fujiwara
Summary: The research finds that the dsx (H) gene controls the mimetic and nonmimetic mimicking effects in mimic butterflies by regulating the way pale-yellow colors react and the structure of wing scales.
Article
Biology
Reiko Tajiri, Haruhiko Fujiwara, Tetsuya Kojima
Summary: Research shows that the cuticle covering the Drosophila larval body expands less efficiently along the body circumference, leading to a change in body shape during growth. This corset property is dependent on specific cuticular proteins, Cuticular protein 11A and Tubby, which work together to alter the larval body shape.
COMMUNICATIONS BIOLOGY
(2021)
Article
Developmental Biology
Kayoko T. Sakurai, Tetsuya Kojima, Toshiro Aigaki, Shigeo Hayashi
DEVELOPMENTAL BIOLOGY
(2007)
Article
Virology
Tomoko Kawashima, Mizuko Osanai, Ryo Futahashi, Tetsuya Kojima, Haruhiko Fujiwara