Article
Biochemistry & Molecular Biology
Jiaxi Zhao, Mindy Liu Perkins, Matthew Norstad, Hernan G. Garcia
Summary: This study combines in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of fruit fly gene ftz. They found that the autoregulatory module of ftz is indeed bistable, and the early element transiently determines the content of the binary cell fate decision. This work confirms the hypothesis that autoregulation can establish developmental fates through bistability.
Article
Genetics & Heredity
Lily Li, Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: The study reveals that the expression of developmental genes is regulated by multiple enhancers and core promoters, which provide both redundancy and specificity. Specific burst properties during transcription, such as burst size and frequency, are most strongly tuned by the combination of promoters and enhancers. The presence of multiple promoters in a locus is due to enhancer preference and a need for redundancy, with broad promoters being common among developmental genes.
Article
Developmental Biology
Nikolay Postika, Paul Schedl, Pavel Georgiev, Olga Kyrchanova
Summary: The Abd-B gene is regulated by four regulatory domains, each responsible for directing its expression in different abdominal segments. Tissue-specific enhancers in the iab-5 domain were found to be required for the proper activation of Abd-B in both A5 and A6. These findings suggest that the iab-5 and iab-6 domains function in an additive manner in the development of the adult cuticle A5 and A6.
Article
Multidisciplinary Sciences
Seth Donoughe, Jordan Hoffmann, Taro Nakamura, Chris H. Rycroft, Cassandra G. Extavour
Summary: The blastoderm formation is a crucial stage of early animal development, and different insects have different cellular behaviors and nuclear movements during this process. A study on the cricket Gryllus bimaculatus reveals that it has a unique solution for blastoderm formation, with nuclear divisions and movements being heterogeneous in space and time and correlated with local nuclear density. A geometric model based on asymmetric pulling forces on nuclei is introduced to explain the patterns of nuclear speeds and orientations. This study sheds light on the cellular and nuclear dynamics during the early stages of insect embryo development.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Moe Yokoshi, Koji Kawasaki, Manuel Cambon, Takashi Fukaya
Summary: Core promoter elements have differential effects on regulating functional parameters of transcriptional bursting in developing Drosophila embryos, including controlling the timing, continuity, and amplitude of bursts. While TATA affects burst amplitude, lnr, MTE, and DPE mainly influence burst frequency. Additionally, core promoter elements play a crucial role in establishing body segments in early embryos.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Anjali Kaushal, Julien Dorier, Bihan Wang, Giriram Mohana, Michael Taschner, Pascal Cousin, Patrice Waridel, Christian Iseli, Anastasiia Semenova, Simon Restrepo, Nicolas Guex, Erez Lieberman Aiden, Maria Cristina Gambetta
Summary: Boundaries in animal genomes play a crucial role in limiting regulatory cross-talk and guiding enhancers to target promoters. This study reveals that the formation and function of boundaries in flies are different from mammals. Unlike mammalian boundaries, most Drosophila boundaries form independently of CTCF and are recruited by Cp190. These boundaries are essential for early development and prevent regulatory cross-talk between specific gene loci, but are dispensable for long-range enhancer-promoter communication.
Article
Biology
Xueying C. Li, Timothy Fuqua, Maria Elize van Breugel, Justin Crocker
Summary: Rapid enhancer and slow promoter evolution have been demonstrated through comparative genomics. However, it is not clear how this information is encoded genetically and if this can be used to place evolution in a predictive context. Here, researchers investigated the evolutionary capacity of promoter variation in Drosophila melanogaster through an unbiased mutation library survey. They found that mutations in promoters had limited to no effect on spatial patterns of gene expression. Compared to developmental enhancers, promoters are more robust to mutations and have more access to mutations that can increase gene expression, suggesting that their low activity might be a result of natural selection.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Tatyana G. Kahn, Mikhail Savitsky, Chikuan Kuong, Caroline Jacquier, Giacomo Cavalli, Jia-Ming Chang, Yuri B. Schwartz
Summary: Drosophila insulators are DNA elements that regulate gene expression by limiting chromatin contacts. By mapping chromatin contacts in Drosophila cells without key insulator proteins CTCF and Cp190, we discovered hundreds of insulator elements. Our findings suggest that Drosophila insulators play a minor role in overall genome folding but have a local impact on chromatin contacts. Our insulator catalog is an important resource for studying genome folding mechanisms.
Article
Multidisciplinary Sciences
Nikolay Postika, Paul Schedl, Pavel Georgiev, Olga Kyrchanova
Summary: The autonomy of segment-specific regulatory domains in the Bithorax complex is conferred by boundary elements and associated Polycomb response elements (PREs). The role of HS1 and HS2 in boundary function suggests that the boundary function of Fab-6 HS1 must be bolstered by a second element that has PRE activity.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Elizabeth A. Urban, Chaim Chernoff, Kayla Viets Layng, Jeong Han, Caitlin Anderson, Daniel Konzman, Robert J. Johnston Jr.
Summary: DNA elements act across long genomic distances to regulate gene expression by mediating transvection. Our study on the stochastic expression of the spineless gene in photoreceptors of fruit flies reveals the biological roles and developmental regulation of transvection. We identify the DNA elements required for activating and repressing transvection and demonstrate that different enhancers participate in transvection at different stages of development, promoting gene expression and specifying cell fates. Our findings have implications for understanding genome organization and architecture.
Review
Biochemistry & Molecular Biology
Matthew D. Gibbons, Yu Fang, Austin P. Spicola, Niko Linzer, Stephen M. Jones, Breanna R. Johnson, Lu Li, Mingyi Xie, Jorg Bungert
Summary: Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast recruit components of the RNA polymerase II transcription machinery. Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA), while UASs in yeast do not recruit the required transcription factor TFIIH. In both systems, Pol II is transferred from enhancers/UASs to promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Linbang Wang, Jingkun Liu, Jiaojiao Tai, Nian Zhou, Tianji Huang, Yuzhou Xue, Zhengxue Quan
Summary: This study identified the crucial role of eRNA WAKMAR2 in immune responses in invasive breast cancer (IBC), suggesting its involvement in regulating the tumour microenvironment and immune-related genes. The downregulation of WAKMAR2 in IBC tissues and its potential as a target for breast cancer treatment were highlighted.
SCIENTIFIC REPORTS
(2021)
Review
Cell Biology
Qianhui Li, Xin Liu, Jingtao Wen, Xi Chen, Bumin Xie, Yang Zhao
Summary: With the advancement of high-throughput sequencing technology, an increasing number of non-coding RNAs have been discovered, including miRNAs, lncRNAs, circRNAs, snoRNAs, and piRNAs. The identification of eRNAs in 2010 has expanded the diversity of non-coding RNAs. eRNAs are non-coding RNA molecules transcribed from enhancer fragments of DNA cis-acting elements. Recent studies have revealed that eRNA transcription may serve as a biological marker for enhancer activity and can participate in the regulation of coding gene transcription. This review discusses the biological characteristics of eRNAs, their functions in transcriptional regulation, the factors regulating eRNA production, and the research progress of eRNAs in different diseases.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Yanfeng He, Shigeo Sato, Chieri Tomomori-Sato, Shiyuan Chen, Zach H. Goode, Joan W. Conaway, Ronald C. Conaway
Summary: The bZIP transcription factor ATF6 alpha is a master regulator of ER stress response genes, with the multifunctional RNA polymerase II transcription factor Elongin identified as a cofactor for ATF6 alpha-dependent transcription activation. Studies show that Elongin facilitates ATF6 alpha-dependent loading of Mediator at the promoters and enhancers of ER stress response genes, and depletion of Elongin leads to impaired transcription and recruitment of Mediator and its CDK8 kinase subunit during the ER stress response. Overall, these findings reveal a crucial role for Elongin as a loading factor for Mediator in the context of ER stress response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Anil K. Panigrahi, David M. Lonard, Bert W. O'Malley
Summary: This study demonstrates the interdependence of transcription between enhancers and target promoters. The results suggest that transcriptional concurrence and coordination throughout the genome are based on the transcriptional interdependence of enhancers and promoters. The study proposes a model where enhancers and promoters are entangled in the form of enhancer-promoter contact, reside in a proteinaceous bubble, and utilize shared transcriptional resources and regulatory inputs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Oncology
Buyuan Chen, Xinji Chen, Xiwei Wu, Xiaoling Wang, Yingjia Wang, Ting-Yu Lin, Jessica Kurata, Jun Wu, Steven Vonderfecht, Guihua Sun, He Huang, Jiing-Kuan Yee, Jianda Hu, Ren-Jang Lin
Article
Neurosciences
Xianzhi Jiang, Don Brown, Nelson Osorio, Chinhui Hsiang, Lily Li, Lucas Chan, Lbachir BenMohamed, Steven L. Wechsler
JOURNAL OF NEUROVIROLOGY
(2015)
Article
Oncology
Sangjun Lee, Eileen L. Heinrich, Lily Li, Jianming Lu, Audrey H. Choi, Rachel A. Levy, Jeffrey E. Wagner, M. L. Richard Yip, Nagarajan Vaidehi, Joseph Kim
MOLECULAR ONCOLOGY
(2015)
Article
Multidisciplinary Sciences
Jinrong Liao, Jinghui Lin, Dong Lin, Changyan Zou, Jessica Kurata, Renjang Lin, Zhiyong He, Ying Su
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Lily Li, Zeba Wunderlich
FRONTIERS IN GENETICS
(2017)
Article
Biochemistry & Molecular Biology
Jessica S. Kurata, Ren-Jang Lin
Article
Gastroenterology & Hepatology
David Luyimbazi, Rebecca A. Nelson, Audrey H. Choi, Lily Li, Joseph Chao, Virginia Sun, John B. Hamner, Joseph Kim
JOURNAL OF GASTROINTESTINAL SURGERY
(2015)
Article
Gastroenterology & Hepatology
Shaila J. Merchant, Lily Li, Joseph Kim
WORLD JOURNAL OF GASTROENTEROLOGY
(2014)
Article
Genetics & Heredity
Lily Li, Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: The study reveals that the expression of developmental genes is regulated by multiple enhancers and core promoters, which provide both redundancy and specificity. Specific burst properties during transcription, such as burst size and frequency, are most strongly tuned by the combination of promoters and enhancers. The presence of multiple promoters in a locus is due to enhancer preference and a need for redundancy, with broad promoters being common among developmental genes.