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
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
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.
Article
Multidisciplinary Sciences
Siqian Feng, Richard S. Mann
Summary: Chromatin immunoprecipitation (ChIP) is a crucial technique for studying protein-DNA interactions, but lacks cell type-specificity in complex tissues. SpyChIP overcomes this limitation by utilizing a specific isopeptide bond to identify cell type-specific transcription factor (TF) binding sites, offering insights into TF mechanisms in different cell types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(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
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
Biotechnology & Applied Microbiology
Henry A. Ertl, Mark S. Hill, Patricia J. Wittkopp
Summary: This study reveals the role of chromatin remodeling factors and their relationship with gene expression and chromatin structure in gene regulatory mechanisms. The findings suggest that variations in chromatin accessibility and Grainy head binding contribute to the evolution of gene expression, shedding light on the complex interactions among molecular layers in gene regulation.
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
Developmental Biology
James D. Price, Susan Lindtner, Athena Ypsilanti, Fadya Binyameen, Jeffrey R. Johnson, Billy W. Newton, Nevan J. Krogan, John L. R. Rubenstein
Summary: This study reveals the crucial role of transcription factors Dlx1/2 and Olig1/2 in determining the fate of subpallium cells. Dlx1/2 interacts with the NuRD complex to regulate gene transcription and cell differentiation. Loss of Dlx1/2 leads to dysregulation of regulatory elements near genes such as Olig2, resulting in increased production of OLIG2(+) cells.
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
Cell Biology
Nikhil Hajirnis, Rakesh K. Mishra
Summary: Hox genes, responsible for regulating the anterior-posterior body axis in animals, exhibit diversity in arrangement across different organisms. Minor changes in gene expression levels play a significant role in the development of biological features, impacting primary axis formation, segment identity, and other crucial processes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Javier Castro Alvarez, Maxime Revel, Judit Carrasco, Fabienne Cleard, Daniel K. Pauli, Valerie P. Hilgers, Francois P. Karch, Robert P. Maeda
Summary: Intergenic transcription is a common feature of eukaryotic genomes, and in the case of the iab-8 ncRNA from the Drosophila Bithorax Complex, it represses gene expression at its 3' end through a sequence-independent mechanism. This repression is limited to the central nervous system, where the ncRNA is specifically extended by the RNA-binding protein, ELAV, resulting in precise tissue-specific gene expression.
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
Genetics & Heredity
Samantha M. Barnada, Andrew Isopi, Daniela Tejada-Martinez, Clement Goubert, Sruti Patoori, Luca Pagliaroli, Mason Tracewell, Marco Trizzino
Summary: The study reveals that SINE-VNTR-Alus (SVAs) are frequently co-opted transposable elements (TEs) in human gene regulation, but the mechanisms are not fully understood. The researchers used CRISPR-interference, computational and functional genomics to investigate the genomic features underlying SVA domestication into human stem-cell gene regulation. They found that around 750 SVAs are functional cis-regulatory elements in human induced pluripotent stem cells and identified a long DNA motif and transcription factors OCT4 and YY1 as important factors in SVA co-option. The repression of active SVAs resulted in altered gene expression.
Article
Multidisciplinary Sciences
Maria Paula Zappia, Yong-Jae Kwon, Anton Westacott, Isabel Liseth, Hyun Min Lee, Abul B. M. M. K. Islam, Jiyeon Kim, Maxim V. Frolov
Summary: The transcription factor E2F is responsible for controlling the expression of cell cycle genes by binding to their promoters. However, its significance in the regulation of metabolic genes is not well understood. In this study, the researchers introduced mutations in the E2F sites of five metabolic genes in fruit flies and found varying effects on E2F recruitment and gene expression, with the glycolytic gene Pgk being the most affected. Loss of E2F regulation on the Pgk gene led to decreased glycolytic flux, ATP content, and abnormal mitochondrial morphology. The study highlights the importance of E2F regulation on metabolic genes and its impact on overall development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Developmental Biology
Matthew J. Borok, Virginia E. Papaioannou, Lori Sussel
DEVELOPMENTAL BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Margaret C. W. Ho, Porfirio Quintero-Cadena, Paul W. Sternberg
Article
Cell Biology
Tingting Xie, Margaret C. W. Ho, Qili Liu, Wakako Horiuchi, Chun-Chieh Lin, Darya Task, Haojiang Luan, Benjamin H. White, Christopher J. Potter, Mark N. Wu
Article
Developmental Biology
Matthew J. Borok, Diana A. Tran, Margaret C. W. Ho, Robert A. Drewell
Article
Medicine, Research & Experimental
Shouhong Xuan, Matthew J. Borok, Kimberly J. Decker, Michele A. Battle, Stephen A. Duncan, Michael A. Hale, Raymond J. Macdonald, Lori Sussel
JOURNAL OF CLINICAL INVESTIGATION
(2012)
Article
Multidisciplinary Sciences
Margaret C. W. Ho, Benjamin J. Schiller, Omar S. Akbari, Esther Bae, Robert A. Drewell
Article
Biochemistry & Molecular Biology
Jagan Srinivasan, Stephan H. von Reuss, Neelanjan Bose, Alon Zaslaver, Parag Mahanti, Margaret C. Ho, Oran G. O'Doherty, Arthur S. Edison, Paul W. Sternberg, Frank C. Schroeder
Article
Biology
Despoina Mademtzoglou, Yoko Asakura, Matthew J. Borok, Sonia Alonso-Martin, Philippos Mourikis, Yusaku Kodaka, Amrudha Mohan, Atsushi Asakura, Frederic Relaix
Article
Neurosciences
Xitong Liang, Margaret C. W. Ho, Yajun Zhang, Yulong Li, Mark N. Wu, Timothy E. Holy, Paul H. Taghert
Article
Cell Biology
Matthew Borok, Nathalie Didier, Francesca Gattazzo, Teoman Ozturk, Aurelien Corneau, Helene Rouard, Frederic Relaix
Summary: The study utilized mass cytometry to track changes in different cell types during muscle regeneration, revealing rapid proteomic changes in various cell types following early activation. After injury induction, there is a drastic reduction in myogenic, vascular, and mesenchymal cell lineages, while immune cells invade the damaged tissue significantly.
Article
Biochemistry & Molecular Biology
Margaret C. W. Ho, Masashi Tabuchi, Xiaojun Xie, Matthew P. Brown, Skylar Luu, Serena Wang, Alex L. Kolodkin, Sha Liu, Mark N. Wu
Summary: The mechanisms underlying the accumulation and release of sleep drive in homeostasis are not well understood. In this study using the fruit fly model, researchers identified R5 neurons as potential sleep drive neurons that promote sleep by signaling to EPG neurons. The connectivity between R5 and EPG neurons strengthens with increased sleep need and triggers sleep when a sufficient number of EPG neurons are activated.
Review
Developmental Biology
Matthew J. Borok, Despoina Mademtzoglou, Frederic Relaix
JOURNAL OF DEVELOPMENTAL BIOLOGY
(2020)
Review
Developmental Biology
Cheng Shi, Pengfei Jiao, Zhiyi Chen, Lan Ma, Siyue Yao
Summary: This review discusses the molecular etiology of congenital craniofacial abnormalities, with a focus on the role and mechanism of noncoding RNAs in regulating craniofacial development. Aberrant expression of noncoding RNAs has been implicated in the pathogenesis of craniofacial abnormalities, providing potential therapeutic targets.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Hideru Togashi, Steven Ray Davis, Makoto Sato
Summary: Tile patterns, regulated by cell adhesion molecules, are regular arrangements of cells that play important functional roles in multicellular organisms. The physical constraints and cell adhesion regulate both cell shape and tissue morphogenesis.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Armen Khanbabei, Lina Segura, Cynthia Petrossian, Aaron Lemus, Ithan Cano, Courtney Frazier, Armen Halajyan, Donnie Ca, Mariano Loza-Coll
Summary: This article investigates the genetic regulatory mechanisms of Drosophila intestinal stem cells. The study found that most target genes co-regulated by Esg and STAT show a consistent gene expression pattern. However, manipulating these validated targets in vivo rarely replicated the effects of manipulating Esg and STAT, suggesting the presence of complex genetic interactions among the downstream targets of these two master regulator genes.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Bayley J. Waters, Zoe R. Birman, Matthew R. Wagner, Julia Lemanski, Barak Blum
Summary: Researchers found that conditional deletion of Robo2 in adult mice led to a significant loss of islet architecture without affecting beta cell identity or function, suggesting that Robo2 plays a role in actively maintaining adult islet architecture. Understanding the factors required for islet architecture maintenance is crucial for developing future diabetes therapies.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Rhiannon Clements, Tyler Smith, Luke Cowart, Jennifer Zhumi, Alan Sherrod, Aidan Cahill, Ginger L. Hunter
Summary: Cell protrusions play a crucial role in regulating cell activities during development. By studying the regulation mechanism in fruit fly sensory bristle patterning, it was found that Myosin XV is essential for the dynamics of signaling filopodia and promotes long-range Notch signaling.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Margaret Keating, Ryan Hagle, Daniel Osorio-Mendez, Anjelica Rodriguez-Parks, Sarah I. Almutawa, Junsu Kang
Summary: Knock-in reporter (KI) animals are essential for studying gene expression in biomedical research. This study developed a new strategy using minicircle technology and a minimal promoter to enhance knock-in events and establish stable KI transgenic reporter lines. The study also highlighted the importance of selecting the proper KI line due to potential inappropriate influence of genome editing on reporter gene expression.
DEVELOPMENTAL BIOLOGY
(2024)
Article
Developmental Biology
Christian Altbuerger, Meta Rath, Daniel Armbruster, Wolfgang Driever
Summary: This study reveals that Neurog1 and Olig2 transcription factors have differential requirements for the development of dopaminergic neurons, and they integrate local patterning signals and Notch neurogenic selection signaling to specify the progenitor population and initiate neurogenesis and differentiation.
DEVELOPMENTAL BIOLOGY
(2024)