Article
Biochemistry & Molecular Biology
Xiaofan Feng, Mario Andrea Marchisio
Summary: New synthetic constitutive promoters for Saccharomyces cerevisiae were constructed and optimized by utilizing foreign core promoters as templates and manipulating the TATA box composition, leading to an expanded pool of yeast promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Tobias Jores, Jackson Tonnies, Travis Wrightsman, Edward S. Buckler, Josh T. Cuperus, Stanley Fields, Christine Queitsch
Summary: A massively parallel reporter assay was used to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum in two assay systems, uncovering the sequence features affecting promoter strength and facilitating promoter strength prediction and synthetic design. The experiments revealed species-specific differences in the contributions of GC content and transcription factors to promoter strength.
Article
Biochemistry & Molecular Biology
Clarice K. Y. Hong, Barak A. Cohen
Summary: In gene regulation, enhancers provide specificity while core promoters provide a modular site for the assembly of the basal transcriptional machinery. The activities of different core promoters are preserved across genomic locations, suggesting that they are modular regulatory elements independently scaled up or down by different genomic environments.
Article
Biochemistry & Molecular Biology
Enoch B. Antwi, Yassine Marrakchi, Ozgun Cicek, Thomas Brox, Barbara Di Ventura
Summary: Researchers manipulate the nuclear localization of a synthetic transcription factor through optogenetics and find that the dynamics of transcription factor can be decoded by the promoter, leading to the ability to obtain different gene expression programs solely based on transcription factor dynamics. This study provides insights into gene expression regulation in mammalian cells and offers the possibility of building complex synthetic circuits guided by transcription factor dynamics.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Agronomy
Ahamed Khan, Noohi Nasim, Baveesh Pudhuvai, Bhupendra Koul, Santosh Kumar Upadhyay, Lini Sethi, Nrisingha Dey
Summary: This review discusses the application of synthetic promoters in plants to overcome the limitations of native promoters in terms of size, distribution, and induction, which ultimately leads to insufficient transcriptional activity. It emphasizes the basic structure and function of the promoter, with a focus on the role of Cis-elements in gene expression regulation. The importance of synthetic promoters in the field of plant biology is highlighted, along with information on two major approaches: conventional methods and advancements in gene editing technology. The efficiency of synthetic promoters and the expression level of transgenes are crucial for successful plant genetic manipulation, making the development of synthetic promoters highly promising for genetic engineering-mediated crop improvement.
Article
Biochemical Research Methods
Abayomi O. Johnson, Susan B. Fowler, Carl Webster, Adam J. Brown, David C. James
Summary: This study describes the de novo design of synthetic promoters specific to dendritic cells (DCs) using computational genome mining approaches. The design rules governing the DC-specific synthetic promoter activity were unraveled, and a library of DC-specific promoters with various transcriptional activities was generated.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Thanh-Hoang Nguyen-Vo, Quang H. Trinh, Loc Nguyen, Phuong-Uyen Nguyen-Hoang, Susanto Rahardja, Binh P. Nguyen
Summary: The study proposes an efficient computational model, iPromoter-Seqvec, which combines bidirectional long short-term memory neural networks and sequence-embedded features to predict TATA and non-TATA promoters in human and mouse genomes. The model outperforms other state-of-the-art methods on independent test sets and achieves high predictive power. Artificial non-promoter sequences were constructed to improve the efficiency of the model.
Article
Plant Sciences
Lini Sethi, Debasish Deb, Badrinath Khadanga, Nrisingha Dey
Summary: Researchers analyzed the synthetic full-length transcript promoter of Blueberry red ringspot virus (BRRV) and developed two chimeric promoters (MBR3 and FBR3) with transcriptional activities equivalent to that of the CaMV35S(2) promoter. These chimeric promoters showed high antimicrobial activities against several pathogens, making them potential useful substitutes for the CaMV35S(2) promoter in plant genetic engineering.
Article
Biochemistry & Molecular Biology
Zong-Heng Fu, Si-Zhe He, Yi Wu, Guang-Rong Zhao
Summary: The combination of synthetic biology and deep learning has revolutionized our ability to decode and recode DNA regulatory grammar. In this study, we focused on B-cell-specific transcriptional regulation and designed a large pool of synthesized B-cell-specific promoters. We deciphered the sequence features that regulate promoter transcriptional using massively parallel reporter assays and developed a deep learning model to predict the transcriptional strength of immunoglobulin V gene promoters. Our findings also highlight the influence of promoter polymorphisms on the transcription of immunoglobulin V genes in the global human population.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Juan F. Santana, Geoffrey S. Collins, Mrutyunjaya Parida, Donal S. Luse, David H. Price
Summary: The effects of depleting different components of RNA polymerase II general transcription factors vary in their impact on promoter activity and are regulated by both core promoter elements and the recruitment of TFIID.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Polina Govorkova, Chee Ka Candice Lam, Kevin Truong
Summary: This paper developed a method to design shorter synthetic mammalian promoters for endogenous genes and found that these synthetic promoters had higher palindromic density than expected. By applying this method, they successfully expressed fluorescent proteins, and the synthetic promoters contained important expression sites.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Vivekanandan Ramalingam, Malini Natarajan, Jeff Johnston, Julia Zeitlinger
Summary: The study found differences between paused promoters with high levels of paused Pol II and TATA promoters showing Pol II occupancy only when the gene is active. These two promoter types are associated with different chromatin accessibility and expression characteristics, potentially optimized for different properties. It is proposed that tissue-specific genes have evolved to use different strategies for their differential expression across tissues.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Euijin Seo, Yun-Nam Choi, Ye Rim Shin, Donghyuk Kim, Jeong Wook Lee
Summary: Researchers use deep generative models and predictive models to design and evaluate synthetic promoters for cyanobacteria. They generate 10,000 synthetic promoter sequences and predict their strengths using a variational autoencoder and convolutional neural network. Through analysis and in vitro experiments, they confirm the validity and functionality of the generated promoter sequences.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Rene Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon
Summary: This study identified preferred downstream positions in human promoters resembling the fruit fly DPE, supporting the presence of Inr+DPE-containing promoters in human genes. Functional characterization of these positions also suggests a spacing dependency on the Inr, indicating the likelihood of common canonical Inr+DPE promoters in metazoan species.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Xizi Chen, Yilun Qi, Zihan Wu, Xinxin Wang, Jiabei Li, Dan Zhao, Haifeng Hou, Yan Li, Zishuo Yu, Weida Liu, Mo Wang, Yulei Ren, Ze Li, Huirong Yang, Yanhui Xu
Summary: This study elucidates the assembly mechanism of human TFIID-based PIC, showing two tracks for modular reorganization and direct promoter deposition, converging at a holo PIC with around 50 subunits. TFIID stabilizes PIC organization and supports CAK-mediated phosphorylation of Pol II.
Article
Cell Biology
Maximiliaan Schillebeeckx, Marjut Pihlajoki, Elisabeth Gretzinger, Wei Yang, Franziska Thol, Theresa Hiller, Ann-Kathrin Loebs, Theresa Roehrig, Anja Schrade, Rebecca Cochran, Patrick Y. Jay, Markku Heikinheimo, Robi D. Mitra, David B. Wilson
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2015)
Retraction
Medicine, Research & Experimental
Haiyang Yu, Mykyta Artomov, Sebastian Braehler, M. Christine Stander, Ghaidan Shamsan, Matthew G. Sampson, J. Michael White, Matthias Kretzler, Jeffrey H. Miner, Sanjay Jain, Cheryl A. Winkler, Robi D. Mitra, Jeffrey B. Kopp, Mark J. Daly, Andrey S. Shaw
JOURNAL OF CLINICAL INVESTIGATION
(2016)
Article
Biochemical Research Methods
Gabe Haller, David Alvarado, Kevin McCall, Robi D. Mitra, Matthew B. Dobbs, Christina A. Gurnett
Article
Biochemistry & Molecular Biology
Erin B. Styles, Karen J. Founk, Lee A. Zamparo, Tina L. Sing, Dogus Altintas, Cyril Ribeyre, Virginie Ribaud, Jacques Rougemont, David Mayhew, Michael Costanzo, Matej Usaj, Adrian J. Verster, Elizabeth N. Koch, Daniele Novarina, Marco Graf, Brian Luke, Marco Muzi-Falconi, Chad L. Myers, Robi David Mitra, David Shore, Grant W. Brown, Zhaolei Zhang, Charles Boone, Brenda J. Andrews
Article
Biochemistry & Molecular Biology
Zongtai Qi, Michael Nathaniel Wilkinson, Xuhua Chen, Sumithra Sankararaman, David Mayhew, Robi David Mitra
NUCLEIC ACIDS RESEARCH
(2017)
Article
Genetics & Heredity
Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra, Michael D. Onken
BMC MEDICAL GENOMICS
(2018)
Article
Multidisciplinary Sciences
Christian A. Shively, Jiayue Liu, Xuhua Chen, Kaiser Loell, Robi D. Mitra
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Yiming Kang, Nikhil R. Patel, Christian Shively, Pamela Samantha Recio, Xuhua Chen, Bernd J. Wranik, Griffin Kim, R. Scott McIsaac, Robi Mitra, Michael R. Brent
Article
Biochemistry & Molecular Biology
Jiayue Liu, Christian A. Shively, Robi D. Mitra
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Alexander J. Cammack, Arnav Moudgil, Jiayang Chen, Michael J. Vasek, Mark Shabsovich, Katherine McCullough, Allen Yen, Tomas Lagunas, Susan E. Maloney, June He, Xuhua Chen, Misha Hooda, Michael N. Wilkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemical Research Methods
Christian A. Shively, Fengping Dong, Robi D. Mitra
Summary: Numerous tools for gene expression knockdown have been developed and characterized in the model organism Saccharomyces cerevisiae and extended to facilitate studies in multicellular models. In this study, the researchers systematically evaluated the efficacy of seven constitutive and inducible knockdown strategies using a panel of essential genes. They also created a tagging vector collection for improved strain construction and successfully adapted an improved protein degradation strategy for one-step strain construction in yeast. This work provides a toolbox for endogenous gene expression knockdown and recommendations for perturbing essential genes.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pamela S. Recio, Nikhil J. Mitra, Christian A. Shively, David Song, Grace Jaramillo, Kristine Shady Lewis, Xuhua Chen, Robi D. Mitra
Summary: Gene expression changes are regulated by transcription factors (TFs) that bind to DNA. Existing models of TF function often do not match experimental measurements, indicating unknown biology. In this study, we analyzed a well-studied TF called Gal4 and built a thermodynamic model to describe its binding. We found that the model failed to predict binding in many cases, but experimental observations showed substantial binding. Further investigation revealed a novel mode of binding in which Gal4 binds unexpectedly to DNA sequences with high densities of half sites. This mode of binding was also found in other zinc cluster TFs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Matthew Lalli, Allen Yen, Urvashi Thopte, Fengping Dong, Arnav Moudgil, Xuhua Chen, Jeffrey Milbrandt, Joseph D. Dougherty, Robi D. Mitra
Summary: The calling cards technology using self-reporting transposons allows the identification of DNA-protein interactions through RNA sequencing. By introducing a DNA barcode and additional barcode during reverse transcription, the cost and labor requirements of bulk calling card experiments can be reduced, and simultaneous transcriptome measurement can be achieved. This method is efficient and powerful for inferring gene regulatory networks in a population of cells.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Clinical Neurology
Alexander J. Cammack, Arnav Moudgil, Tomas Lagunas, Michael J. Vasek, Mark Shabsovich, June He, Xuhua Chen, Michael N. Willkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty
ANNALS OF NEUROLOGY
(2019)
Article
Cell Biology
Theresa Roehrig, Marjut Pihlajoki, Ricarda Ziegler, Rebecca S. Cochran, Anja Schrade, Maximiliaan Schillebeeckx, Robi D. Mitra, Markku Heikinheimo, David B. Wilson
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2015)