Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Francisco Carranza, Hossein Shenasa, Klemens J. Hertel
Summary: Alternative splicing is a highly combinatorial mechanism that allows higher eukaryotes to increase mRNA diversity. The selection of alternative splice sites is influenced by sequence, cis-regulatory elements, exon and intron length, and RNA secondary structures. The study showed that the mode of splice site recognition, either intron or exon definition, plays a role in alternative splicing decisions.
Article
Biochemistry & Molecular Biology
Ling Liu, Urmi Das, Samuel Ogunsola, Jiuyong Xie
Summary: This study focuses on the pairing of splice sites across introns or exons in rat GH3 pituitary cells, revealing correlations between RISE indexes at specific introns or exons and inversely correlated with adjacent exons usage. The modulation of paired indexes by depolarization and disruptible by 5-aza-Cytidine was also observed. The nucleotide matrices of RISE-positive splice sites deviated significantly from rat consensus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Cell Biology
Triveni Menon, Rebecca D. Burdine
Summary: The asymmetric expression of transcription factor Pitx2 is crucial for proper organ asymmetry during development. A recent study in Science reveals that Pitx2 expression, independent of Nodal, functions as a brake to counteract BMP4 signaling on the right side, leading to gut tilting.
DEVELOPMENTAL CELL
(2022)
Article
Microbiology
Judith Ryll, Rebecca Rothering, Francesco Catania
Summary: The conventional distinction between exons and introns in eukaryotic genes is actually blurred. This article provides evidence, through studies on Paramecium, that resolves the disconnect between traditional views on introns and the role of RNA splicing.
Review
Biochemistry & Molecular Biology
Kun Li, Ziqiang Wang
Summary: SRSF2, a splicing factor, is regulated by HSV-1 infection and can in turn modulate the levels of immune checkpoint molecules in exhausted T cells, thus playing a crucial role in disease progression.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
John G. Conboy
Summary: A translationally silent single nucleotide mutation in exon 44 of the von Willebrand factor gene is associated with inefficient splicing in a von Willebrand disease patient. The mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor intron retention. Competition between the cryptic site and annotated site may affect splicing efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Yamile Marquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy, Manuel Irimia
Summary: ExOrthist is a Nextflow-based software that enables inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. It evaluates exon sequence conservation by considering the surrounding exon-intron context to derive genome-wide multi-species exon homologies.
Article
Plant Sciences
Ling Chen, Zhihui Xu, Jie Huang, Haidong Shu, Yufan Hui, Danling Zhu, Yufeng Wu, Suomeng Dong, Zhe Wu
Summary: This study reveals the mechanism of SKRP in regulating pre-mRNA splicing and plant immunity. It interacts with spliceosome components and splicing factors to control the splicing of pre-mRNA, thereby affecting plant resistance against Phytophthora pathogens.
Article
Biotechnology & Applied Microbiology
A. Gallo, D. Dolfini, A. Bernardini, N. Gnesutta, R. Mantovani
Summary: NF-YA, the regulatory subunit of the trimeric CCAAT-binding transcription factor NF-Y, has multiple alternative spliced isoforms, and NF-YAx and NF-YAg are enriched in Aves and play a major role in early chicken embryo development. In addition, the absence of exon-5 in NF-YAg leads to a global reduction of beta-stranded elements, while removal of the disordered exon-3 sequence has limited effects on TAD architecture.
Article
Plant Sciences
Qiqi Chen, Pan Shen, Ralph Bock, Shengchun Li, Jiang Zhang
Summary: A global survey of plastid gene expression during fruit ripening in kiwifruit reveals cis-elements that can potentially trigger high-level transgene expression in edible tissues, providing valuable resources for analyzing plastid gene expression and future efforts to engineer the plastid genome of kiwifruit.
PLANT CELL REPORTS
(2022)
Article
Multidisciplinary Sciences
Georgia Katsioudi, Rene Dreos, Enes S. Arpa, Sevasti Gaspari, Angelica Liechti, Miho Sato, Christian H. Gabriel, Achim Kramer, Steven A. Brown, David Gatfield
Summary: The study demonstrates the importance of nonsense-mediated mRNA decay (NMD) in physiological control, particularly in regulating the circadian clock and gene expression.
Article
Plant Sciences
Jennifer P. C. To, Ian W. Davis, Matthew S. Marengo, Aabid Shariff, Catherine Baublite, Keith Decker, Rafaelo M. Galvao, Zhihuan Gao, Olivia Haragutchi, Jee W. Jung, Hong Li, Brent O'Brien, Anagha Sant, Tedd D. Elich
Summary: New expression elements were computationally generated for effective transgene expression in crops, showing precise initiation of transcripts, effective splicing of introns, and predictable processing of transcript ends. These elements have the potential to optimize gene expression in future plant biotechnology traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Fahad Ullah, Saira Jabeen, Maayan Salton, Anireddy S. N. Reddy, Asa Ben-Hur
Summary: In this study, evidence is provided for the hypothesis that transcription factors are involved in the regulation of intron retention. By studying regions of open chromatin, deep learning models were used to distinguish between open chromatin regions in retained and non-retained introns. Motifs enriched in intron retention events with hits to known human transcription factors, particularly from the zinc finger family, were identified.
Article
Plant Sciences
Keiko Inaba-Hasegawa, Ayumi Ohmura, Masayo Nomura, Masahiro Sugiura
Summary: Chloroplast genomes in land plants contain approximately 20 intron-containing genes, similar to group II introns found in fungi, algae, and some bacteria, but lacking self-splicing capability. Researchers developed an in vitro system using tobacco chloroplasts to study splicing reactions, revealing differences in splicing mechanisms between chloroplast pre-mRNA and self-splicing group II introns.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Scott Medler, Athar Ansari
SCIENTIFIC REPORTS
(2015)
Article
Genetics & Heredity
Neha Agarwal, Athar Ansari
Article
Multidisciplinary Sciences
Nadra Al-Husini, Ali Sharifi, Seyed Ahmad Mousavi, Hamidreza Chitsaz, Athar Ansari
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Zuzer Dhoondia, Ricci Tarockoff, Nadra Alhusini, Scott Medler, Neha Agarwal, Athar Ansari
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2017)
Article
Biochemistry & Molecular Biology
Banupriya Mukundan, Athar Ansari
JOURNAL OF BIOLOGICAL CHEMISTRY
(2013)
Article
Multidisciplinary Sciences
Aboudi M. Moabbi, Neha Agarwal, Belal El Kaderi, Athar Ansari
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Genetics & Heredity
Nadra Al Husini, Paul Kudla, Athar Ansari
Article
Biochemistry & Molecular Biology
Paula Allepuz-Fuster, Michael J. O'Brien, Noelia Gonzalez-Polo, Bianca Pereira, Zuzer Dhoondia, Athar Ansari, Olga Calvo
NUCLEIC ACIDS RESEARCH
(2019)
Review
Biochemistry & Molecular Biology
Nadra Al-Husini, Scott Medler, Athar Ansari
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2020)
Article
Biochemistry & Molecular Biology
Zuzer Dhoondia, Hesham Elewa, Marva Malik, Zahidur Arif, Roger Pique-Regi, Athar Ansari
Summary: The study reveals a novel role of Rat1 in mRNA splicing in budding yeast. Rat1 interacts with splicing factors such as Clf1, Isy1, Yju2, Prp43, and Sub2, and recruitment of these splicing factors on the intron is compromised in Rat1 mutants. Rat1 is not a general splicing factor and crosslinks to only long introns with an average length of 400 nucleotides.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Michael J. O'Brien, Athar Ansari
Summary: Viral infections depend on host transcription and translation machinery to replicate viral genes and express proteins, with the transcription factor TFIIB frequently targeted by viruses. Direct interactions between viral transcriptional regulators and host TFIIB may offer potential for antiviral therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Genetics & Heredity
Michael J. O'Brien, Athar Ansari
Summary: The general transcription factor TFIIB is not only involved in transcription initiation, but also plays a role in transcription termination. It interacts with termination factors at the 3' end of genes, potentially leading to gene looping and providing promoter directionality. This pleiotropic role of TFIIB in the transcription cycle may explain why it is preferentially targeted by viruses and warrants further study in the context of viral pathogenesis.
Editorial Material
Biochemistry & Molecular Biology
Olga Calvo, Athar Ansari, Francisco Navarro
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)