Article
Multidisciplinary Sciences
Tianxiong Yu, Kaili Fan, Deniz M. Ozata, Gen Zhang, Yu Fu, William E. Theurkauf, Phillip D. Zamore, Zhiping Weng
Summary: An unusually long first exon or a long, unspliced transcript is associated with germline-specific transcription and piRNA production in pachytene piRNA clusters. Additionally, a highly methylated promoter containing a low or intermediate level of CG dinucleotides correlates with germline expression and somatic silencing of pachytene piRNA clusters. Furthermore, pachytene piRNA precursor transcripts bind THOC1 and THOC2, contributing to the production of piRNAs.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hoang Thu Trang Do, Siba Shanak, Ahmad Barghash, Volkhard Helms
Summary: Alternative exon usage affects a large portion of genes in mammalian genomes. Analysis of data from the Human Epigenome Atlas shows that the differential usage of exons in different developmental stages of human cells and tissues is associated with differential epigenetic modifications. Many genes that are differentially regulated at the exon level and show deregulated histone marks are functionally associated with development and metabolism.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Mariano Soliman, Maricel Podio, Gianpiero Marconi, Marco Di Marsico, Juan Pablo A. Ortiz, Emidio Albertini, Luciana Delgado
Summary: Apomixis in Paspalum rufum may arise from the deregulation of preexisting genes related to sexuality, potentially involving genetic and epigenetic mechanisms, leading to the formation of clonal seeds in diploid individuals. By comparing DNA methylation levels, differential methylated contigs (DMCs) were identified between apomictic and sexual samples, with homologies to genes associated with flower growth, development, and apomixis, indicating a potential role in apomixis success at diploid and tetraploid levels.
Editorial Material
Multidisciplinary Sciences
Serge McGraw, Sarah Kimmins
Summary: Using a mouse model with targeted DNA methylation, researchers aim to understand how epigenetic marks can be inherited from parents to offspring.
Article
Genetics & Heredity
Chaonan Zhu, Nina Baumgarten, Meiqian Wu, Yue Wang, Arka Provo Das, Jaskiran Kaur, Fatemeh Behjati Ardakani, Thanh Thuy Duong, Minh Duc Pham, Maria Duda, Stefanie Dimmeler, Ting Yuan, Marcel H. Schulz, Jaya Krishnan
Summary: Cardiovascular diseases are a major cause of death globally. A study found that many single nucleotide polymorphisms (SNPs) associated with cardiovascular diseases occur in non-coding genomic regions. This study identified a novel non-coding RNA (ncRNA) called IGBP1P1, which plays a key regulatory role in modulating cardiomyocyte size and cardiac function.
Review
Biochemical Research Methods
Peter A. Crisp, Pooja Bhatnagar-Mathur, Penny Hundleby, Ian D. Godwin, Peter M. Waterhouse, Lee T. Hickey
Summary: Traditional plant breeding has achieved certain success, but it is facing the challenge of meeting the growing demand. To fill the yield gaps and meet consumer preferences, new breeding strategies and sources of genetic variation are needed, and it is important to go beyond the traditional gene-centric thinking and consider the roles of epigenetic variation and cis-regulatory variation in plant traits.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Shahid Ali, Naeem Khan, Yulin Tang
Summary: Abiotic stressors significantly impact agricultural output. Plants have adaptive systems to respond to these stressors through epigenetic modifications, which play a functional role in gene expression. This study summarizes the epigenetic mechanisms, such as DNA methylation, histone modifications, and metabolites, involved in plant responses to environmental stress. Understanding these mechanisms is crucial for crop improvement, and genome editing offers sustainable genetic tools for agricultural engineering.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jing Xue, Feng Chen, Li Su, Xiaowen Cao, Min Bai, Yue Zhao, Chunhai Fan, Yongxi Zhao
Summary: This study demonstrates the differentiated visualization of 5fC or 5hmC spatial positioning and their pairwise proximity in single cells, providing insights into regulation functions and mechanisms of chromatin modifications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Darya A. A. Tourzani, Qiangzong Yin, Erica A. A. Jackson, Oliver J. J. Rando, Pablo E. E. Visconti, Maria G. G. Gervasi
Summary: The sperm energy restriction and recovery (SER) treatment developed in the laboratory improves fertilization and blastocyst development in mice. The effects of SER on early embryogenesis were investigated, showing advanced progression through the pronuclear stages and changes in histone modifications and gene expression. These findings suggest that sperm incubation conditions can impact early embryo development and improve assisted reproductive technology outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Ariadna Gomez-Vilarrubla, Berta Mas-Pares, Gemma Carreras-Badosa, Silvia Xargay-Torrent, Anna Prats-Puig, Alexandra Bonmati-Santane, Francis de Zegher, Lourdes Ibanez, Abel Lopez-Bermejo, Judit Bassols
Summary: This study aimed to identify placental DNA methylation marks associated with gestational weight gain (GWG) and study their association with offspring obesity parameters. The results suggest that placental regulation of FRAT1, SNX5, and KCNK3 relates to obesity parameters in offspring exposed to excessive GWG.
Article
Biochemistry & Molecular Biology
Tzu-Hsien Yang, Ya-Chiao Yang, Kai-Chi Tu
Summary: Transcription regulation is controlled by transcription factors binding to specific DNA sequences. Understanding the distribution of regulatory modules in the genome is important for constructing transcriptional regulatory networks. Traditional methods for identifying these modules are costly and low-throughput, so computational algorithms are often used. However, existing methods have limitations. To overcome these limitations, a novel identification pipeline called regCNN was designed and shown to have improved accuracy and prediction capabilities compared to other tools.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Ioannis Konstantinidis, Dafni Anastasiadi, Pal Saetrom, Artem V. Nedoluzhko, Robin Mjelle, Tomasz Podgorniak, Francesc Piferrer, Jorge M. O. Fernandes
Summary: This study reveals the tissue-specific localization of 5-hydroxymethylcytosines within the somatotropic axis, highlighting their important role in gene regulation and contribution to phenotypic plasticity of growth.
Article
Genetics & Heredity
Ling Zeng, Mei Wang, Jinzhao Zhou, Xiaofei Wang, Yanwei Zhang, Ping Su
Summary: The interaction between gametic epigenetic marks and retrotransposons plays a crucial role in the transmission of parental acquired traits during early embryonic development.
Article
Biochemistry & Molecular Biology
Yue Gao, Xin Li, Shipeng Shang, Shuang Guo, Peng Wang, Dailin Sun, Jing Gan, Jie Sun, Yakun Zhang, Junwei Wang, Xinyue Wang, Xia Li, Yunpeng Zhang, Shangwei Ning
Summary: LincSNP 3.0 is an updated comprehensive database that focuses on documenting and annotating disease or phenotype-associated variants in human long non-coding RNAs and circular RNAs, with expanded types of variants and regulatory elements, as well as identified associations among them.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Immunology
Mankgopo Magdeline Kgatle, Ismaheel Opeyemi Lawal, Gabriel Mashabela, Tebatso Moshoeu Gillian Boshomane, Palesa Caroline Koatale, Phetole Walter Mahasha, Honest Ndlovu, Mariza Vorster, Hosana Gomes Rodrigues, Jan Rijn Zeevaart, Siamon Gordon, Pedro Moura-Alves, Mike Machaba Sathekge
Summary: Severe cases of COVID-19 may be influenced by metabolic and epigenetic mechanisms, including DNA methylation and histone/chromatin alterations. These epigenetic phenomena may lead to enhanced viral replication, resulting in severe symptoms and fatalities.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Evolutionary Biology
Zoe Vance, Lukasz Niezabitowski, Laurence D. Hurst, Aoife McLysaght
Summary: Research has shown that duplicated genes evolve at a faster rate compared to singleton genes in multiple lineages. This phenomenon is not restricted to a single lineage and has implications for the interpretation of gene duplication. Additionally, some singleton genes appear to evolve faster due to homology detection failure and unidentified paralogs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Alexander T. Ho, Laurence D. Hurst
Summary: The recognition of stop codons by release factors (RF1 and RF2) and the adaptations of RF ratios to stop codon usage across bacterial species have been studied to explain TGA/TAG relative usage. The results suggest that RF1/RF2 ratios may adapt to stop codon usage, rather than vice versa, and that the specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. The causal relationships for the evolution of synonymous stop codon usage may be different from those affecting synonymous sense codon usage, particularly in transitions between TGA and TAG.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Yanxiao Jia, Chao Qin, Milton Brian Traw, Xiaonan Chen, Ying He, Jing Kai, Sihai Yang, Long Wang, Laurence D. Hurst
Summary: The introduction of frameshifting non-3n indels enables the identification of gene-trait associations. However, the recovery of the original reading frame due to non-canonical splice forms is rare, and most frame-restoring isoforms induced by indels are low in abundance and potentially disruptive to proteins, suggesting that such rescue is uncommon. Despite this, it is important to consider the RNA level effects of non-3n indels and explore multiple non-3n indels in any given gene for probing trait associations.
Article
Biochemical Research Methods
Stefanie Muhlhausen, Laurence D. Hurst
Summary: Transgene-design is a web application that assists in designing transgenes for mammalian studies. It utilizes the discovery that transgenes without introns and native retrogenes can be highly expressed if the GC content at exonic synonymous sites is high. The application allows for the manipulation of exonic splice enhancers and the option to retain the first intron and protect or avoid specific motifs.
Article
Cell & Tissue Engineering
Hanwen Yu, Manqi Chen, Yuanlang Hu, Songbang Ou, Xiu Yu, Shiqi Liang, Niannian Li, Mingzhu Yang, Xuhui Kong, Chuanbo Sun, Shiqi Jia, Qingxue Zhang, Lin Liu, Laurence D. Hurst, Ruiqi Li, Wenjun Wang, Jichang Wang
Summary: Reprogramming of H3K9me3-dependent heterochromatin plays an important role in early human development, affecting the interaction between specific promoters and enhancers, regulating zygotic genome activation and transcription of inner cell mass-specific genes.
Article
Evolutionary Biology
Alexander T. Ho, Laurence D. Hurst
Summary: The usage of the TGA stop codon in protein coding genes is influenced by G + C content, while TAA may be the universally optimal stop codon. Despite being influenced by mutation bias and selection, G + C pressure is the main determinant of trends in TGA usage between different species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Laurence D. Hurst
Summary: It has been found that many human embryos die due to abnormal chromosome numbers, which is mainly caused by the failure of chromosome separation during maternal meiosis. Additionally, the asymmetry of chromosome division is susceptible to the influence of centromeres, leading to aneuploidy. In mammals, the continuous provisioning during in utero and postnatal stages helps mitigate the costs of early death. Therefore, natural selection may favor centromeres that induce lethal aneuploidy as this increases the chances of survival.
Article
Biochemistry & Molecular Biology
Tamas Rasko, Amit Pande, Kathrin Radscheit, Annika Zink, Manvendra Singh, Christian Sommer, Gerda Wachtl, Orsolya Kolacsek, Gizem Inak, Attila Szvetnik, Spyros Petrakis, Mario Bunse, Vikas Bansal, Matthias Selbach, Tamas Orban, Alessandro Prigione, Laurence D. Hurst, Zsuzsanna Izsvak
Summary: The study characterizes a new gene PGBD1, specific to nonmonotreme mammals, under purifying selection, retaining original DNA transposon features and capturing additional domains. PGBD1 was found to have important regulatory functions on genes related to neuronal development, with specific binding activity in the core structural RNA NEAT1 of paraspeckles.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Cristina Fonseca, Jonathan Pettitt, Alison D. Woollard, Adam Rutherford, Wendy Bickmore, Anne Ferguson-Smith, Laurence Hurst
Summary: People have varying attitudes towards well-evidenced science, especially in the context of genetics and allied sciences. Recent research shows that individuals with strongly negative attitudes towards specific genetic technologies often do not objectively understand the science but believe that they do. A study on UK adults further reveals that those with extremely positive or negative attitudes towards genetics are more likely to believe that they understand the science, but only those with positive attitudes have justified self-confidence, regardless of specific technologies.
Article
Multidisciplinary Sciences
Sofia Radrizzani, Cristina D. Fonseca, Alison Woollard, Jonathan Pettitt, Laurence Hurst
Summary: Based on the study on changes in trust in science during the COVID-19 pandemic, we found that factors such as age and pre-pandemic trust level have an impact on trust changes. The increase in trust towards scientists is more significant than the decrease, indicating trust polarization and a backfire effect. These changes have significant implications for public health, as they are predictive of willingness to receive the COVID-19 vaccine.
Article
Biochemistry & Molecular Biology
Manvendra Singh, Aleksandra M. Kondrashkina, Thomas J. Widmann, Jose L. Cortes, Vikas L. Bansal, Jichang D. Wang, Christine Roemer, Marta Garcia-Canadas, Jose L. Garcia-Perez, Laurence D. Hurst, Zsuzsanna Izsvak
Summary: There is much that remains unknown about early human development, including the nature of cell types affected by apoptosis and the definition of the inner cell mass (ICM). In this study, a multi-method analysis of early human embryos was conducted to understand these issues. The discovery of a previously unknown class of cells, called REject cells, helps to define the viable ontogenetic sisters of ICM cells.
Letter
Multidisciplinary Sciences
Long Wang, Alexander T. T. Ho, Laurence D. D. Hurst, Sihai Yang
Article
Biochemical Research Methods
Loveday E. Lewin, Kate G. Daniels, Laurence D. Hurst
Summary: It has been found that initiation optimality codons, which are synonymous codons that promote efficient translation initiation, are not commonly used in native genes encoding highly abundant proteins. However, initiation optimality scores derived from transgene experiments may be relevant for in silico transgene design for a wide range of bacteria.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Stephen Richer, Yuan Tian, Stefan Schoenfelder, Laurence Hurst, Adele Murrell, Giuseppina Pisignano
Summary: This study investigates the differences in three-dimensional chromatin conformation between heterozygous loci, taking into consideration parent-of-origin differences and genome-wide allele-specific chromatin conformation associations. A bioinformatic pipeline called HiCFlow is developed for haplotype assembly and visualization of parental chromatin architecture. The study identifies stable allele-specific interactions at specific gene loci and detects allele-specific differences in A/B compartmentalization. The findings highlight the widespread differences in chromatin conformation and provide insights into allele-specific expressed genes, including previously unidentified ones.
Article
Biochemistry & Molecular Biology
Alexander Thomas Ho, Laurence Daniel Hurst
Summary: The assumption that conservation of sequence implies the action of purifying selection is central to different methodologies, but GC-biased gene conversion (gBGC) can mimic the action of selection. This study focuses on mammalian stop codon evolution and provides evidence supporting the hypothesis that gBGC mimics purifying selection. The findings suggest that sequence conservation may not always indicate purifying selection.