Since their initial discovery in maize, transposable elements (TEs) have emerged as being integral to the evolution of maize, accounting for 80% of its genome. However, the repetitive nature of TEs has hindered our understanding of their regulatory potential. Here, we demonstrate that long-read chromatin fiber sequencing (Fiber-seq) permits the comprehensive annotation of the regulatory potential of maize TEs. We uncover that only 94 LTR retrotransposons contain the functional epigenetic architecture required for mobilization within maize leaves. This epigenetic architecture degenerates with evolutionary age, resulting in solo TE enhancers being preferentially marked by simultaneous hyper-CpG methylation and chromatin accessibility, an architecture markedly divergent from canonical enhancers. We find that TEs shape maize gene regulation by creating novel promoters within the TE itself as well as through TE-mediated gene amplification. Lastly, we uncover a pervasive epigenetic code directing TEs to specific loci, including that locus that sparked McClintock's discovery of TEs.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11257541PMC
http://dx.doi.org/10.1101/2024.07.10.602892DOI Listing

Publication Analysis

Top Keywords

regulatory potential
12
transposable elements
8
epigenetic architecture
8
maize
6
tes
6
potential transposable
4
elements maize
4
maize initial
4
initial discovery
4
discovery maize
4

Similar Publications

Influencers are content creators who post online about their lives and can amass a significant following. Influencers can be dangerous by negatively affecting their followers' body image and marketing products in a deceptive way. The limited academic writings which consider influencer regulation note an incongruency between influencer conduct and the corresponding regulatory system.

View Article and Find Full Text PDF

Taurine prevents mitochondrial dysfunction and protects mitochondria from reactive oxygen species and deuterium toxicity.

Amino Acids

January 2025

Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece.

Taurine, although not a coding amino acid, is the most common free amino acid in the body. Taurine has multiple and complex functions in protecting mitochondria against oxidative-nitrosative stress. In this comprehensive review paper, we introduce a novel potential role for taurine in protecting from deuterium (heavy hydrogen) toxicity.

View Article and Find Full Text PDF

Drug-induced eosinophilic pneumonia (EP) is an uncommon adverse drug reaction. Many drugs have been reported to cause EP, the evidence mainly being in the form of case reports/case series. This study aims to conduct an exploratory analysis of the United States Food and Drug Administration adverse event reporting system (FAERS) database to identify previously unknown drugs that can cause EP and supplement the available evidence for known culprit drugs.

View Article and Find Full Text PDF

RNF138 contributes to cisplatin resistance in nasopharyngeal carcinoma cells.

Sci Rep

January 2025

Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), No. 999 Donghai Avenue, Taizhou City, 318000, Zhejiang Province, China.

Resistance to chemotherapy is a significant concern in the treatment of nasopharyngeal carcinoma (NPC), and occurs due to various mechanisms. This study is aimed to evaluate the effects of RING finger protein 138 (RNF138) in the development of cisplatin resistance to NPC. After gene overexpression and silencing, the expression levels of RNF138 were evaluated.

View Article and Find Full Text PDF

The therapeutic potential of circular RNAs.

Nat Rev Genet

January 2025

Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.

Over the past decade, research into circular RNA (circRNA) has increased rapidly, and over the past few years, circRNA has emerged as a promising therapeutic platform. The regulatory functions of circRNAs, including their roles in templating protein translation and regulating protein and RNA functions, as well as their unique characteristics, such as increased stability and a favourable immunological profile compared with mRNAs, make them attractive candidates for RNA-based therapies. Here, we describe the properties of circRNAs, their therapeutic potential and technologies for their synthesis.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!