Genome-Wide Identification and Diversity Analysis of DGAT1, DGAT2, LPAT2, WRI1, FAD2, FAD3, and FAE1 Genes in Terms of Breeding Importance in Brassica carinata - Cytology and Genetics

Abstract Abyssinian mustard, or carinata (Brassica carinata), is currently considered one of the most promising alternative oilseed crops, particularly for liquid biofuel production. Breeding and genetic engineering studies that enhance seed oil quality and yield have become increasingly important as the agricultural use of this crop expands. Leveraging publicly available genomic resources for carinata simplifies crop improvement and enables a targeted focus on loci or genes involved in lipid and fatty acid biosynthesis. This study aimed to conduct a genome-wide identification and comprehensive analysis of genes regulating fatty acid and neutral lipid synthesis (DGAT1, DGAT2, LPAT2, WRI1, FAD2, FAD3, and FAE1) in the allopolyploid species B. carinata. A total of 24 genes were identified, with each enzyme encoded by multiple homoeologs. These genes shared a high degree of sequence similarity but differed in noncoding regions (introns and promoter sequences), which allowed us to identify several microsatellite loci specific to each gene family. The results support the development of highly accurate molecular markers for marker-assisted breeding, which will accelerate the creation of B. carinata varieties with enhanced oil quality and increased seed oil content.

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators - Nature Communications

Splicing is a vital biological reaction and a druggable pathway to treat infection, genetic diseases and cancer. Here, the authors describe how splicing is modulated by small molecules that target the conserved splicing active site in the group II introns.

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Mechanisms of Intron-Mediated Enhancement of Expression: Welcome to the Hotel California - Cytology and Genetics

Abstract The phenomenon of the positive influence of introns on the expression of a corresponding gene, which is called intron-mediated enhancement (IME), is characteristic of a wide variety of organisms, including nematodes, insects, mammals, fungi, and plants, and occurs due to an as-yet-undefined fundamental mechanism. IME introns have been used for a long time, in particular, in plant biotechnology. Understanding the mechanisms of this phenomenon allows predicting and easily generating stimulatory introns with the given properties and creating highly advantageous phenotypes. It will also give the greenlight to the use of IME in gene therapy and to improve the production of pharmaceutical proteins. In this review, we analysed previously proposed models of IME functioning mechanisms and identified factors that can directly or indirectly determine IME under different conditions and at different levels of gene expression, such as experimental methods of IME research, regulatory RNAs, sequence properties, intron position and orientation, factors at the levels of DNA, transcription, splicing, mRNA, translation, genes in which IME is detected, tissue specificity, repression and how some factors relate to each other by importance. Since there is no single mechanism of IME, and the effect may differ in different species, when modelling this process, only the cases of IME affecting the same level of expression should be compared with each other, taking into account the experimental conditions. Identifying the biological factors that may determine IME and the relationship between them will help in the future to create a corresponding data set suitable for machine learning and try to solve the mystery of the IME phenomenon using machine learning.

Noncoding translation mitigation - Nature

Combining genome-wide CRISPR screens with massively parallel analyses of human and random DNA sequences reveal a unified mechanism for the surveillance and evolution of translation products from annotated noncoding DNA.

The position of the longest intron is related to biological functions in some human genes

The evidence that introns can influence different levels of transfer of genetic information between DNA and the final product is increasing. Longer first introns were found to be a general property of eukaryotic gene structure and shown to contain a higher ...

Long-standing genomic mystery about the origins of introns explained in new study

One of the most long-standing, fundamental mysteries of biology surrounds the poorly understood origins of introns. Introns are segments of noncoding DNA that must be removed from the genetic code before it is translated in the process of making proteins. Introns are an ancient feature found across all eukaryotic life, a wide range of organisms that spans all animals, plants, fungi, and protists, but are absent in prokaryotic genomes such as those of bacteria. There is a massive variation in the number of introns found in different species' genomes, even between closely related species.