Mammalian genomes contain highly conserved sequences that are not functionally transcribed. These sequences are single copy and comprise approximately 1-2% of the human genome. Evolutionary analysis strongly supports their functional conservation, although their potentially diverse, functional attributes remain unknown. It is likely that genomic variation in conserved non-genic sequences is associated with phenotypic variability and human disorders. So how might their function and contribution to human disorders be examined?
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http://dx.doi.org/10.1038/nrg1527 | DOI Listing |
Biology (Basel)
July 2024
Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece.
Small open reading frames (sORFs; <300 nucleotides or <100 amino acids) are widespread across all genomes, and an increasing variety of them appear to be translating from non-genic regions. Over the past few decades, peptides produced from sORFs have been identified as functional in various organisms, from bacteria to humans. Despite recent advances in next-generation sequencing and proteomics, accurate annotation and classification of sORFs remain a rate-limiting step toward reliable and high-throughput detection of small proteins from non-genic regions.
View Article and Find Full Text PDFPlant Genome
June 2024
ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India.
Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach.
View Article and Find Full Text PDFNat Struct Mol Biol
March 2024
School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
Genomes encode for genes and non-coding DNA, both capable of transcriptional activity. However, unlike canonical genes, many transcripts from non-coding DNA have limited evidence of conservation or function. Here, to determine how much biological noise is expected from non-genic sequences, we quantify the regulatory activity of evolutionarily naive DNA using RNA-seq in yeast and computational predictions in humans.
View Article and Find Full Text PDFiScience
December 2022
Unidad de Genómica Avanzada (UGA-Langebio), CINVESTAV-IPN, Irapuato, Mexico.
Evolution has long been considered to be a conservative process in which new genes arise from pre-existing genes through gene duplication, domain shuffling, horizontal transfer, overprinting, retrotransposition, etc. However, this view is changing as new genes originating from non-genic sequences are discovered in different organisms. Still, rather limited functional information is available.
View Article and Find Full Text PDFWestern redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self-compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non-genic regions, we genotyped 44 parent trees and 1520 offspring trees representing 26 polycross (PX) families collected from three progeny test sites using 45,378 SNPs. Trees were phenotyped for eight traits related to growth, heartwood and foliar chemistry associated with wood durability and deer browse resistance.
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