Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data

Frontiers in Genetics
Min Tu, Yin Li

Abstract

Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3' untranslated regions (3'UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3'UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3'UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3'UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3'UTRs. Importantly, the high-confidence alternative 3'UTR genes significantly overlapped with the genesets that are associated with RNA N6-methyladenosine (m6A) modification, suggesting a clear indication between alternative 3'UTR and m6A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3'UTR usage. In summary, our work exemplifies a transc...Continue Reading

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Citations

May 25, 2021·Frontiers in Genetics·Yin LiRay Ming

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Datasets Mentioned

BETA
PRJNA413691

Methods Mentioned

BETA
RNA-seq
PA-seq

Software Mentioned

priUTR )
PAQR
priUTR
DB
IGV
PolyA
clusterProfiler
Kleat
PlantAPA
Integrative Genomics Viewer ( IGV

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