Genome‐wide profiling of circular RNAs, alternative splicing, and R‐loops in stem‐differentiating xylem of Populus trichocarpa

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.

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Genome-wide Analysis of Alternative Pre-mRNA Splicing

Journal of Biological Chemistry ◽

10.1074/jbc.r700033200 ◽

2007 ◽

Vol 283 (3) ◽

pp. 1229-1233 ◽

Cited By ~ 80

Author(s):

Claudia Ben-Dov ◽

Britta Hartmann ◽

Josefin Lundgren ◽

Juan Valcárcel

Keyword(s):

Alternative Splicing ◽

Large Scale ◽

Mrna Splicing ◽

Diagnostic Tools ◽

Primary Transcript ◽

Genome Wide ◽

Human Genes ◽

Multicellular Organisms ◽

Eukaryotic Genomes ◽

Key Questions

Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.

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Genome-Wide Identification of Evolutionarily Conserved Alternative Splicing Events in Flowering Plants

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2015.00033 ◽

2015 ◽

Vol 3 ◽

Cited By ~ 47

Author(s):

Srikar Chamala ◽

Guanqiao Feng ◽

Carolina Chavarro ◽

W. Brad Barbazuk

Keyword(s):

Alternative Splicing ◽

Flowering Plants ◽

Genome Wide ◽

Evolutionarily Conserved ◽

Alternative Splicing Events

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Ovary-derived circular RNAs profile analysis during the onset of puberty in gilts

BMC Genomics ◽

10.1186/s12864-021-07786-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiangchun Pan ◽

Wentao Gong ◽

Yingting He ◽

Nian Li ◽

Hao Zhang ◽

...

Keyword(s):

Alternative Splicing ◽

Signaling Pathway ◽

Gene Networks ◽

Profile Analysis ◽

Mirna Gene ◽

Mapk Signaling ◽

Circular Rnas ◽

Ras Signaling ◽

Female Reproduction ◽

Non Coding Rna

Abstract Background In mammals, the ovary is the essential system of female reproduction for the onset of puberty, and the abnormal puberty has negative outcomes on health. CircRNA is a non-coding RNA produced by non-canonical alternative splicing (AS). Several studies have reported that circRNA is involved in the gene regulation and plays an important role in some human diseases. However, the contribution of circRNA has received little known within the onset of puberty in ovary. Results Here, the profiles of ovarian circRNAs across pre-, in- and post-pubertal stages were established by RNA-sEq. In total, 972 circRNAs were identified, including 631 stage-specific circRNAs and 8 tissue-specific circRNAs. The biological functions of parental genes of circRNAs were enriched in steroid biosynthesis, autophagy-animal, MAPK signaling pathway, progesterone-mediated oocyte maturation and ras signaling pathway. Moreover, 5 circRNAs derived from 4 puberty-related genes (ESR1, JAK2, NF1 and ARNT) were found in this study. The A3SS events were the most alternative splicing, but IR events were likely to be arose in post-pubertal ovaries. Besides, the circRNA-miRNA-gene networks were explored for 10 differentially expressed circRNAs. Furthermore, the head-to-tail exon as well as the expressions of 10 circRNAs were validated by the divergent RT-qPCR and sanger sequencing. Conclusions In summary, the profiles of ovarian circRNAs were provided during pubertal transition in gilts, and these results provided useful information for the investigation on the onset of puberty at the ovarian-circRNAs-level in mammals.

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