Large Introns of 5 to 10 Kilo Base Pairs Can Be Spliced out in Arabidopsis

Chang, Ning; Sun, Qingqing; Hu, Jinglei; An, Chuanjing; Gao, and Hongbo

doi:10.3390/genes8080200

Cited by 19 publications

(19 citation statements)

References 17 publications

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“…Trimmed files were then mapped to the genome by STAR using --outFilterMultimapNmax 1 --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterScoreMinOverLread 0.9 options. Intron length limit (10,000 bp) were set based on the characteristics of the Arabidopsis genome (Chang et al, 2017). Please consult Supplemental Table 2 for basic statistics applied on RNA-seq datasets.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Tissue-specific transcriptome profiling of theArabidopsis thalianainflorescence stem reveals local cellular signatures

Shi¹,

Jouannet²,

Agustí

et al. 2020

Preprint

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One sentence summary:A genome-wide high-resolution gene expression map of the Arabidopsis inflorescence stem is established. AbstractGenome-wide gene expression maps with a high spatial resolution have substantially accelerated molecular plant science. However, the number of characterized tissues and growth stages is still small because of the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterize transcriptomes of xylem vessels, fibers, the proximal and the distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classify more than 15,000 genes as being differentially expressed among different stem tissues and reveal known and novel tissue-specific cellular signatures. By determining transcription factor binding regions enriched in promoter regions of differentially expressed genes, we furthermore provide candidates for tissue-specific transcriptional regulators. Our datasets predict expression profiles of an exceptional amount of genes and allow generating hypotheses toward the spatial organization of physiological processes. Moreover, we demonstrate that information on gene expression in a broad range of mature plant tissues can be established with high spatial resolution by nuclear mRNA profiling.

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Section: Bioinformatic Analysesmentioning

confidence: 99%

Tissue-specific transcriptome profiling of theArabidopsis thalianainflorescence stem reveals local cellular signatures

Shi¹,

Jouannet²,

Agustí

et al. 2020

Preprint

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“…According to data shown in the TAIR 10.0 annotation of the Arabidopsis genome and our previous analysis ( Chang et al. 2017 ), the Arabidopsis genome has 62,565 introns that are shorter than 100 bp, and these constitute 48.93% of all the introns in the genome.…”

Section: Resultsmentioning

confidence: 91%

“…During evolution, introns show signs of extension and retraction. We have shown that transposable elements and large indels could be the causes of this phenomenon for large introns in Arabidopsis ( Chang et al. 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The Putative Smallest Introns in the Arabidopsis Genome

Cheng

Zhou

Miao

et al. 2018

Genome Biology and Evolution

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Most eukaryotic genes contain introns, which are noncoding sequences that are removed during premRNA processing. Introns are usually preserved across evolutionary time. However, the sizes of introns vary greatly. In Arabidopsis, some introns are longer than 10 kilo base pairs (bp) and others are predicted to be shorter than 10 bp. To identify the shortest intron in the genome, we analyzed the predicted introns in annotated version 10 of the Arabidopsis thaliana genome and found 103 predicted introns that are 30 bp or shorter, which make up only 0.08% of all introns in the genome. However, our own bioinformatics and experimental analyses found no evidence for the existence of these predicted introns. The predicted introns of 30–39 bp, 40–49 bp, and 50–59 bp in length are also rare and constitute only 0.07%, 0.2%, and 0.28% of all introns in the genome, respectively. An analysis of 30 predicted introns 31–59 bp long verified two in this range, both of which were 59 bp long. Thus, this study suggests that there is a limit to how small introns in A. thaliana can be, which is useful for the understanding of the evolution and processing of small introns in plants in general.

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“…We have found such large introns in other genes involved in meiosis such as FIGL1 , HEI10 , KU70 , Met1A , and MSH2 but their significance remains to be determined. It is possible that they could relate to gene expression regulation as reported in Drosophila where large introns can promote alternative splicing ( Kandul and Noor, 2009 ) although only 16 such large introns (>5kbp) were found in Arabidopsis ( Chang et al, 2017 ). Although we detected eight RTEL1 transcripts in barley anther and meiocyte transcriptome ( Barakate et al, 2021 ), only one isoform was expressed.…”

Section: Discussionmentioning

confidence: 99%

Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers

et al. 2021

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Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helicase 1 (RTEL1) DNA helicase was previously shown to enforce the number of meiotic COs in Caenorhabditis elegans but its function in plants has been studied only in the vegetative phase. Here, we characterised barley RTEL1 gene structure and expression using RNA-seq data previously obtained from vegetative and reproductive organs and tissues. Using RNAi, we downregulated RTEL1 expression specifically in reproductive tissues and analysed its impact on recombination using a barley 50k iSelect SNP Array. Unlike in C. elegans, in a population segregating for RTEL1 downregulated by RNAi, high resolution genome-wide genetic analysis revealed a significant increase of COs at distal chromosomal regions of barley without a change in their total number. Our data reveal the important role of RTEL1 helicase in plant meiosis and control of recombination.

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Large Introns of 5 to 10 Kilo Base Pairs Can Be Spliced out in Arabidopsis

Cited by 19 publications

References 17 publications

Tissue-specific transcriptome profiling of theArabidopsis thalianainflorescence stem reveals local cellular signatures

Tissue-specific transcriptome profiling of theArabidopsis thalianainflorescence stem reveals local cellular signatures

The Putative Smallest Introns in the Arabidopsis Genome

Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers

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