Brachypodium distachyon Long Noncoding RNAs: Genome-Wide Identification and Expression Analysis

Quattro, Concetta De; Mica, Erica; Pè, Mario Enrico; Bertolini, Edoardo

doi:10.1007/978-1-4939-7278-4_3

Cited by 7 publications

(7 citation statements)

References 25 publications

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“…Improvements in nucleotide sequencing technology have revealed the existence of lncRNAs, some of which act as the regulators of a range of eukaryotic cellular processes [15,37,[46][47][48]. The number of lncRNAs identified by transcriptomic analyses reflects the depth of the sequencing method applied.…”

Section: Discussionmentioning

confidence: 99%

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Tian

Guo

Zhang³

et al. 2020

BMC Plant Biol

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Background: Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Results: A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions: This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

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Section: Discussionmentioning

confidence: 99%

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Tian

Guo

Zhang³

et al. 2020

BMC Plant Biol

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“…High-confidence lncRNAs were annotated according to De Quattro et al [56,113]. Non-redundant transcripts assembled from the RNA-seq data were scanned using published criteria for defining lncRNA transcripts [58,114]: we filtered out sequences that i) were less than 200 bp, ii) were open reading frame encoding proteins with more than 100 amino acids, iii) were known functional protein domains deposited in the database Pfam v30 [115] (BLASTX cutoff E-value ≤1.0E − 3), iv) had the potential to encode functional proteins based on the program CPC [116], and/or v) had homology with maize structural RNA domains deposited in the database Rfam v12 [117] (BLASTN cutoff E-value 1.0E ≤ − 10).…”

Section: Annotation and Quantification Of Long Non-coding Rnasmentioning

confidence: 99%

The regulatory landscape of early maize inflorescence development

et al. 2020

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Background: The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Result: Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3′ ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long noncoding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. Conclusions: These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

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“…High-confidence lncRNAs were annotated according to De Quattro et al [48,122]. Non-redundant transcripts assembled from the RNA-seq data were scanned using published criteria for defining lncRNA transcripts [50,123]: we filtered out sequences that i) were less than 200 bp, ii) were open reading frame encoding proteins with more than 100 amino acids, iii) were known functional protein domains deposited in the database Pfam v30 [124] (BLASTX cutoff E-value ≤ 1.0E -3), iv) had the potential to encode functional proteins based on the program CPC [125], and/or v) had homology with maize structural RNA domains deposited in the database Rfam v12 [126] (BLASTN cutoff E-value 1.0E ≤ -10).…”

Section: Annotation and Quantification Of Long Non-coding Rnasmentioning

confidence: 99%

The regulatory landscape of early maize inflorescence development

Parvathaneni

Bertolini

Shamimuzzaman

et al. 2019

Preprint

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The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profiled accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classified approximately 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach mapped regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor (TF) occupancy data were used to annotate regulatory factors, such as combinatorial TF binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity revealed new SNP-trait associations in known regulators of inflorescence development as well as new candidates. These analyses provide a comprehensive look into the cisregulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

show abstract

Brachypodium distachyon Long Noncoding RNAs: Genome-Wide Identification and Expression Analysis

Cited by 7 publications

References 25 publications

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

The regulatory landscape of early maize inflorescence development

The regulatory landscape of early maize inflorescence development

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