- characterization of intermediate-size non- coding RNAs in maize. - In the study of maize, an important crop for both humans and animals, aside from microRNAs and long non-coding RNAs, few studies have been. - Results: We constructed a homogenized cDNA library of 50 – 500 nt RNAs in the maize inbred line Chang 7 – 2.. - Forty of the novel ncRNAs were specific to the Panicoideae, and 24% of them are located on sense-strand of the 5 ′ or 3 ′ terminus of protein coding genes on chromosome. - Expression analysis showed that 43 ncRNAs exhibited significantly altered expression in different tissues or developmental stages of maize seedlings, eight ncRNAs had tissue-specific expression and five ncRNAs were strictly accumulated in the early stage of leaf development. - Further analysis showed that 3 of the 5 stage-specific ncRNAs (Zm-3, Zm-18, and Zm-73) can be highly induced under drought and salt stress, while one snoRNA Zm-8 can be repressed under PEG-simulated drought condition.. - Conclusions: We provided a genome-wide identification and functional analysis of ncRNAs with a size range of 50 – 500 nt in maize. - Full list of author information is available at the end of the article. - 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - transposable-element-derived long intergenic non-coding RNAs (TE-lincRNAs) can be induced or inhibited by cold, heat, drought, salt or highlight stress in rice and maize [22].. - 500 nt) in maize is rare. - Maize (Zea mays L.) is one of the most important food crops in the world. - The maize genome has been sequenced, and nearly 85% of the 3.2 GB genome sequence is com- posed of hundreds of families of transposable elements [43]. - Because the vast majority of the maize genome con- sists of non-protein-coding regions, there is great potential for discovering more ncRNAs in maize.. - seedling and developing grain total RNAs of the maize inbred line Chang 7–2. - Total RNAs were isolated from seven tissues harvested at eleven developmental stages of maize seedlings and five stages of developing grains. - Of the 169 ncRNAs, 58 were known ncRNAs, which contained 42 snRNAs, 7 snoRNAs, 5 Signal recognition particle RNAs (SRPs) and 4 tRNAs. - Results showed that 76 of the 169 unique ncRNAs had counterparts in the three plant genomes, including 3 snRNA families (57 unique snRNAs), 8 snoRNAs, 4 SRPs, 5 tRNAs, and 2 unclassi- fied ncRNAs (Zm-79 and Zm-80). - Almost all of the ncRNAs in maize (166 of 169 transcripts) had counter- parts in the closely-related Sorghum bicolor genome (with identity more than 90. - We also found 128 (76%) ncRNAs had counterparts in the rice genome (with identity more than 95. - ACA box snoRNAs could guide to 30 2’-O-methylation and 8 pseudouridylation sites of maize rRNAs and snRNAs, respectively. - Genomic organization of maize ncRNAs. - We compared the genomic locations of the novel ncRNAs with annotated protein-coding genes in the maize genome. - Results showed that more than half of novel ncRNAs were located in the intergenic regions and 15% in introns (Additional file 2: Table S1), 70%. - host genes of the intronic ncRNAs encode ribosomal proteins (Additional file 2: Figure S1), which is similar to other organisms [23]. - This is similar to rice, in which more than half of the intermediate-size ncRNAs were located around the plus-strand of the 5′ and 3′ terminus of the coding se- quences [45]. - However, different to rice (in which the number of ncRNAs on the 3’ UTR is nearly two-fold as that on the 5’ UTR), 67% of the UTR-origin ncRNAs in maize are located on the 5’ UTR, and 78% of the UTR-origin ncRNAs are snoRNAs, but most of them have no predicated targets to rRNAs or snRNAs, which indicated that they might be orphan snoRNAs.. - To verify that UTR-origin ncRNAs are not degrad- ation products of protein-coding genes, 21 of the 27 UTR-origin ncRNAs were detected by the northern blot.. - Moreover, 93% of the host genes of UTR-origin ncRNAs are annotated as hypothetical or pseudogenes (Additional file 2: Figure S3). - The host genes of the 8 snRNAs are annotated as pseudogenes with cDNA length between 141 nt and 400 nt. - In contrast to rice, in which all snoRNA clusters are in intron and intergenic regions, there are only five intronic and three intergenic snoRNA clusters in maize, and the other 11 snoRNA clusters are located in the UTR regions of protein-coding genes (Additional file 1).. - In rice, half of the snoRNA gene families expanded in the genome through tandem duplications [45]. - In maize, many less tandem duplications were involved in the ori- gination of ncRNAs. - The counterparts of these tandem repeats are also observed in the sorghum and rice genomes, but with different repeat numbers. - They also have counter- parts of tandem repeats in the sorghum, rice, and Arabidopsis genomes with less repeat numbers, indicat- ing that these tandem repeats are highly conserved be- tween monocots and dicots.. - We used northern blots to compare the expression of the intermediate-size ncRNAs in different tissues and developmental stages of maize. - Nearly 65% of the differentially-expressed snoRNAs had no predicted tar- gets and might be orphan snoRNAs.. - Most of the intronic and UTR-origin ncRNAs exhib- ited a similar expression pattern with their host genes in different tissues (Additional file 2: Figure S2 and S5).. - Inter- estingly, Zm-46 had two transcript isoforms in the blade and developing kernel (Additional file 2: Figure S5),. - (a) Expression pattern of three C/D box snoRNAs (Zm-6, Zm-18, and Zm-38) and one unclassified ncRNA (Zm-73) in different tissues of maize by northern blot.. - (b) Expression pattern of four tRNAs in different tissues of maize by northern blot. - (c) Expression pattern of the neighboring genes of Zm-6, tRNA Leu (TAG), and tRNA Ser (GGA) in different tissues of maize by semi-quantitative RT-PCR. - Such as Zm-6, had more expression in the flag leaf, stem apex, and developing kernel, but little or no detectable ex- pression in the blade and root (Fig. - however, its anti- sense upstream gene GRMZM2G099056-T01(roothairless) (genomic position was shown in Additional file 2: Figure S4) accumulated more in the blade and root (Fig. - 2c), indi- cating that Zm-6 might play reverse role in the regulation of roothairless during maize root development.. - We found that each tRNA had multiple copies in the genome. - For example, there are 25 copies of tRNA Ser (GGA) in the maize genome, and all of them are located on the antisense strand of LTR/Copia retro- transposons. - 2b and c), indicating that the tissue-differential expressed tRNAs might function together with their neighboring genes in the leaf development of maize.. - ncRNAs accumulated more in juvenile stage of maize seedling. - With Northern blots analysis, we found that 11 ncRNAs can accumulated more in the. - From 8 to 11 DAG, maize enters into the trefoil stage, the seedling begins transition from juvenile to adult, a lot of protein-coding genes had differential expressions before and after the conversion, such as Teopod genes, the accumulation of Tp1, Tp2, and Tp3 before the transition can promote juvenility of maize seedling [51, 52]. - In our results, the accumulation of snoR- NAs in leaves before the 14th day of seedling indicated their roles in juvenile maintainence of maize.. - 3 Expression pattern of ncRNAs specific (a) and enriched (b) in the early stage of leaf development by northern blot. - Divergency of Monocot and dicot was taken placed around 200 mya ago [56, 57], during the last ~ 3 million years, the size of the maize genome has ex- panded to 2.3 GB via a proliferation of long terminal re- peat retrotransposons (LTR retrotransposons) in the intergenic region . - The large number of Panicoideae-specific ncRNAs being located in the inter- genic region of maize genome indicated that these. - The distribution of maize-novel ncRNAs on chromo- somes was varied, 51% loci were intergenic and 15%. - Twenty-four percent of the novel ncRNAs originated from the 5′ or 3’ UTR of protein coding genes, moreover, a large number of their host genes are annotated as pseudogenes. - Guo et al. - We found the expres- sion of tissue-specific tRNAs accumulated more in the leaf organs of maize, with less or none in the root, meri- stem, and developing kernel. - Stress-induced intermediate-size ncRNAs of maize Plants are exposed to ever-changing environmental con- ditions including drought, freezing, and salinity. - Furthermore, analysis of the expression profiles of the novel ncRNAs showed that 43 ncRNAs changed signifi- cantly during maize development, three ncRNAs can be strongly induced under drought and salt stress, suggest- ing their roles in maize stress response.. - Construction of the cDNA library of 50 – 500 nt ncRNAs in maize. - To construct a full-length intermediate-size (50–500 nt) ncRNA library of maize (Zea mays L.) inbred line Chang 7–2 (gift from Dr. - Jihua Tang of Henan Agricultural University), total RNAs were isolated from seven tissues harvested at eleven developmental stages of maize seed- lings and five stages of developing grains. - First, the seeds of maize were surface-sterilized in 0.1% HgCl 2 for 10 min and rinsed in distilled water 10 times, then soaked in the dark overnight and placed on filter papers soaked with distilled water for another 24 h. - petiole, flag leaf, stem apex and hypocotyl were collected from eleven developmental stages of maize seedlings, the and 42 days after germination (DAG). - Stress treatments of maize seedling. - Maize seeds were surface-sterilized in 0.1% HgCl 2 for 10 min, then rinsed in distilled water 10 times and soaked in the dark overnight at room temperature. - Expression of UTR-origin ncRNAs (A and B) and their host genes (C) as well as ORF-origin U1 snRNAs (D) in different tissues of maize. - Expression of intron-origin ncRNAs and their host genes in different tissues of maize. - Expression of intergenic-origin ncRNAs (A) and their neighboring genes (B) in different tissues of maize. - Genome location of novel ncRNAs of maize. - ncRNAs: Non-coding RNAs. - TE- lincRNAs: Transposable-element-origin long intergenic non-coding RNAs;. - Maize were planted in the farmland of Henan Agricultural University by Dr.. - Seedlings of maize were cultured in the phytotron of Nanyang Normal University. - Long non-coding RNAs: insights into functions. - Harnessing NGS and big data optimally: comparison of miRNA prediction from assembled versus non-assembled sequencing data--the case of the grass Aegilops tauschii Complex genome. - Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. - Transposon-derived non-coding RNAs and their function in plants.. - Genome-wide identification of miRNAs and their targets involved in the developing internodes under maize ears by responding to hormone signaling. - Genome-wide discovery and characterization of maize long non-coding RNAs. - Identification of maize long non-coding RNAs responsive to drought stress. - Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L. - Long non-coding RNAs responsive to salt and boron stress in the hyper-arid Lluteno maize from Atacama Desert. - The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. - Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. - A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. - The effect of a heterochronic mutation, Teopod2, on the cell lineage of the maize shoot. - A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. - Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. - Gene loss and movement in the maize genome. - The paleontology of intergene retrotransposons of maize. - Uneven chromosome contraction and expansion in the maize genome. - The pseudogene-derived long non- coding RNA SFTA1P suppresses cell proliferation, migration, and invasion in gastric cancer. - Genome-wide identification and analysis of microRNA responding to long-term waterlogging in crown roots of maize seedlings. - Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection.. - Long non- coding genes implicated in response to stripe rust pathogen stress in wheat (Triticum aestivum L. - Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. - Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori
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