IC4R002-lncRNA-2014-25517485 - Revision history

Zhennan: /* Research Findings */

2016-06-23T03:24:26Z

‎Research Findings

Zhennan: /* Research Findings */

2016-06-23T03:21:47Z

‎Research Findings

Zhennan: /* Plant Culture & Treatment */

2016-06-23T03:14:53Z

‎Plant Culture & Treatment

Zhennan: /* Plant Culture & Treatment */

2016-06-23T03:14:35Z

‎Plant Culture & Treatment

Zhennan: /* Plant Culture & Treatment */

2016-06-23T03:14:07Z

‎Plant Culture & Treatment

Zhennan: /* Research Findings */

2016-06-23T03:12:21Z

‎Research Findings

Zhennan: /* Research Findings */

2016-06-23T03:08:43Z

‎Research Findings

Zhennan: /* Plant Culture & Treatment */

2016-06-23T03:04:09Z

‎Plant Culture & Treatment

Zhennan: /* Plant Culture & Treatment */

2016-06-23T03:03:59Z

‎Plant Culture & Treatment

Zhennan: /* Corresponding Author */

2016-06-23T03:02:04Z

‎Corresponding Author

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 ==Research Findings==
 * To systematically identify lncRNAs related to rice reproduction, we performed whole transcriptome ssRNA-seq of rice anthers, pistils, seeds that were harvested 5 DAP and shoots that were harvested 14 DAG (the sequencing results included 3.89×10 8 reads; Additional file 1; Sequence Read Archive (SRA) accession number SRP047482). We then developed a rice lncRNA computational identification pipeline based on RNA-seq data ('''Figure 1''') using 4 whole transcriptome ssRNA-seq data sets and 40 available poly(A) RNA-seq data sets (1.23×10 9 reads). These datasets covered most of the organs and stages involved in rice reproduction (Additional file 1) and were suitable for the identification of reproduction-related lncRNAs. Our lncRNA identification strategy comprised three key procedures ('''Figure 1''').First, the rice transcriptome was reconstructed from all of the RNA-seq datasets using Cufflink2.0. After filtering out infrequently expressed transcripts (those showing FPKM (fragments per kilobase of transcript per million mapped reads) scores <0.5 in all samples) and transcripts without strand information, we recovered 77.4% (30,219/39,045) of the non-transposable element (non-TE)-related mRNAs in the datasets (the mRNAs discussed in the following sections are non-TE related mRNAs unless otherwise specified). The efficient recovery of known protein-coding genes indicated that the dataset employed here was suitable for the recovery of novel transcribed regions of the rice genome.
-[[File:IC4R004-GWAS-2015-25371505-2.PNG|500px|thumb|right|'''Table 1''' ''Effect of ozone stress on phenotypic values'']]
+[[File:IC4R002-lncRNA-2014-25517485-2.PNG|500px|thumb|right|'''Figure 2''' '' Properties of rice lncRNAs.'']]
 * We characterized the basic genomic features of the obtained lncRNAs and compared these features with the available features of Arabidopsis or human lncRNAs or to rice protein-coding genes where appropriate. We found that only a small fraction (median percentage, 6.5%) of the sequence of most of the lncNATs was antisense overlapped by protein-coding mRNA (Figure 2A) and that lincRNAs and lncNATs are similar in many aspects ('''Figure 2'''). To display the characteristics of lincRNAs and lncNATs more clearly, we analyzed the characteristics of lincRNAs and lncNATs separately in the following comparisons. Similar to findings for Arabidopsis, only around half of lncRNAs were spliced (46.5% for lincRNAs, 65.9% for lncNATs). In contrast, more than 98% of human lncRNAs are spliced ('''Figure 2B'''). Rice lncRNAs have fewer exons than mRNAs (2.21 versus 4.67 on average, respectively; 2.10 exons for lincRNAs and 2.42 exons for lncNATs), but their exon lengths (median length of 323 nucleotides; 322 nucleotides for lincRNAs, 298 nucleotides for lncNATs) are longer than those of mRNA (median length of 159 nucleotides) ('''Figure 2C'''). Full-length rice lncRNA transcripts (median length of852 nucleotides; 800 nucleotides for lincRNAs, 950 nucleotides for lncNATs) are longer than Arabidoposis lncRNA transcripts (median length of 285 nucleotides) and human lncRNA transcripts (median length of 592 nucleotides), and are generally shorter than protein-coding transcripts (median length of 1,411 nucleotides) (Figure 2D). Rice lncRNAs generally do not overlap with repeat sequences ('''Figure 2E'''); fewer repeats-overlapped rice lncRNAs than repeats overlapped rice mRNAs and repeats-overlapped human lncRNAs. Like Arabidopsis lncRNAs, only a small proportion of rice lncRNAs (122 of 1,624 lincRNAs, 7.5%; 44 of 600 lncNATs, 7.3%) generate sRNAs (Additional file 3), implying that these lncRNAs might function through generating sRNAs. Interestingly, rice lncRNAs were much more A/U-rich than the coding sequences and the 5′UTRs of protein-coding genes but were less A/U-rich than 3′to appear in divergent orientations with respect to the closest neighboring protein-coding genes. However, we did not observe a stronger correlation between the expression of rice lincRNAs and their nearest neighbors than that between adjacent protein-coding genes (Figure 2G), although the expression of lncNATs is more highly correlated with convergent and divergent overlapped mRNA than with tandem overlapped mRNAs. UTRs that use A/U-rich elements to regulate mRNA degradation ('''Figure 2F'''). This characteristic is conserved in Arabidopsis and animal lncRNAs, implying that this feature might be related to the functions of lncRNAs. Rice lincRNAs are most likely to appear in divergent orientations with respect to the closest neighboring protein-coding genes. However, we did not observe a stronger correlation between the expression of rice lincRNAs and their nearest neighbors than that between adjacent protein-coding genes ('''Figure 2G'''), although the expression of lncNATs is more highly correlated with convergent and divergent overlapped mRNA than with tandem overlapped mRNAs.

@@ Line 15: / Line 15: @@
 [[File:IC4R004-GWAS-2015-25371505-2.PNG|500px|thumb|right|'''Table 1''' ''Effect of ozone stress on phenotypic values'']]
+* We characterized the basic genomic features of the obtained lncRNAs and compared these features with the available features of Arabidopsis or human lncRNAs or to rice protein-coding genes where appropriate. We found that only a small fraction (median percentage, 6.5%) of the sequence of most of the lncNATs was antisense overlapped by protein-coding mRNA (Figure 2A) and that lincRNAs and lncNATs are similar in many aspects ('''Figure 2'''). To display the characteristics of lincRNAs and lncNATs more clearly, we analyzed the characteristics of lincRNAs and lncNATs separately in the following comparisons. Similar to findings for Arabidopsis, only around half of lncRNAs were spliced (46.5% for lincRNAs, 65.9% for lncNATs). In contrast, more than 98% of human lncRNAs are spliced ('''Figure 2B'''). Rice lncRNAs have fewer exons than mRNAs (2.21 versus 4.67 on average, respectively; 2.10 exons for lincRNAs and 2.42 exons for lncNATs), but their exon lengths (median length of 323 nucleotides; 322 nucleotides for lincRNAs, 298 nucleotides for lncNATs) are longer than those of mRNA (median length of 159 nucleotides) ('''Figure 2C'''). Full-length rice lncRNA transcripts (median length of852 nucleotides; 800 nucleotides for lincRNAs, 950 nucleotides for lncNATs) are longer than Arabidoposis lncRNA transcripts (median length of 285 nucleotides) and human lncRNA transcripts (median length of 592 nucleotides), and are generally shorter than protein-coding transcripts (median length of 1,411 nucleotides) (Figure 2D). Rice lncRNAs generally do not overlap with repeat sequences ('''Figure 2E'''); fewer repeats-overlapped rice lncRNAs than repeats overlapped rice mRNAs and repeats-overlapped human lncRNAs. Like Arabidopsis lncRNAs, only a small proportion of rice lncRNAs (122 of 1,624 lincRNAs, 7.5%; 44 of 600 lncNATs, 7.3%) generate sRNAs (Additional file 3), implying that these lncRNAs might function through generating sRNAs. Interestingly, rice lncRNAs were much more A/U-rich than the coding sequences and the 5′UTRs of protein-coding genes but were less A/U-rich than 3′to appear in divergent orientations with respect to the closest neighboring protein-coding genes. However, we did not observe a stronger correlation between the expression of rice lincRNAs and their nearest neighbors than that between adjacent protein-coding genes (Figure 2G), although the expression of lncNATs is more highly correlated with convergent and divergent overlapped mRNA than with tandem overlapped mRNAs. UTRs that use A/U-rich elements to regulate mRNA degradation ('''Figure 2F'''). This characteristic is conserved in Arabidopsis and animal lncRNAs, implying that this feature might be related to the functions of lncRNAs. Rice lincRNAs are most likely to appear in divergent orientations with respect to the closest neighboring protein-coding genes. However, we did not observe a stronger correlation between the expression of rice lincRNAs and their nearest neighbors than that between adjacent protein-coding genes ('''Figure 2G'''), although the expression of lncNATs is more highly correlated with convergent and divergent overlapped mRNA than with tandem overlapped mRNAs.
 == Labs working on this Project ==

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 ==Plant Culture & Treatment==
 * Total RNA was obtained from rice anthers before flowering, pistils before flowering, spikelets 5 DAP and shoots 14 DAG; these samples were used for sequencing. The preparation of whole transcriptome libraries and deep sequencing were performed by the Annoroad Gene Technology Corporation (Beijing, PR China). Whole transcriptome libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system and qPCR (Kapa Biosystems, Woburn, MA, USA). The resulting libraries were sequenced initially on a HiSeq 2000 instrument that generated paired-end reads of 100 nucleotides. The sequencing data have been submitted to the NCBI Sequence Read Archive (SRA accession number SRP047482).
-[[File:IC4R002-lncRNA-2014-25517485-1.PNG|1000px|thumb|right|'''Figure 1''' ''An integrative computational pipeline for the systematic identification of lncRNAs in rice.'']]
+[[File:IC4R002-lncRNA-2014-25517485-1.PNG|1000px|thumb|center|'''Figure 1''' ''An integrative computational pipeline for the systematic identification of lncRNAs in rice.'']]
 ==Research Findings==

@@ Line 9: / Line 9: @@
 ==Plant Culture & Treatment==
 * Total RNA was obtained from rice anthers before flowering, pistils before flowering, spikelets 5 DAP and shoots 14 DAG; these samples were used for sequencing. The preparation of whole transcriptome libraries and deep sequencing were performed by the Annoroad Gene Technology Corporation (Beijing, PR China). Whole transcriptome libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system and qPCR (Kapa Biosystems, Woburn, MA, USA). The resulting libraries were sequenced initially on a HiSeq 2000 instrument that generated paired-end reads of 100 nucleotides. The sequencing data have been submitted to the NCBI Sequence Read Archive (SRA accession number SRP047482).
-[[File:IC4R002-lncRNA-2014-25517485-1.PNG|1000px|thumb|center|'''Figure 1''' ''An integrative computational pipeline for the systematic identification of lncRNAs in rice.'']]
+[[File:IC4R002-lncRNA-2014-25517485-1.PNG|1000px|thumb|right|'''Figure 1''' ''An integrative computational pipeline for the systematic identification of lncRNAs in rice.'']]
 ==Research Findings==

@@ Line 9: / Line 9: @@
 ==Plant Culture & Treatment==
 * Total RNA was obtained from rice anthers before flowering, pistils before flowering, spikelets 5 DAP and shoots 14 DAG; these samples were used for sequencing. The preparation of whole transcriptome libraries and deep sequencing were performed by the Annoroad Gene Technology Corporation (Beijing, PR China). Whole transcriptome libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system and qPCR (Kapa Biosystems, Woburn, MA, USA). The resulting libraries were sequenced initially on a HiSeq 2000 instrument that generated paired-end reads of 100 nucleotides. The sequencing data have been submitted to the NCBI Sequence Read Archive (SRA accession number SRP047482).
-[[File:|1000px|thumb|center|'''Figure 1''' '' Box plots for relative phenotypic values. The median of each trait is shown as the horizontal bar in the box, and the upper and lower sides of a box represent the first and third quartile values of the distribution, respectively. Whiskers extended to 1.5 times the interquartile range (box size) or to the maximum/minimum values.'']]
+[[File:IC4R002-lncRNA-2014-25517485-1.PNG|1000px|thumb|center|'''Figure 1''' ''An integrative computational pipeline for the systematic identification of lncRNAs in rice.'']]
 ==Research Findings==

← Older revision		Revision as of 03:08, 23 June 2016
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	[[File:IC4R004-GWAS-2015-25371505-2.PNG\|500px\|thumb\|right\|'''Table 1''' ''Effect of ozone stress on phenotypic values'']]		[[File:IC4R004-GWAS-2015-25371505-2.PNG\|500px\|thumb\|right\|'''Table 1''' ''Effect of ozone stress on phenotypic values'']]

−	*	+	*

	== Labs working on this Project ==		== Labs working on this Project ==

← Older revision		Revision as of 03:02, 23 June 2016
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	==Corresponding Author==		==Corresponding Author==
−	* ''' '''()	+	* ''' Yue-Qin Chen '''(lsscyq@mail.sysu.edu.cn)