scholarly journals High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

2017 ◽  
Vol 49 (12) ◽  
pp. 1731-1740 ◽  
Author(s):  
Julien Lagarde ◽  
Barbara Uszczynska-Ratajczak ◽  
Silvia Carbonell ◽  
Sílvia Pérez-Lluch ◽  
Amaya Abad ◽  
...  
Keyword(s):  
High Throughput ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Long Read

scholarly journals High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing

2017 ◽  
Author(s):  
Julien Lagarde ◽  
Barbara Uszczynska-Ratajczak ◽  
Silvia Carbonell ◽  
SÍlvia Pérez-Lluch ◽  
Amaya Abad ◽  
...  
Keyword(s):  
High Throughput ◽  
Single Molecule ◽  
Noncoding Rnas ◽  
Splice Junction ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Novel Transcript ◽  
Mouse Tissues ◽  
Long Read ◽  
Full Length Transcript

AbstractAccurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, reference gene collections remain incomplete: many gene models are fragmentary, while thousands more remain uncatalogued–particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third-generation long-read sequencing. We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively. CLS approximately doubles the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter- and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.Abbreviationsbpbase pairFLfull lengthntnucleotideROIread of insert, i.e. PacBio readSJsplice junctionSMRTsingle-molecule real-timeTMtranscript model

Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS)

2020 ◽  
pp. 133-159
Author(s):  
Sílvia Carbonell Sala ◽  
Barbara Uszczyńska-Ratajczak ◽  
Julien Lagarde ◽  
Rory Johnson ◽  
Roderic Guigó
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Long Read

scholarly journals The small peptide world in long noncoding RNAs

2019 ◽  
Vol 20 (5) ◽  
pp. 1853-1864 ◽  
Author(s):  
Seo-Won Choi ◽  
Hyun-Woo Kim ◽  
Jin-Wu Nam
Keyword(s):  
High Throughput ◽  
Functional Significance ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Small Peptides ◽  
Small Peptide ◽  
Plant Genomes ◽  
The Past ◽  
Sequencing Technologies ◽  
Coding Potential

Abstract Long noncoding RNAs (lncRNAs) are a group of transcripts that are longer than 200 nucleotides (nt) without coding potential. Over the past decade, tens of thousands of novel lncRNAs have been annotated in animal and plant genomes because of advanced high-throughput RNA sequencing technologies and with the aid of coding transcript classifiers. Further, a considerable number of reports have revealed the existence of stable, functional small peptides (also known as micropeptides), translated from lncRNAs. In this review, we discuss the methods of lncRNA classification, the investigations regarding their coding potential and the functional significance of the peptides they encode.

scholarly journals Full-length annotation with multi-strategy RNA-seq uncovers transcriptional regulation of lncRNAs in diploid cotton G. arboreum1

2020 ◽  
Author(s):  
Xiaomin Zheng ◽  
Yanjun Chen ◽  
Yifan Zhou ◽  
Danyang Li ◽  
Keke Shi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Rna Seq ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Protein Coding ◽  
Diploid Cotton ◽  
Cap Analysis

AbstractLong noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. High-throughput and accurate identification of lncRNAs is still lacking in plants. To build an accurate atlas of lncRNA in cotton, we combined Isoform-sequencing (Iso-seq), strand-specific RNA-seq (ssRNA-seq), cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA (PULL) to integrate multi-omics data. A total of 9240 lncRNAs from 21 tissue samples of the diploid cotton Gossypium arboreum were identified. We revealed that alternative usage of transcription start site (TSS) and transcription end site (TES) of lncRNAs occurs pervasively during plant growth and responses to stress. We identified the lncRNAs which co-expressed or be linked to the protein coding genes (PCGs) or GWAS studied SNPs associated with ovule and fiber development. We also mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing (ChIRP-seq) and validated the trans transcriptional regulation of lnc-Ga13g0352 via virus induced gene suppression (VIGS) assay. These findings provide valuable research resources for plant community and broaden our understandings of biogenesis and regulation function of plant lncRNAs.One sentence summaryThe full-length annotation and transcriptional regulation of long noncoding RNAs in cotton.

Annotating full-length long noncoding RNAs

2018 ◽  
Vol 15 (1) ◽  
pp. 16-16
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length

scholarly journals Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ying Wan ◽  
Xiaoyang Liu ◽  
Dongwang Zheng ◽  
Yuying Wang ◽  
Huan Chen ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Systematic Identification

scholarly journals HIT-scISOseq: High-throughput and High-accuracy Single-cell Full-length Isoform Sequencing for Corneal Epithelium

2020 ◽  
Author(s):  
Ying-Feng Zheng ◽  
Zhi-Chao Chen ◽  
Zhuo-Xing Shi ◽  
Kun-Hua Hu ◽  
Jia-Yong Zhong ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Cost Effective ◽  
Pcr Primers ◽  
Cell Types ◽  
High Accuracy ◽  
Full Length ◽  
Pacbio Sequencing ◽  
Simple Method ◽  
Long Read

AbstractSingle-cell isoform sequencing can reveal transcriptomic dynamics in individual cells invisible to bulk- and single-cell RNA analysis based on short-read sequencing. However, current long-read single-cell sequencing technologies have been limited by low throughput and high error rate. Here we introduce HIT-scISOseq for high-throughput single-cell isoform sequencing. This method was made possible by full-length cDNA capture using biotinylated PCR primers, and by our novel library preparation procedure that combines head-to-tail concatemeric full-length cDNAs into a long SMRTbell insert for high-accuracy PacBio sequencing. HIT-scISOseq yields > 10 million high-accuracy full-length isoforms in a single PacBio Sequel II 8M SMRT Cell, providing > 8 times more data output than the standard single-cell isoform PacBio sequencing protocol. We exemplified HIT-scISOseq by first studying transcriptome profiles of 4,000 normal and 8,000 injured corneal epitheliums from cynomolgus monkeys. We constructed dynamic transcriptome landscapes of known and rare cell types, revealed novel isoforms, and identified injury-related splicing and switching events that are previously not accessible with low throughput isoform sequencing. HIT-scISOseq represents a high-throughput, cost-effective, and technically simple method to accelerate the burgeoning field of long-read single-cell transcriptomics.

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