scholarly journals Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach

Genomics ◽  
2019 ◽  
Vol 111 (4) ◽  
pp. 973-979 ◽  
Author(s):  
Jung-A Kim ◽  
Neha Samir Roy ◽  
Inn-hye Lee ◽  
Ah-Young Choi ◽  
Beom-Soon Choi ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Transcriptome Profiling ◽  
Genome Wide

scholarly journals Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Weipeng Mo ◽  
Bo Liu ◽  
Hong Zhang ◽  
Xianhao Jin ◽  
Dongdong Lu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Transcription Initiation ◽  
Transcription Termination ◽  
Trna Genes ◽  
Genome Wide ◽  
Chimeric Transcripts ◽  
Wide Range ◽  
Wide Scale ◽  
Nascent Rna

Abstract Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5′ Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. Conclusions Our method is applicable to establish a comprehensive termination landscape in a broad range of species.

Comparative Transcriptome Profiling of Disruptive Technology, Single- Molecule Direct RNA Sequencing

2020 ◽  
Vol 15 (2) ◽  
pp. 165-172
Author(s):  
Chaithra Pradeep ◽  
Dharam Nandan ◽  
Arya A. Das ◽  
Dinesh Velayutham
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Transcriptome Assembly ◽  
Transcriptome Profiling ◽  
Read Length ◽  
Complex Nature ◽  
Disruptive Technology ◽  
Sequencing Technology ◽  
Sequencing Technologies ◽  
Long Read

Background: The standard approach for transcriptomic profiling involves high throughput short-read sequencing technology, mainly dominated by Illumina. However, the short reads have limitations in transcriptome assembly and in obtaining full-length transcripts due to the complex nature of transcriptomes with variable length and multiple alternative spliced isoforms. Recent advances in long read sequencing by the Oxford Nanopore Technologies (ONT) offered both cDNA as well as direct RNA sequencing and has brought a paradigm change in the sequencing technology to greatly improve the assembly and expression estimates. ONT enables molecules to be sequenced without fragmentation resulting in ultra-long read length enabling the entire genes and transcripts to be fully characterized. The direct RNA sequencing method, in addition, circumvents the reverse transcription and amplification steps. Objective: In this study, RNA sequencing methods were assessed by comparing data from Illumina (ILM), ONT cDNA (OCD) and ONT direct RNA (ODR). Methods: The sensitivity & specificity of the isoform detection was determined from the data generated by Illumina, ONT cDNA and ONT direct RNA sequencing technologies using Saccharomyces cerevisiae as model. Comparative studies were conducted with two pipelines to detect the isoforms, novel genes and variable gene length. Results: Mapping metrics and qualitative profiles for different pipelines are presented to understand these disruptive technologies. The variability in sequencing technology and the analysis pipeline were studied.

Genome-Wide Transcriptome Profiling of the Neoplastic Giant Cell Tumor of Bone Stromal Cells by RNA Sequencing

2017 ◽  
Vol 118 (6) ◽  
pp. 1349-1360 ◽  
Author(s):  
Carol P.Y. Lau ◽  
Jamie S.L. Kwok ◽  
Joseph C.C. Tsui ◽  
Lin Huang ◽  
Kevin Y. Yang ◽  
...  
Keyword(s):  
Giant Cell Tumor ◽  
Giant Cell ◽  
Rna Sequencing ◽  
Stromal Cells ◽  
Transcriptome Profiling ◽  
Cell Tumor ◽  
Genome Wide

scholarly journals Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer’s disease

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Joseph S. Reddy ◽  
Mariet Allen ◽  
Charlotte C. G. Ho ◽  
Stephanie R. Oatman ◽  
Özkan İş ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Genome Wide Association Study ◽  
Transcriptome Profiling ◽  
Brain Regions ◽  
Common Finding ◽  
Amyloid Angiopathy ◽  
Genome Wide ◽  
A Genome ◽  
Male Sex

AbstractCerebral amyloid angiopathy (CAA) contributes to accelerated cognitive decline in Alzheimer’s disease (AD) dementia and is a common finding at autopsy. The APOEε4 allele and male sex have previously been reported to associate with increased CAA in AD. To inform biomarker and therapeutic target discovery, we aimed to identify additional genetic risk factors and biological pathways involved in this vascular component of AD etiology. We present a genome-wide association study of CAA pathology in AD cases and report sex- and APOE-stratified assessment of this phenotype. Genome-wide genotypes were collected from 853 neuropathology-confirmed AD cases scored for CAA across five brain regions, and imputed to the Haplotype Reference Consortium panel. Key variables and genome-wide genotypes were tested for association with CAA in all individuals and in sex and APOEε4 stratified subsets. Pathway enrichment was run for each of the genetic analyses. Implicated loci were further investigated for functional consequences using brain transcriptome data from 1,186 samples representing seven brain regions profiled as part of the AMP-AD consortium. We confirmed association of male sex, AD neuropathology and APOEε4 with increased CAA, and identified a novel locus, LINC-PINT, associated with lower CAA amongst APOEε4-negative individuals (rs10234094-C, beta = −3.70 [95% CI −0.49—−0.24]; p = 1.63E-08). Transcriptome profiling revealed higher LINC-PINT expression levels in AD cases, and association of rs10234094-C with altered LINC-PINT splicing. Pathway analysis indicates variation in genes involved in neuronal health and function are linked to CAA in AD patients. Further studies in additional and diverse cohorts are needed to assess broader translation of our findings.

Sign in / Sign up

Export Citation Format

Share Document