scholarly journals Extremely fast and incredibly close: co-transcriptional splicing in budding yeast

2016 ◽  
Author(s):  
Edward W.J. Wallace ◽  
Jean D. Beggs
Keyword(s):  
Next Generation Sequencing ◽  
Ribosomal Protein ◽  
Rna Polymerase Ii ◽  
Rna Processing ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Budding Yeast ◽  
List Type ◽  
Next Generation ◽  
Generation Sequencing

AbstractRNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that quantify co-transcriptional splicing in budding yeast. Splicing in yeast is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3’ splice site. Ribosomal protein mRNAs are spliced particularly fast and co-transcriptionally. Intron-mediated regulation of some genes is also likely to be co-transcriptional. We suggest that intermediates of the splicing reaction, missing from current datasets, may hold key information about splicing kinetics.TrendsIndependent next-generation sequencing methods quantify co-transcriptional splicing in budding yeastRibosomal protein mRNAs are spliced particularly fast and co-transcriptionallyIntron-mediated regulation of DBP2 and RPS9A is likely co-transcriptionalSplicing intermediates, missing from current datasets, may hold key information

scholarly journals The genetic analysis of Chinese patients with clonal cytopenias using targeted next-generation sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lijuan Zhang ◽  
YuYe Shi ◽  
Yue Chen ◽  
Shandong Tao ◽  
Wenting Shi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myelodysplastic Syndromes ◽  
Rna Splicing ◽  
Myeloproliferative Neoplasms ◽  
Chinese Patients ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Significant Difference ◽  
Generation Sequencing

Abstract Background Clonal hematopoiesis (CH) can be found in various myeloid neoplasms (MN), such as myelodysplastic syndromes (MDS), myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN), also in pre-MDS conditions. Methods Cytogenetics is an independent prognostic factor in MDS, and fluorescence in-situ hybridization (FISH) can be used as an adjunct to karyotype analysis. In the past 5 years, only 35 of 100 newly diagnosed MDS and MDS/MPN patients were identified abnormalities, who underwent the FISH panel. In addition, we examined a cohort of 51 cytopenic patients suspected MDS or MDS/MPN with a 20-gene next generation sequencing (NGS), including 35 newly diagnosed MN patients and 16 clonal cytopenias of undetermined significance (CCUS) patients. Results Compared with the CCUS group, the MN group had higher male ratio (22/13 vs 10/6), cytogenetics abnormalities rate (41.4% vs 21.4%) and frequency of a series of mutations, such as ASXL1 (28.6% vs 25%), U2AF1 (25.7% vs 25%), RUNX1 (20% vs 0.0%); also, higher adverse mutations proportion (75% vs 85.2%), and double or multiple mutations (54.3% vs 43.75%). There were 7 MN patients and 4 CCUS patients who experienced cardio-cerebrovascular embolism events demonstrated a significant difference between the two groups (25% vs 20%). Ten of the 11 patients had somatic mutations, half had DNA methylation, while the other half had RNA splicing. Additionally, six patients had disease transformation, and four patients had mutated U2AF1, including two CCUS cases and two MDS-EB cases. Following up to January 2021, there was no significant difference in over survival between the CCUS and MN groups. Conclusion NGS facilitates the diagnosis of unexplained cytopenias. The monitoring and management of CCUS is necessary, also cardio-cerebrovascular embolism events in patients with CH need attention in the clinical practice.

scholarly journals 112 Axonal polyneuropathy with onset in young adulthood due to TUBB3 mutation

2019 ◽  
Vol 90 (e7) ◽  
pp. A36.2-A36
Author(s):  
Po Sheng Yang ◽  
Kimberley K Forrest ◽  
Ian B Wilson
Keyword(s):  
Next Generation Sequencing ◽  
Axonal Neuropathy ◽  
Extraocular Muscles ◽  
Diagnostic Process ◽  
List Type ◽  
Next Generation ◽  
Sensorimotor Polyneuropathy ◽  
Axonal Polyneuropathy ◽  
Congenital Fibrosis ◽  
Generation Sequencing

IntroductionThe TUBB3 gene encodes the protein Beta-tubulin isotype III, a component of the microtubule cytoskeleton. Mutations in this gene have been associated with axonal polyneuropathy, however usually associated with congenital fibrosis of the extraocular muscles (CFOEM) and other abnormalities of cerebral development.1 2 We report a case of isolated neuropathy associated with a TUBB3 mutation.MethodsCase report - clinical information and next generation sequencing results were obtained.ResultsA 64 year old man presented with a severe, progressive, length dependent sensorimotor polyneuropathy which commenced in his late twenties. There was no clinical involvement of the extraocular muscles and cognition was normal. Family history was limited, but there were no other members affected.The patient had previously been extensively investigated including sural nerve biopsy, which confirmed axonal neuropathy without a specific diagnosis. Intravenous immunoglobulins and steroids had been trialled without benefit.A neuromuscular gene panel utilising next generation sequencing was performed and demonstrated heterozygosity for a variant of the TUBB3 gene (D417N substitution).Case series describing TUBB3 mutations show a large heterogeneity in phenotypic expression depending on the amino acid substitution.2–4 There is also heterogeneity in patients with D417N mutations, although a small number have been reported to develop a polyneuropathy without CFOEM1.ConclusionsThis case strengthens previous reports that TUBB3 mutation can be associated with a pure, axonal, sensorimotor polyneuropathy and highlights the use of next generation sequencing in streamlining the diagnostic process.ReferenceTischfield M, et al. Human TUBB3 mutations perturb microtubule dynamics, kinesin interactions, and axon guidance. Cell 2010;140(1):pp.74–87.Ncbi.nlm.nih.gov. (2019). Congenital fibrosis of the extraocular muscles - Conditions - GTR - NCBI. [online] Available at: https://www.ncbi.nlm.nih.gov/gtr/conditions/CN043677/ [Accessed 14 Feb. 2019].Omim.org. (2019). OMIM Entry - * 602661 - TUBULIN, BETA-3; TUBB3. [online] Available at: https://www.omim.org/entry/602661 [Accessed 14 Feb. 2019].Krupa, K. and Bekiesinska-Figatowska, M. (2013). Congenital and Acquired Abnormalities of the Corpus Callosum: A Pictorial Essay. BioMed Research International, 2013, pp.1–14.

scholarly journals Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach

2019 ◽  
Author(s):  
M. Crotti ◽  
C.E. Adams ◽  
K.R. Elmer
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
List Type ◽  
Summary Statistics ◽  
Next Generation ◽  
Population Genomic ◽  
Genome Wide ◽  
Generation Sequencing

SummaryEpigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses.We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we compared the number of SNPs retained, population genetic summary statistics, and population genetic structure between data drawn from ddRADseq and epiRADseq library preparations.We find that SNPs drawn from epiRADseq are similar in number to those drawn from ddRADseq, with a 55-83% of SNPs being identified by both methods. Genotyping error rate was <5% in both approaches. For summary statistics such as heterozygosity and nucleotide diversity, there is a strong correlation between methods (Spearman’s rho > 0.88). Furthermore, identical patterns of population genetic structure were recovered using SNPs from epiRADseq and ddRADseq approaches.We show that SNPs obtained from epiRADseq are highly similar to those from ddRADseq and are equivalent for estimating genetic diversity and population structure. This finding is particularly relevant to researchers interested in genetics and epigenetics on the same individuals because using a single epigenomic approach to generate two datasets greatly reduces the time and financial costs compared to using these techniques separately. It also efficiently enables correction of epigenetic estimates with population genetic data. Many studies will benefit from a combinatorial approach with genetic and epigenetic markers and this demonstrates a single, efficient method to do so.

scholarly journals QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

2017 ◽  
Author(s):  
Ben N. Mansfeld ◽  
Rebecca Grumet
Keyword(s):  
Next Generation Sequencing ◽  
Bulk Segregant Analysis ◽  
Statistical Significance ◽  
Simulation Method ◽  
R Package ◽  
List Type ◽  
Next Generation ◽  
Snp Data ◽  
R Packages ◽  
Generation Sequencing

1AbstractNext Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G’. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr, can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G’ values, and log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr.Core ideasAn R package that performs Next Generation Sequencing Bulk Segregant Analysis was developedTwo methods for analysis are provided: QTL-seq and G’The QTLseqr package is quick and produces publication quality figures and tables

scholarly journals Pheochromocytoma due to a novel SDHD variant presenting as unilateral visual loss

2021 ◽  
Vol 2021 ◽  
Author(s):  
Clare Miller ◽  
Agnieszka Pazderska ◽  
John Reynolds ◽  
Patricia Gou ◽  
Barbara Dunne ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Organ Damage ◽  
Secondary Hypertension ◽  
Cystoid Macular Oedema ◽  
List Type ◽  
Next Generation ◽  
Novel Variants ◽  
High Heritability ◽  
Learning Points ◽  
Generation Sequencing

Summary A 53-year-old female presented to a tertiary ophthalmology referral centre complaining of unilateral painless loss of vision. Subsequent assessment revealed malignant hypertension causing right-sided cystoid macular oedema. During the course of secondary hypertension workup, she was diagnosed with a 7.8 cm phaeochromocytoma which was resected. Testing for a panel of all predisposing phaeochromocytoma-causing variants using next-generation sequencing resulted in the diagnosis of a novel SDHD variant. Learning points Screening for secondary causes of hypertension is indicated when there is evidence of hypertension-mediated end-organ damage (1). Testing for a predisposing variant should be considered in all patients with phaeochromocytoma or paraganglioma due to the high heritability rate and prevalence of somatic variants (2, 3, 4). Novel variants are commonly uncovered in the Succinate Dehydrogenase (SDH) subunit; proving pathogenicity is a complex, time-consuming process and one challenge of next-generation sequencing (3). SDHB immunohistochemistry as a tool for demonstrating pathogenicity is associated with reduced sensitivity when assessing SDHD variants (5, 6).

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

2020 ◽  
Vol 48 (6) ◽  
pp. 2399-2414
Author(s):  
Anireddy S.N. Reddy ◽  
Jie Huang ◽  
Naeem H. Syed ◽  
Asa Ben-Hur ◽  
Suomeng Dong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Global Analysis ◽  
Tail Length ◽  
Optimal Growth ◽  
Transcriptional Level ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.

scholarly journals Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Kidney Disease-Related Genes in Patients with Diabetic Kidney Disease

2020 ◽  
Author(s):  
Jose Lazaro-Guevara ◽  
Julio Fierro Morales ◽  
A. Hunter Wright ◽  
River Gunville ◽  
Scott G. Frodsham ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Kidney Disease ◽  
Diabetic Kidney Disease ◽  
List Type ◽  
Next Generation ◽  
Diabetic Kidney ◽  
Pathogenic Variants ◽  
Patients With Diabetes ◽  
Disease Related Genes ◽  
Generation Sequencing

AbstractDiabetes is the most common cause of chronic kidney disease (CKD). For patients with diabetes and CKD, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes. Without histopathological confirmation, however, the underlying cause of their kidney disease is unclear. Recent studies have shown that next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease. Here, we set out to investigate the genetic basis of disease in non-diabetic kidney disease (NDKD) and diabetic kidney disease (DKD) patients by performing targeted NGS using a custom panel comprised of 345 kidney disease-related genes. Our analysis identified rare diagnostic variants that were consistent with the clinical diagnosis of 19% of the NDKD patients included in this study. Similarly, 22% of DKD patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel. Genetic variants suggestive of NDKD were detected in 3% of the diabetic patients included in this study. Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Key MessagesWhat is already known about this subject? For patients with diabetes and chronic kidney disease, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes; without histopathological confirmation, however, the underlying cause of their kidney disease is unclear.Next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease.What are the new findings? Using targeted NGS and a custom panel comprised of 345 kidney disease-related genes, we found that 22% of diabetic kidney disease patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel.Genetic variants suggestive of non-diabetic kidney disease were detected in 3% of the diabetic patients included in this study.How might these results change the focus of research or clinical practice? Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Importantly, improved understanding of the underlying disease process in diabetic kidney disease could have major implications in terms of patient care and monitoring as well as for research studies in this field.

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