SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark DOI Creative Commons
Jorge Mestre-Tomás, Tianyuan Liu, Francisco J. Pardo-Palacios

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 24, 2023

Long-read RNA-seq has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods identifying annotated and novel transcripts remains challenge. Here, we present SQANTI-SIM, versatile utility that wraps around popular long-read simulators to allow precise management novelty based on structural categories defined by SQANTI3. By selectively excluding specific from reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, provides customizable features supports simulation additional types data, representing first multi-omics lrRNA-seq field. We demonstrate effectiveness benchmarking five transcriptome reconstruction pipelines using simulated data.

Language: Английский

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing DOI Creative Commons

Mélanie Sagniez,

Anshul Budhraja,

Bastien Paré

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 23, 2024

Abstract Resolving the transcriptomes of higher eukaryotes is more tangible with advent long read sequencing, which greatly facilitates identification new transcripts and their splicing isoforms. However, computational analysis RNA sequencing data remains challenging as it difficult to disentangle technical artifacts from bona fide biological information. To address this, we evaluated performance multiple leading transcriptome assembly algorithms on ability accurately reconstruct transcript We specifically focused deep nanopore synthetic spike-in controls (Sequins™ SIRVs) across different chemistries, including cDNA direct protocols. Our systematic comparative benchmarking exposes strengths limitations surveyed strategies. also highlight conceptual challenges annotation formalization quality metrics. results complement similar recent endeavors, helping forge a path towards gold standard analytical pipeline for assembly.

Language: Английский

Citations

1
Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner DOI Creative Commons
Hyun Joo Ji, Mihaela Pertea

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 16, 2024

Recently developed long–read RNA sequencing technologies promise to provide a more accurate and comprehensive view of transcriptomes compared short-read sequencers, primarily due their capability achieve full–length transcripts. However, realizing this potential requires computational tools tailored process long reads, which exhibit higher error rate than short reads. Existing methods for assembling quantifying data often disagree on expressed transcripts abundance levels, leading researchers lack confidence in the produced using data. One approach address uncertainties transcriptome assembly quantification is by assigning reads transcripts, enabling detailed characterization transcript support at read level. Here, we introduce TranSigner, versatile tool that assigns any input transcriptome. TranSigner consists three consecutive modules performing: alignment given computation compatibility scores based positions, execution an expectation–maximization algorithm probabilistically assign fractions while estimating abundances. Using simulated experimental datasets from well studied organisms — Homo Sapiens, Arabidopsis thaliana Mus musculus demonstrate achieves accuracy estimation assignment existing tools.

Language: Английский

Citations

1
A proteogenomic atlas of the human neural retina DOI Open Access
Tabea Riepe, Merel Stemerdink, Renee Salz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 24, 2024

The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific but limitations in detailing transcript isoforms. To address this, we generated proteogenomic atlas that combines PacBio long-read data mass spectrometry whole genome sequencing three healthy samples. We identified nearly 60,000 isoforms, which approximately one-third are novel. Additionally, ten novel peptides confirmed For instance, IMPDH1 isoform combination known exons supported by peptide evidence. Our research underscores the potential in-depth tissue-specific transcriptomic analysis enhance our grasp underlying available via EGA identifier EGAD50000000101, ProteomeXchange PXD045187, accessible through UCSC browser.

Language: Английский

Citations

1
Gene expansions contributing to human brain evolution DOI Creative Commons
Daniela C. Soto, José M. Uribe‐Salazar, Gulhan Kaya

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including increased complexity synaptic connections between neurons and dramatic expansion neocortex. Discovering duplicate is challenging because similarity paralogs makes them prone sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere genome sequence (T2T-CHM13) identified 213 duplicated gene families containing (>98% identity). Positing that important universal features should exist with at least one copy all modern humans exhibit expression brain, narrowed on 362 across thousands ancestrally diverse genomes present transcriptomes. Of these, 38 co-express modules enriched for autism-associated potentially contribute language cognition. We 13 are fixed among show convincing patterns. Using long-read DNA sequencing revealed hidden variation 200 ancestries, uncovering signatures selection not previously identified, possible balancing

Language: Английский

Citations

1
RNA sequencing depth guidelines for the study of alternative splicing DOI Creative Commons
Olga Tsoy, Sabine Ameling, Sören Franzenburg

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 13, 2024

ABSTRACT A key parameter in the experimental design of RNA-seq projects is choice sequencing depth. Considering a limited budget, one needs to find tradeoff between number samples and sensitivity analysis, particularly concerning lowly expressed genes. While previous studies have proposed lower bound for comprehensive analysis differential gene expression, alternative splicing, it has only been human adipose tissue. However, splicing differs across tissues conditions. We analyzed publicly available newly generated deep-sequenced paired-end (between 150 >500 million reads, read length 50-150 bp) from buffy coat cells diverse sets tissues, including gluteal subcutaneous fat, heart, hypothalamus. Our results show that depth typically used published cohorts not sufficient comprehensively capture landscape splicing. This motivates use deeper or long-read technologies future studies. Toward this goal, we offer guidelines choosing suitable GRAPHICAL

Language: Английский

Citations

1
The polyadenylation landscape afterin vivolong-term potentiation in the rat brain DOI Creative Commons
Natalia Gumińska, François Philippe Pauzin, Bożena Kuźniewska

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 8, 2024

Abstract Local protein synthesis in neurons is vital for synaptic plasticity, yet the regulatory mechanisms, particularly cytoplasmic polyadenylation, are not fully understood. This study employed nanopore sequencing to examine transcriptomic responses rat hippocampi during vivo long-term potentiation (LTP) and synaptoneurosomes after vitro stimulation. Our long-read dataset allows detailed analysis of mRNA 3′-ends, poly(A) tail lengths, composition. We observed dynamic shifts polyadenylation site preference post-LTP induction, with significant lengthening restricted transcriptionally induced mRNAs. Poly(A) tails these genes showed increased non-adenosine abundance. In synaptoneurosomes, chemical stimulation led shortening on preexisting mRNAs, indicating translation-induced deadenylation. Additionally, we discovered a group neuronal transcripts abundant residues. These semi-templated derived from extremely adenosine-rich 3′UTRs. provides comprehensive overview 3′-end dynamics LTP, offering insights into post-transcriptional regulation activation.

Language: Английский

Citations

0
How to choose the optimal RNA-Seq library characteristics for alternative splicing analysis DOI

Annika Ladwig,

Melina Klostermann, Kathi Zarnack

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 13, 2024

Abstract Alternative splicing (AS) is a key layer of regulation in eukaryotic gene expression that investigated all areas life sciences. Differences AS between conditions can be quantified from transcriptome-wide short-read RNA sequencing (RNA-Seq) data with designated computational tools. However, not RNA-Seq are equally suited for analysis. Here, we perform an exemplary analysis to showcase the impact library characteristics on obtained results. Using three standard ENCODE datasets widespread changes, modulate read length, depth and number replicates compare their influence detection, quantification classification events state-of-the-art algorithm MAJIQ. We find longer reads higher most effective measures improve sensitivity precision From our results, provide recommendation how best choose specifications

Language: Английский

Citations

0
A proteogenomic atlas of the human neural retina DOI Creative Commons
Tabea Riepe, Merel Stemerdink, Renee Salz

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 19, 2024

The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific but limitations in detailing transcript isoforms. To address this, we generated proteogenomic atlas that combines PacBio long-read data mass spectrometry whole genome sequencing three healthy samples. We identified nearly 60,000 isoforms, which approximately one-third are novel. Additionally, ten novel peptides confirmed For instance, IMPDH1 isoform combination known exons supported by peptide evidence. Our research underscores the potential in-depth tissue-specific transcriptomic analysis enhance our grasp underlying available via EGA identifier EGAD50000000101, ProteomeXchange PXD045187, accessible through UCSC browser.

Language: Английский

Citations

0
Single-cell profiling identifies LIN28A mRNA targets in the mouse pluripotent-to-2C-like transition and somatic cell reprogramming DOI Creative Commons
Jieyi Hu,

Jianwen Yuan,

Quan Shi

et al.

Journal of Biological Chemistry, Journal Year: 2024, Volume and Issue: 300(11), P. 107824 - 107824

Published: Sept. 27, 2024

Language: Английский

Citations

0
Long-read transcriptomics in neurodegeneration DOI
Emil K. Gustavsson, Hannah Macpherson

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 183 - 204

Published: Oct. 1, 2024

Language: Английский

Citations

0