Pan‐tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation

Li, Yisheng; Schaefke, Bernhard; Zou, Xudong; Zhang, Min; Heyd, Florian; Sun, Wei; Zhang, Bin; Li, Guipeng; Liang, Weizheng; He, Yuhao; Zhou, Juexiao; Li, Yunfei; Fang, Liang; Hu, Yuhui; Chen, Wei

doi:10.15252/msb.20199367

Cited by 6 publications

(6 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of the 2,443 events, only 85 (3.5%) events exhibited opposite signs of ΔPSI T in the two tissues, fitting scenario 1. This shows that cis -divergence causing opposite allelic changes between tissues is rare, similar to the previously observed patterns for alternative polyadenylation ( Li et al, 2020 ). Among the remaining events, 247 fit scenario 2 with parallel changes in isoform abundance between tissues and 456 fit scenario 4 with equal divergence across tissues, whereas the majority (1,655, 67.7%) fit scenario 3 with only one allele showing tissue-dependent splicing.…”

Section: Resultssupporting

confidence: 88%

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

et al. 2021

Self Cite

View full text Add to dashboard Cite

Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.

show abstract

Section: Resultssupporting

confidence: 88%

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…APAs likely play a role in many processes involved in gene expression, including nuclear export, localization, stability, degradation, repression, translation, and protein diversification [104]. Additionally, APAs associated with differentiation, proliferation, and tissue-specific expression have been reported [105]. APAs at the gene-level can be discovered using EST, microarray, RNA-Seq, 3' RNA-Seq, and qRT-PCR methodologies.…”

Section: Alternative Polyadenylation (Apa) Site Usagementioning

confidence: 99%

Recent Applications of RNA Sequencing in Food and Agriculture

Sripathi¹,

Anche²,

Gossett³

et al. 2021

Applications of RNA-Seq in Biology and Medicine

View full text Add to dashboard Cite

RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.

show abstract

“…Nevertheless, several studies have been pointing out that these capsules may cause unwanted fibrotic reactions. [150] As a result, new formulations have been envisaged for cell encap sulation including alginatechitosan microcapsules [151] and decellularized liver matrixalginate gel beads. [148] Experiments using comicroencapsulated hepatocytes and HUVECs, trans planted intraperitoneally into rat models of fulminant hepatic failure (FHF), showed that hepatocytespecific functions were significantly better than the transplant of isolated hepatocytes or even microcapsules with hepatocytes only.…”

Section: D Culturingmentioning

confidence: 99%

Advanced Biomaterials and Processing Methods for Liver Regeneration: State‐of‐the‐Art and Future Trends

Morais

Vieira

Zhao

et al. 2020

Adv Healthcare Materials

View full text Add to dashboard Cite

Liver diseases contribute markedly to the global burden of mortality and disease. The limited organ disposal for orthotopic liver transplantation results in a continuing need for alternative strategies. Over the past years, important progress has been made in the field of tissue engineering (TE). Many of the early trials to improve the development of an engineered tissue construct are based on seeding cells onto biomaterial scaffolds. Nowadays, several TE approaches have been developed and are applied to one vital organ: the liver. Essential elements must be considered in liver TE—cells and culturing systems, bioactive agents or growth factors (GF), and biomaterials and processing methods. The potential of hepatocytes, mesenchymal stem cells, and others as cell sources is demonstrated. They need engineered biomaterial‐based scaffolds with perfect biocompatibility and bioactivity to support cell proliferation and hepatic differentiation as well as allowing extracellular matrix deposition and vascularization. Moreover, they require a microenvironment provided using conventional or advanced processing technologies in order to supply oxygen, nutrients, and GF. Herein the biomaterials and the conventional and advanced processing technologies, including cell‐sheets process, 3D bioprinting, and microfluidic systems, as well as the future trends in these major fields are discussed.

show abstract

Pan‐tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation

Cited by 6 publications

References 57 publications

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

Recent Applications of RNA Sequencing in Food and Agriculture

Advanced Biomaterials and Processing Methods for Liver Regeneration: State‐of‐the‐Art and Future Trends

Contact Info

Product

Resources

About