Detection of Schistosoma mansoni long non-coding RNAs in the infected C57BL/6 mouse liver

Abstract Background: While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for lncRNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection.Results: Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNAs were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3). Conclusions: Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and disease.

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The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages

Scientific Reports ◽

10.1038/s41598-017-10853-6 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 20

Author(s):

Elton J. R. Vasconcelos ◽

Lucas F. daSilva ◽

David S. Pires ◽

Guilherme M. Lavezzo ◽

Adriana S. A. Pereira ◽

...

Keyword(s):

Life Cycle ◽

Schistosoma Mansoni ◽

Parasite Life Cycle ◽

Life Cycle Stages ◽

Non Coding Rnas

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Visualization of oxygen radical production in mouse liver in response to infection with Schistosoma mansoni

Liver International ◽

10.1111/j.1478-3231.1999.tb00082.x ◽

1999 ◽

Vol 19 (6) ◽

pp. 495-500 ◽

Cited By ~ 33

Author(s):

Ould M. S. Abdallahi ◽

Stéphane Hanna ◽

Max Reggi ◽

Bouchra Gharib

Keyword(s):

Schistosoma Mansoni ◽

Mouse Liver ◽

Oxygen Radical ◽

Radical Production ◽

Oxygen Radical Production

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Mitochondrial dynamics in the mouse liver infected by Schistosoma mansoni

Acta Tropica ◽

10.1016/j.actatropica.2015.04.004 ◽

2015 ◽

Vol 148 ◽

pp. 13-23 ◽

Cited By ~ 8

Author(s):

Tina Tu-Wen Chen ◽

Lawrence Shih Hsin Wu ◽

Paul Wei-Che Hsu ◽

Cheng-Yoong Pang ◽

Kin-Mu Lee ◽

...

Keyword(s):

Schistosoma Mansoni ◽

Mouse Liver ◽

Mitochondrial Dynamics

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Long Non-coding RNA Signatures Associated With Liver Aging in Senescence-Accelerated Mouse Prone 8 Model

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.698442 ◽

2021 ◽

Vol 9 ◽

Author(s):

Shuai Zhang ◽

Juanjuan Duan ◽

Yu Du ◽

Jinlu Xie ◽

Haijing Zhang ◽

...

Keyword(s):

Mouse Liver ◽

Systematic Research ◽

Physiological Processes ◽

Age Related ◽

Non Coding Rna ◽

Genome Wide ◽

Potential Link ◽

Non Coding Rnas ◽

Long Non Coding Rna ◽

Senescence Accelerated Mouse

The liver is sensitive to aging because the risk of hepatopathy, including fatty liver, hepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma, increases dramatically with age. Long non-coding RNAs (lncRNAs) are >200 nucleotides long and affect many pathological and physiological processes. A potential link was recently discovered between lncRNAs and liver aging; however, comprehensive and systematic research on this topic is still limited. In this study, the mouse liver genome-wide lncRNA profiles of 8-month-old SAMP8 and SAMR1 models were explored through deep RNA sequencing. A total of 605,801,688 clean reads were generated. Among the 2,182 identified lncRNAs, 28 were differentially expressed between SAMP8 and SAMR1 mice. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) surveys showed that these substantially dysregulated lncRNAs participated in liver aging from different aspects, such as lipid catabolic (GO: 0016042) and metabolic pathways. Further assessment was conducted on lncRNAs that are most likely to be involved in liver aging and related diseases, such as LNC_000027, LNC_000204E, NSMUST00000144661.1, and ENSMUST00000181906.1 acted on Ces1g. This study provided the first comprehensive dissection of lncRNA landscape in SAMP8 mouse liver. These lncRNAs could be exploited as potential targets for the molecular-based diagnosis and therapy of age-related liver diseases.

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Identification and characterization of long intergenic non-coding RNAs related to mouse liver development

Molecular Genetics and Genomics ◽

10.1007/s00438-014-0882-9 ◽

2014 ◽

Vol 289 (6) ◽

pp. 1225-1235 ◽

Cited By ~ 15

Author(s):

Jie Lv ◽

Zhijun Huang ◽

Hui Liu ◽

Hongbo Liu ◽

Wei Cui ◽

...

Keyword(s):

Mouse Liver ◽

Liver Development ◽

Non Coding Rnas ◽

Identification And Characterization

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Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs

10.1101/2021.01.14.426753 ◽

2021 ◽

Author(s):

Christine N. Goldfarb ◽

David J. Waxman

Keyword(s):

Mouse Liver ◽

Global Analysis ◽

Constitutive Androstane Receptor ◽

Protein Coding ◽

Transcript Processing ◽

Topologically Associating Domains ◽

Liver Transcriptome ◽

Non Coding Rnas ◽

Density Ratios ◽

Exonic Sequence

AbstractWhile nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for lncRNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection. Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNAs were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3). Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and diseases.

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Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs

BMC Genomics ◽

10.1186/s12864-021-07478-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Christine N. Goldfarb ◽

David J. Waxman

Keyword(s):

Mouse Liver ◽

Global Analysis ◽

Constitutive Androstane Receptor ◽

Protein Coding ◽

Transcript Processing ◽

Topologically Associating Domains ◽

Liver Transcriptome ◽

Non Coding Rnas ◽

Density Ratios ◽

Exonic Sequence

Abstract Background While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for long non-coding (lnc)RNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection. Results Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNA transcripts were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to TCPOBOP a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3). Conclusions Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and disease.

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