Discovery of alternatively spliced isoforms and long non-coding RNA in full length brain transcriptomes of anadromous Hilsa shad, Tenualosa ilisha (Hamilton, 1822)

The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.

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The Full‑Length Transcriptome Sequencing and Identification of Na+/H+ Antiporter Genes in Halophyte Nitraria tangutorum Bobrov

Genes ◽

10.3390/genes12060836 ◽

2021 ◽

Vol 12 (6) ◽

pp. 836

Author(s):

Liming Zhu ◽

Lu Lu ◽

Liming Yang ◽

Zhaodong Hao ◽

Jinhui Chen ◽

...

Keyword(s):

Single Molecule ◽

Transcriptome Sequencing ◽

Reference Genome ◽

Full Length ◽

Tolerance Mechanism ◽

Non Coding Rna ◽

Nitraria Tangutorum ◽

Long Non Coding Rna ◽

Gene Information ◽

Simple Sequence

Nitraria tangutorum Bobrov is a halophyte that is resistant to salt and alkali and is widely distributed in northwestern China. However, its genome has not been sequenced, thereby limiting studies on this particular species. For species without a reference genome, the full-length transcriptome is a convenient and rapid way to obtain reference gene information. To better study N. tangutorum, we used PacBio single-molecule real-time technology to perform full-length transcriptome analysis of this halophyte. In this study, a total of 21.83 Gb of data were obtained, and 198,300 transcripts, 51,875 SSRs (simple sequence repeats), 55,574 CDS (coding sequence), and 74,913 lncRNAs (long non-coding RNA) were identified. In addition, using this full-length transcriptome, we identified the key Na+/H+ antiporter (NHX) genes that maintain ion balance in plants and found that these are induced to express under salt stress. The results indicate that the full-length transcriptome of N. tangutorum can be used as a database and be utilized in elucidating the salt tolerance mechanism of N. tangutorum.

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Epstein-Barr virus long non-coding RNA RPMS1 full-length spliceome in transformed epithelial tissue

10.1101/2021.02.07.430139 ◽

2021 ◽

Author(s):

Isak Holmqvist ◽

Alan Bäckerholm ◽

Guojiang Xie ◽

Yarong Tian ◽

Kaisa Thorell ◽

...

Keyword(s):

Gastric Adenocarcinoma ◽

Epstein Barr Virus ◽

Full Length ◽

Epithelial Tissue ◽

Sequencing Data ◽

Comprehensive Overview ◽

Barr Virus ◽

Non Coding Rna ◽

Epstein Barr ◽

Long Non Coding Rna

AbstractEpstein-Barr virus is associated with two types of epithelial neoplasms, nasopharyngeal carcinoma and gastric adenocarcinoma. The viral long non-coding RNA RPMS1 is the most abundantly expressed poly-adenylated viral RNA in these malignant tissues. The RPMS1 gene is known to contain two cassette exons, exon Ia and Ib, and several alternative splicing variants have been described in low-throughput studies. To characterize the entire RPMS1 spliceome we combined long-read sequencing data from the nasopharyngeal cell line C666-1 and a primary gastric adenocarcinoma, with complementary short-read sequencing datasets. We developed FLAME, a Python-based bioinformatics package that can generate complete high resolution characterization of RNA splicing at full-length. Using FLAME, we identified 32 novel exons in the RPMS1 gene, primarily within the large constitutive exons III, V and VII. Two of the novel exons contained retention of the intron between exon III and exon IV, and a novel cassette exon was identified between VI and exon VII. All previously described transcript variants of RPMS1 containing putative ORFs were identified at various levels. Similarly, native transcripts with the potential to form previously reported circular RNA elements were detected. Our work illuminates the multifaceted nature of viral transcriptional repertoires. FLAME provides a comprehensive overview of the relative abundance of alternative splice variants and allows for a wealth of previously unknown splicing events to be unveiled.

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Full-length transcriptome and long non-coding RNA profiling of whiteleg shrimp Penaeus vannamei hemocytes in response to Spiroplasma eriocheiris infection

Fish & Shellfish Immunology ◽

10.1016/j.fsi.2020.06.057 ◽

2020 ◽

Vol 106 ◽

pp. 876-886

Author(s):

Yaoqing Ren ◽

Jingyu Li ◽

Liang Guo ◽

Jian Ning Liu ◽

Hui Wan ◽

...

Keyword(s):

Full Length ◽

Penaeus Vannamei ◽

Rna Profiling ◽

Non Coding Rna ◽

Whiteleg Shrimp ◽

Long Non Coding Rna

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Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host-gene

Scientific Reports ◽

10.1038/s41598-021-89080-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Karim Rahimi ◽

Annette Christine Füchtbauer ◽

Fardin Fathi ◽

Seyed Javad Mowla ◽

Ernst-Martin Füchtbauer

Keyword(s):

Transcriptional Control ◽

Regulatory Elements ◽

Host Gene ◽

Regulatory Sequences ◽

Mirna Cluster ◽

Cellular Functions ◽

Non Coding Rna ◽

Alternatively Spliced ◽

Long Non Coding Rna ◽

Rna Genes

AbstractMicroRNAs are important regulators of cellular functions. MiR-302/367 is a polycistronic miRNA cluster that can induce and maintain pluripotency. Here we investigate the transcriptional control and the processing of the miR-302 host-gene in mice. Our results indicate that the mmu-miR-302 host-gene is alternatively spliced, polyadenylated and exported from the nucleus. The regulatory sequences extend at least 2 kb upstream of the transcription start site and contain several conserved binding sites for both transcriptional activators and repressors. The gene structure and regulatory elements are highly conserved between mouse and human. So far, regulating miR-302 expression is the only known function of the miR-302 host-gene. Even though we here only provide one example, regulation of microRNA transcription might be a so far little recognized function of long non-coding RNA genes.

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Long Non-Coding RNA Expression Levels Modulate Cell-Type Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins

10.20944/preprints201906.0259.v1 ◽

2019 ◽

Author(s):

Felipe Wendt Porto ◽

Swapna Vidhur Daulatabad ◽

Sarath Chandra Janga

Keyword(s):

Alternative Splicing ◽

Rna Binding ◽

Cell Type ◽

Non Coding Rna ◽

Specific Manner ◽

Alternatively Spliced ◽

A Cell ◽

Cell Type Specific ◽

Rna Interaction ◽

Long Non Coding Rna

Background: Recent developments in our understanding of the interactions between long non-coding RNA (lncRNA) and cellular components have improved treatment approaches for various human diseases including cancer, vascular diseases, and neurological diseases. Although investigation of specific lncRNAs revealed their role in the metabolism of cellular RNA, our understanding of their contribution to post-transcriptional regulation is relatively limited. In this study, we explore the role of lncRNAs in modulating alternative splicing and their impact on downstream protein-RNA interaction networks. Results: Analysis of alternative splicing events across 39 lncRNA wildtype and knockout RNA-sequencing datasets from three human cell lines: HeLa (Cervical Cancer), K562 (Myeloid Leukemia), and U87 (Glioblastoma), resulted in high confidence (fdr < 0.01) identification of 4432 skipped exon events and 2474 retained intron events, implicating 759 genes to be impacted at post-transcriptional level due to the loss of lncRNAs. We observed that a majority of the alternatively spliced genes in a lncRNA knockout were specific to the cell type, in agreement with the finding that genes affected by alternative splicing also displayed enriched functions in a cell type specific manner. To understand the mechanism behind this cell-type specific alternative splicing patterns, we analyzed RNA binding protein (RBP)-RNA interaction profiles across the spliced regions. Conclusions: Despite limited RBP binding data across cell lines, alternatively spliced events detected in lncRNA perturbation experiments were associated with RBPs binding in proximal intron-exon junctions, in a cell type specific manner. The cellular functions affected by alternative splicing were also affected in a cell type specific manner. Based on the RBP binding profiles in HeLa and K562 cells, we hypothesize that several lncRNAs are likely to exhibit a sponge effect in disease contexts, resulting in the functional disruption of RBPs due to altered titration of the RBPs from their target loci. We propose that such lncRNA sponges can extensively rewire the post-transcriptional gene regulatory networks by altering the protein-RNA interaction landscape in a cell-type specific manner.

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The Neglected Insulin: IGF-II, a Metabolic Regulator with Implications for Diabetes, Obesity, and Cancer

Cells ◽

10.3390/cells8101207 ◽

2019 ◽

Vol 8 (10) ◽

pp. 1207 ◽

Cited By ~ 11

Author(s):

Holly ◽

Biernacka ◽

Perks

Keyword(s):

Antisense Rna ◽

Metabolic Regulation ◽

Micro Rna ◽

Metabolic Reprogramming ◽

Non Coding Rna ◽

Alternatively Spliced ◽

Insulin Activity ◽

Parent Of Origin ◽

Obesity And Cancer ◽

Long Non Coding Rna

When originally discovered, one of the initial observations was that, when all of the insulin peptide was depleted from serum, the vast majority of the insulin activity remained and this was due to a single additional peptide, IGF-II. The IGF-II gene is adjacent to the insulin gene, which is a result of gene duplication, but has evolved to be considerably more complicated. It was one of the first genes recognised to be imprinted and expressed in a parent-of-origin specific manner. The gene codes for IGF-II mRNA, but, in addition, also codes for antisense RNA, long non-coding RNA, and several micro RNA. Recent evidence suggests that each of these have important independent roles in metabolic regulation. It has also become clear that an alternatively spliced form of the insulin receptor may be the principle IGF-II receptor. These recent discoveries have important implications for metabolic disorders and also for cancer, for which there is renewed acknowledgement of the importance of metabolic reprogramming.

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