An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines

Pérez‐Molina, Rosario; Arzate-Mejía, Rodrigo G.; Ayala-Ortega, Erandi; Guerrero, Georgina; Meier, Karin; Suaste-Olmos, Fernando; Recillas‐Targa, Félix

doi:10.3389/fgene.2020.00928

Cited by 4 publications

(2 citation statements)

References 32 publications

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“…Many of the AluSx elements are intronic 81,82 . More generally, in both NPCs and neurons, we observe binding sites mapping predominantly in or around (+/-1 kb) protein coding genes (~84%) (Extended Data Fig.…”

Section: Pgbd1 Genomically Binds Protein Coding Genes and The Consensus Motif Of Scan Domain Family Membersmentioning

confidence: 99%

PiggyBac Transposable Element-derived 1 controls Neuronal Progenitor Identity, Stress Sensing and mammal-specific paraspeckles

Raskó

Pande

Radscheit

et al. 2021

Preprint

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The evolution and functional integration of new genes, especially those that become core to key functions, remains enigmatic. We consider the mammal-specific gene, piggyBac transposable element derived 1 (PGBD1), implicated in neuronal disorders. While it no longer recognises piggyBac transposon-like inverted repeats and transposase functionality having been lost, it has evolved a core role in neural homeostasis. Depletion of PGBD1 triggers accumulation of mammal-specific paraspeckles and neural differentiation. It acts by two modalities, DNA binding and protein-protein interaction. As a transcriptional repressor of (lnc)NEAT1, the backbone of paraspeckles, it inhibits paraspeckle formation in neural progenitor cells (NPCs). At the protein level it is associated with the stress response system, a function partially shared with (lnc)NEAT1. PGBD1 thus presents as an unusual exemplar of new gene creation, being a recently acquired multi-function, multi-modal gene. Mammalian specificity associated with control of a mammal-specific structure implies coevolution of new genes with new functions.

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Section: Pgbd1 Genomically Binds Protein Coding Genes and The Consensus Motif Of Scan Domain Family Membersmentioning

confidence: 99%

PiggyBac Transposable Element-derived 1 controls Neuronal Progenitor Identity, Stress Sensing and mammal-specific paraspeckles

Raskó

Pande

Radscheit

et al. 2021

Preprint

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show abstract

“…Several reports have emphasised the functional role of Alu elements embedded in lncRNAs [9,13,17]. Alu elements embedded within introns can introduce alternative splicesites in both pre-mRNA and lncRNA.…”

Section: Introductionmentioning

confidence: 99%

Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene

Emblem

Knutsen

Jørgensen

et al. 2022

ncRNA

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Many severe inflammation conditions are complement-dependent with the complement component C5a-C5aR1 axis as an important driver. At the RNA level, the blood transcriptome undergoes programmed expression of coding and long non-coding RNAs to combat invading microorganisms. Understanding the expression of long non-coding RNAs containing Alu elements in inflammation is important for reconstructing cell fate trajectories leading to severe disease. We have assembled a pipeline for computation mining of new Alu-containing long non-coding RNAs by intersecting immune genes with known Alu coordinates in the human genome. By applying the pipeline to patient bulk RNA-seq data with sepsis, we found immune genes containing 48 Alu insertion as robust candidates for further study. Interestingly, 1 of the 48 candidates was located within the complement system receptor gene C5aR1 and holds promise as a target for RNA therapeutics.

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A novel AluYb8 insertion-associated non-coding RNA, lncMUTYH, impairs mitochondrial function and dampens the M2-like polarization of macrophages

Dong,

Yin,

Liang

et al. 2024

Free Radical Research

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An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines

Cited by 4 publications

References 32 publications

PiggyBac Transposable Element-derived 1 controls Neuronal Progenitor Identity, Stress Sensing and mammal-specific paraspeckles

PiggyBac Transposable Element-derived 1 controls Neuronal Progenitor Identity, Stress Sensing and mammal-specific paraspeckles

Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene

A novel AluYb8 insertion-associated non-coding RNA, lncMUTYH, impairs mitochondrial function and dampens the M2-like polarization of macrophages

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