Emerging roles of non-coding RNAs in epigenetic regulation

Chen, Juan; Xue, Yuanchao

doi:10.1007/s11427-016-5010-0

Cited by 55 publications

(22 citation statements)

References 71 publications

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“…Non-coding RNAs are classified according to their length, with those less than 200 nucleotides (nt) being classified as microRNAs, while the remainder are lncRNAs19. lncRNAs were initially believed to have no biological function, but recent studies have suggested that they are widely involved in X-chromosome silencing, genomic imprinting, chromatin modification, transcriptional activation, interference, nuclear transport and other important regulatory processes20212223. By RNA sequencing (RNA-seq) technology and bioinformatic analysis, thousands of lncRNAs have been discovered in organisms from fruit flies to humans and their functions have been predicted.…”

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confidence: 99%

Differential transcription profiles of long non-coding RNAs in primary human brain microvascular endothelial cells in response to meningitic Escherichia coli

Yang

Huang²,

et al. 2016

Sci Rep

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Accumulating studies have indicated the influence of long non-coding RNAs (lncRNAs) on various biological processes as well as disease development and progression. However, the lncRNAs involved in bacterial meningitis and their regulatory effects are largely unknown. By RNA-sequencing, the transcriptional profiles of host lncRNAs in primary human brain microvascular endothelial cells (hBMECs) in response to meningitic Escherichia coli were demonstrated. Here, 25,257 lncRNAs were identified, including 24,645 annotated lncRNAs and 612 newly found ones. A total of 895 lncRNAs exhibited significant differences upon infection, among which 382 were upregulated and 513 were downregulated (≥2-fold, p < 0.05). Via bioinformatic analysis, the features of these lncRNAs, their possible functions, and the potential regulatory relationships between lncRNAs and mRNAs were predicted. Moreover, we compared the transcriptional specificity of these differential lncRNAs among hBMECs, human astrocyte cell U251, and human umbilical vein endothelial cells, and demonstrated the novel regulatory effects of proinflammatory cytokines on these differential lncRNAs. To our knowledge, this is the first time the transcriptional profiles of host lncRNAs involved in E. coli-induced meningitis have been reported, which shall provide novel insight into the regulatory mechanisms behind bacterial meningitis involving lncRNAs, and contribute to better prevention and therapy of CNS infection.

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confidence: 99%

Differential transcription profiles of long non-coding RNAs in primary human brain microvascular endothelial cells in response to meningitic Escherichia coli

Yang

Huang²,

et al. 2016

Sci Rep

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“… 44 As different RBPs tend to associate with one another to form various macromolecular complexes, each RBP in the complex may uniquely contribute to RNA code recognition, thus generating a combinational RNA code to institute the complex specificity observed in the cell. 55 The AID “mutator complex” may contain other proteins that indirectly interact with AID, 56 , 57 including several hnRNP proteins that work together with ROD1 to restrict AID targeting.…”

Section: Discussionmentioning

confidence: 99%

The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes

et al. 2018

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Activation-induced cytidine deaminase (AID) mediates class switching by binding to a small fraction of single-stranded DNA (ssDNA) to diversify the antibody repertoire. The precise mechanism for highly selective AID targeting in the genome has remained elusive. Here, we report an RNA-binding protein, ROD1 (also known as PTBP3), that is both required and sufficient to define AID-binding sites genome-wide in activated B cells. ROD1 interacts with AID via an ultraconserved loop, which proves to be critical for the recruitment of AID to ssDNA using bi-directionally transcribed nascent RNAs as stepping stones. Strikingly, AID-specific mutations identified in human patients with hyper-IgM syndrome type 2 (HIGM2) completely disrupt the AID interacting surface with ROD1, thereby abolishing the recruitment of AID to immunoglobulin (Ig) loci. Together, our results suggest that bi-directionally transcribed RNA traps the RNA-binding protein ROD1, which serves as a guiding system for AID to load onto specific genomic loci to induce DNA rearrangement during immune responses.

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“…In addition, possible roles of non-coding RNAs, which can be derived from pseudogenes, in epigenetic regulation (e.g. histone modification and chromatin remodeling) still remain an open question (Chen and Xue, 2016).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary direction of processed pseudogenes

Liu

Cui

Liang

et al. 2016

Sci. China Life Sci.

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While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection. GC content, mutual information, transcription factor binding motifs, mutational bias, recombination Citation:Liu, G

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Emerging roles of non-coding RNAs in epigenetic regulation

Cited by 55 publications

References 71 publications

Differential transcription profiles of long non-coding RNAs in primary human brain microvascular endothelial cells in response to meningitic Escherichia coli

Differential transcription profiles of long non-coding RNAs in primary human brain microvascular endothelial cells in response to meningitic Escherichia coli

The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes

Evolutionary direction of processed pseudogenes

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