An imprinted long noncoding RNA located between genes Meg8 and Meg9 in the cattle Dlk1-Dio3 domain

Zhang, Mingyue; Zhao, Yijie; Wang, Guannan; Li, Dongjie; Chen, Weina; Zhang, Cui; Li, Shijie

doi:10.1007/s10709-016-9939-5

Cited by 8 publications

(10 citation statements)

References 25 publications

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“…The complete cp genome of P. trunciflora is 159,512 bp in size and was submitted to GenBank (accession number: KU318111). The size is similar to that of other Myrtaceae species ( Eguiluz et al , 2017 ; Machado et al , 2017 ). The cp genome included an LSC region of 88,097 bp, an SSC region of 18,587 bp and a pair of inverted repeats (IRa and IRb) of 26,414 bp each ( Figure 1 ).…”

supporting

confidence: 76%

“…Coding regions comprise 47.2%, 13.3% correspond to rRNAs and tRNAs, and 39.5% of the genome comprises non-coding regions, including introns, pseudogenes and intergenic spacers ( Table 1 ). In general, all genomic features showed similarity in structure and gene abundance with other Myrtaceae species ( Bayly et al , 2013 ; Eguiluz et al , 2017 ; Machado et al , 2017 ). The genome contained 131 genes in total, which includes 111 single-copy genes corresponding to 77 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal genes (rRNA) ( Figure 1 , Table 1 ).…”

mentioning

confidence: 86%

“…Despite the high degree of conservation in its structure, gene content and organization, the presence of mutations, duplications and rearrangements of genes make it an attractive option for phylogenetic studies ( Costa et al , 2016 ). In the case of Myrtaceae, there are only few phylogenetic and evolutionary studies based on cp genes ( Craven and Biffin 2005 ; Payn et al , 2007 ; Biffin et al , 2010 ; Bayly et al , 2013 ; Eguiluz et al , 2017 ; Machado et al , 2017 ), and there are even less that include the Plinia genus ( Vasconcelos et al , 2017 ).…”

mentioning

confidence: 99%

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Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

et al. 2017

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Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding, 30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding genes demonstrated that P. trunciflora, Eugenia uniflora and Acca sellowiana form a cluster with closer relationship to Syzygium cumini than with Eucalyptus. The complete cp sequence reported here can be used in evolutionary and population genetics studies, contributing to resolve the complex taxonomy of this species and fill the gap in genetic characterization.

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supporting

confidence: 76%

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confidence: 86%

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confidence: 99%

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Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

et al. 2017

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“…The Dlk1 - Dio3 imprinted domain and their predominant patterns of allelic expression are highly conserved in humans [ 91 ] and multiple mammalian species [ 85 , 92 , 93 , 94 , 95 ].…”

Section: Genomic Imprinting Of Dio3mentioning

confidence: 99%

The Type 3 Deiodinase: Epigenetic Control of Brain Thyroid Hormone Action and Neurological Function

Hernández

Stohn

2018

IJMS

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Thyroid hormones (THs) influence multiple processes in the developing and adult central nervous system, and their local availability needs to be maintained at levels that are tailored to the requirements of their biological targets. The local complement of TH transporters, deiodinase enzymes, and receptors is critical to ensure specific levels of TH action in neural cells. The type 3 iodothyronine deiodinase (DIO3) inactivates THs and is highly present in the developing and adult brain, where it limits their availability and action. DIO3 deficiency in mice results in a host of neurodevelopmental and behavioral abnormalities, demonstrating the deleterious effects of TH excess, and revealing the critical role of DIO3 in the regulation of TH action in the brain. The fact the Dio3 is an imprinted gene and that its allelic expression pattern varies across brain regions and during development introduces an additional level of control to deliver specific levels of hormone action in the central nervous system (CNS). The sensitive epigenetic nature of the mechanisms controlling the genomic imprinting of Dio3 renders brain TH action particularly susceptible to disruption due to exogenous treatments and environmental exposures, with potential implications for the etiology of human neurodevelopmental disorders.

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“…Lambros et al used RNA-Seq data from 18 bovine tissue samples to identify and annotate 9778 new lncRNAs, including the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and HOX transcript antisense RNA (HOTAIR), which are well-known lncRNAs in humans and mice [21]. Other lncRNAs reported in cattle include MEG8, MEG8-IT1, MEG8-IT2, MEG8-IT3, and LINC24061 [22,23]. These studies enrich the annotation of the cattle genome and provide valuable resources for the subsequent functional identification of lncRNAs.…”

Section: Introductionmentioning

confidence: 99%

MIR221HG Is a Novel Long Noncoding RNA that Inhibits Bovine Adipocyte Differentiation

Gao

Tian

et al. 2019

Genes

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Adipogenesis is a complicated but precisely orchestrated process mediated by a series of transcription factors. Our previous study has identified a novel long noncoding RNA (lncRNA) that was differentially expressed during bovine adipocyte differentiation. Because this lncRNA overlaps with miR-221 in the genome, it was named miR-221 host gene (MIR221HG). The purpose of this study was to clone the full length of MIR221HG, detect its subcellular localization, and determine the effects of MIR221HG on bovine adipocyte differentiation. The 5′ rapid amplification of cDNA ends (RACE) and 3′ RACE analyses demonstrated that MIR221HG is a transcript of 1064 nucleotides, is located on the bovine X chromosome, and contains a single exon. Bioinformatics analyses suggested that MIR221HG is an lncRNA and the promoter of MIR221HG includes the binding consensus sequences of the forkhead box C1 (FOXC1) and krüppel-like factor5 (KLF5). The semi-quantitative PCR and quantitative real-time PCR (qRT-PCR) of nuclear and cytoplasmic fractions revealed that MIR221HG mainly resides in the nucleus. Inhibition of MIR221HG significantly increased adipocyte differentiation, as indicated by a dramatic increment in the number of mature adipocytes and in the expression of the respective adipogenic markers, peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer-binding protein α (C/EBPα), and fatty acid binding protein 4 (FABP4). Our results provide a basis for elucidating the mechanism by which MIR221HG regulates adipocyte differentiation.

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An imprinted long noncoding RNA located between genes Meg8 and Meg9 in the cattle Dlk1-Dio3 domain

Cited by 8 publications

References 25 publications

Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

The Type 3 Deiodinase: Epigenetic Control of Brain Thyroid Hormone Action and Neurological Function

MIR221HG Is a Novel Long Noncoding RNA that Inhibits Bovine Adipocyte Differentiation

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