Genomic Analyses of Non-Coding RNAs Overlapping Transposable Elements and Its Implication to Human Diseases

Park, Eun Gyung; Ha, Hong-Seok; Lee, Du‐Hyeong; Kim, Woo Ryung; Lee, Yun Ju; Bae, Woo Hyeon; Kim, Heui‐Soo

doi:10.3390/ijms23168950

Cited by 17 publications

(13 citation statements)

References 87 publications

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“…We conducted a statistical analysis for each type of TEs contained within the lncRNA, following the methods reported in published papers. [ 19 ] By analyzing the RNA‐Seq data of pigs (GSE163620) and comparing the expression levels at various stages of pre‐implantation development, we observed that TEs‐associated lncRNAs exhibit higher expression levels during the 4–8‐cell stage ( Figure 1 A,B ), which is a critical period for ZGA in porcine. [ 20 ] To validate this finding, we performed the same analysis on porcine RNA‐Seq data (CRA004237) once again and obtained consistent results (Figure S1A , Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

SINE‐Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation

He,

Peng,

Yang

et al. 2023

Advanced Science

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In mice, retrotransposon‐associated long noncoding RNAs (lncRNA) play important regulatory roles in pre‐implantation development; however, it is largely unknown whether they function in the pre‐implantation development in pigs. The current study aims to screen for retrotransposon‐associated lncRNA in porcine early embryos and identifies a porcine 8‐cell embryo‐specific SINE‐associated nuclear long noncoding RNA named SAWPA. SAWPA is essential for porcine embryonic development as depletion of SAWPA results in a developmental arrest at the 8‐cell stage, accompanied by the inhibition of the JNK‐MAPK signaling pathway. Mechanistically, SAWPA works in trans as a transcription factor for JNK through the formation of an RNA‐protein complex with HNRNPA1 and MED8 binding the SINE elements upstream of JNK. Therefore, as the first functional SINE‐associated long noncoding RNAs in pigs, SAWPA provides novel insights for the mechanism research on retrotransposons in mammalian pre‐implantation development.

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Section: Resultsmentioning

confidence: 99%

SINE‐Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation

He,

Peng,

Yang

et al. 2023

Advanced Science

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“…It is estimated that up to 80% of the human genome is transcribed into RNA molecules, but less than 2% of the genome codes for proteins, the remaining RNA transcripts that are not translated into proteins are called non-coding RNAs (ncRNAs). 1 LncRNAs are a type of ncRNA with a length greater than 200 nucleotides. 2 Research shows that lncRNA plays a crucial regulatory role in the onset and progression of various human diseases.…”

Section: Introductionmentioning

confidence: 99%

The role of lncRNA HCG18 in human diseases

Long,

Zhou,

Zhang

et al. 2024

Cell Biochemistry & Function

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A substantial number of long noncoding RNAs (lncRNAs) have been identified as potent regulators of human disease. Human leukocyte antigen complex group 18 (HCG18) is a new type of lncRNA that has recently been proven to play an important role in the occurrence and development of various diseases. Studies have found that abnormal expression of HCG18 is closely related to the clinicopathological characteristics of many diseases. More importantly, HCG18 was also found to promote disease progression by affecting a series of cell biological processes. This article mainly discusses the expression characteristics, clinical characteristics, biological effects and related regulatory mechanisms of HCG18 in different human diseases, providing a scientific theoretical basis for its early clinical application.

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“…The human genome has the potential to generate hundreds of cell types through a vast repertoire of gene expression patterns. This is shown by the low percentage (1.5%) of the genome allocated to encoding proteins [ 1 ], whilst the remaining 98.5% codes for regulatory elements, the functions of most of which are still largely unknown. The approximately 6 billion bases of DNA are wrapped around 30 million nucleosome octamers, forming a complex macromolecular environment named chromatin.…”

Section: Introductionmentioning

confidence: 99%

“…These regions are often insulated from each other by loops pinched by CCCTC-binding factors (CTCFs) and cohesin [ 3 ]. TADs comprise DNA segments ranging in size from 100 kilobases (kb) up to several megabases and they are supposed to segregate genes and their distal regulatory elements into compartments crucial for tailored gene regulation [ 1 ]. Recently, it was shown that TADs can be further subdivided into smaller chromatin nanodomains (CNDs), the sizes of which are around 100 nm and which embed about 10–100 kb.…”

Section: Introductionmentioning

confidence: 99%

On the Advent of Super-Resolution Microscopy in the Realm of Polycomb Proteins

Nepita

Piazza

Ruglioni

et al. 2023

Biology

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The genomes of metazoans are organized at multiple spatial scales, ranging from the double helix of DNA to whole chromosomes. The intermediate genomic scale of kilobases to megabases, which corresponds to the 50–300 nm spatial scale, is particularly interesting, as the 3D arrangement of chromatin is implicated in multiple regulatory mechanisms. In this context, polycomb group (PcG) proteins stand as major epigenetic modulators of chromatin function, acting prevalently as repressors of gene transcription by combining chemical modifications of target histones with physical crosslinking of distal genomic regions and phase separation. The recent development of super-resolution microscopy (SRM) has strongly contributed to improving our comprehension of several aspects of nano-/mesoscale (10–200 nm) chromatin domains. Here, we review the current state-of-the-art SRM applied to PcG proteins, showing that the application of SRM to PcG activity and organization is still quite limited and mainly focused on the 3D assembly of PcG-controlled genomic loci. In this context, SRM approaches have mostly been applied to multilabel fluorescence in situ hybridization (FISH). However, SRM data have complemented the maps obtained from chromosome capture experiments and have opened a new window to observe how 3D chromatin topology is modulated by PcGs.

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Genomic Analyses of Non-Coding RNAs Overlapping Transposable Elements and Its Implication to Human Diseases

Cited by 17 publications

References 87 publications

SINE‐Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation

SINE‐Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation

The role of lncRNA HCG18 in human diseases

On the Advent of Super-Resolution Microscopy in the Realm of Polycomb Proteins

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