The integrated comprehension of lncRNA HOXA-AS3 implication on human diseases

Yao, Qiong; Wang, Cuili; Wang, Yucheng; Zhang, Xiuyuan; Jiang, Hong; Chen, Dajin

doi:10.1007/s12094-022-02920-w

Cited by 8 publications

(5 citation statements)

References 84 publications

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“…Our results show several potentially DMR-regulated lncRNAs associated with epithelial cell proliferation and migration, including HOXA-AS2 and HOXA-AS3 [ 52 , 53 ]. Interestingly, these lncRNAs are under DMR regulation and are downregulated in UC.…”

Section: Discussionmentioning

confidence: 99%

Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis

Fenton,

Ray,

Meng

et al. 2023

IJMS

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Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.

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Section: Discussionmentioning

confidence: 99%

Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis

Fenton,

Ray,

Meng

et al. 2023

IJMS

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“…Our mesoscale chromatin model has high-resolution particles (9-bp), so it is compatible with Micro-C, which can have resolution as high as 100 bp. Three sets of data are obtained for five gene systems as follows: (i–iii) the NXN ( 54 ), HOXC ( 55 , 56 ) and HOXA ( 57 , 58 ) genes in mouse embryonic stem cells (mESC). We focused on these three regions for validation purposes using Micro-C data from ( 53 ) (GEO accession: GSE130275) with 100 bp resolution.…”

Section: Methodsmentioning

confidence: 99%

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

Li,

Schlick

2023

Nucleic Acids Research

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The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.

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“…These findings emphasize the significance of HOXA-AS3 in the pathogenesis and advancement of non-cancerous diseases. HOXA-AS3 abnormal expression and functional roles also position it as a potential biomarker and therapeutic target for both cancers and non-cancerous diseases [ 108 ].…”

Section: Lncrnas As Potential Theranostic Agents (Diagnostic Prognost...mentioning

confidence: 99%

MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions

Zeinelabdeen,

Abaza,

Yasser

et al. 2024

Non-coding RNA Research

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The integrated comprehension of lncRNA HOXA-AS3 implication on human diseases

Cited by 8 publications

References 84 publications

Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis

Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions

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