PICALM rs3851179 Variant Confers Susceptibility to Alzheimer’s Disease in Chinese Population

Liu, Guiyou; Xu, Yining; Jiang, Yixiang; Zhang, Liangcai; Feng, Rennan; Jiang, Qinghua

doi:10.1007/s12035-016-9886-2

Cited by 57 publications

(42 citation statements)

References 27 publications

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“…However, Fit-Hi-C, like other peak-calling methods (Jin et al, 2013; Rao et al, 2014; Xu et al, 2015, 2016), is sensitive to sequencing depth, and therefore we found considerable variation in total chromatin contacts between samples, precluding any statistically rigorous comparative peak-calling analysis across tissues. However, upon closer examination of the chromatin contacts near the contact matrix diagonal (+/- 200kb from the matrix diagonal), we noticed that some regions exhibit unusually high levels of local contact frequency in a tissue type dependent manner (Figure 2a).…”

Section: Resultsmentioning

confidence: 83%

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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

et al. 2016

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Summary The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we found topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate function of non-coding sequence variants.

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Section: Resultsmentioning

confidence: 83%

“…Here, rs3851179 is within a brain-specific super-enhancer, while rs536841 is outside the super-enhancer. Interestingly, this brain-specific FIRE overlaps with PICALM , which contains the SNP (rs3851179) previously related to late-onset Alzheimer's disease incidence (Liu et al, 2016). …”

Section: Resultsmentioning

confidence: 90%

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

et al. 2016

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“…This search was performed by two independent individuals to identify potential publications meeting our inclusion criteria (see below), with differences resolved by discussion with a third reviewer. More detailed information about the search strategy is described in previous studies [33–35]. …”

Section: Methodsmentioning

confidence: 99%

“…The following inclusion criteria were used to select all potential publications for the meta-analysis: (1) use a case-control design; (2) evaluate the association between rs9929218 and CRC; (3) provide odds ratio (OR) with 95% confidence interval (CI) for allele model (see below); or (4) provide sufficient data to calculate the OR and 95% CI for allele model; For any publication, it is excluded from the meta-analysis, if (1) not for cancer research; (2) not use a case-control design including case population; case reports, conference abstract, reviews; (3) not provide OR with 95% CI for allele model (see below); or (4) not provide sufficient data to calculate the OR and 95% CI for allele model; More detailed information is described in previous studies [33–35]. …”

Section: Methodsmentioning

confidence: 99%

CDH1 rs9929218 variant at 16q22.1 contributes to colorectal cancer susceptibility

Han

Liu

Lü³

et al. 2016

Oncotarget

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Colorectal cancer (CRC) is the third most common cancer. Large-scale genome-wide association studies (GWAS) have been performed and reported some novel CRC susceptibility variants in European ancestry including the CDH1 rs9929218. Following GWAS and candidate studies evaluated the association between the CDH1 rs9929218 polymorphism and CRC in European, Asian and American populations. However, these studies reported inconsistent associations. Evidence shows that rs9929218 may regulate different gene expressions in different human tissues. Here, we reevaluated this association using large-scale samples from 16 studies (n=131768) using a meta-analysis method. In heterogeneity test, we did not identify significant heterogeneity among these studies. Meta-analysis using fixed effect model showed significant association between rs9929218 and CRC (P=6.16E-21, odds ratio (OR) =0.92, 95% confidence interval (CI) 0.91-0.94). In order to validate the effect of rs9929218 variant on CDH1 expression, we further performed a functional analysis using two large-scale expression datasets. We identified significant regulation relation between rs9929218 variant and the expression of CDH1, ZFP90, RP11-354M1.2 and MCOLN2 by both cis-effect and trans-effect. In summary, our analysis highlights significant association between rs9929218 polymorphism and CRC susceptibility.

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“…Alzheimer's disease (AD) is a neurodegenerative disease with unknown etiology [1–3]. The main clinical manifestation is intelligence damage.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional Regulation of lncRNA Genes by Histone Modification in Alzheimer’s Disease

Wan

Zhou

et al. 2016

BioMed Research International

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Increasing studies have revealed that long noncoding RNAs (lncRNAs) are not transcriptional noise but play important roles in the regulation of a wide range of biological processes, and the dysregulation of lncRNA genes is associated with disease development. Alzheimer's disease (AD) is a chronic neurodegenerative disease that usually starts slowly and gets worse over time. However, little is known about the roles of lncRNA genes in AD and how the lncRNA genes are transcriptionally regulated. Herein, we analyzed RNA-seq data and ChIP-seq histone modification data from CK-p25 AD model and control mice and identified 72 differentially expressed lncRNA genes, 4,917 differential peaks of H3K4me3, and 1,624 differential peaks of H3K27me3 between AD and control samples, respectively. Furthermore, we found 92 differential peaks of histone modification H3K4me3 are located in the promoter of 39 differentially expressed lncRNA genes and 8 differential peaks of histone modification H3K27me3 are located upstream of 7 differentially expressed lncRNA genes, which suggest that the majority of lncRNA genes may be transcriptionally regulated by histone modification in AD.

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PICALM rs3851179 Variant Confers Susceptibility to Alzheimer’s Disease in Chinese Population

Cited by 57 publications

References 27 publications

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

CDH1 rs9929218 variant at 16q22.1 contributes to colorectal cancer susceptibility

Transcriptional Regulation of lncRNA Genes by Histone Modification in Alzheimer’s Disease

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