MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data

Khakmardan, Saman; Rezvani, Mohsen; Pouyan, Ali A.; Fateh, Mansoor; Alinejad‐Rokny, Hamid

doi:10.1186/s12864-020-6636-7

Cited by 17 publications

(15 citation statements)

References 11 publications

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“…Interestingly, CATG00000053385 encompasses two NDD related GWAS SNPs, while SLC13A3 , the eQTL linked gene, does not overlap with either GWAS SNPs or ASD related CNVs. MHiC tool [72] has been used to generate the figure.…”

Section: Resultsmentioning

confidence: 99%

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders

Asgari

Heng

Lovell

et al. 2020

Preprint

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Noncoding RNAs (ncRNAs) comprise a significant proportion of the mammalian genome, but their biological significance in neurodevelopment and in diseases is poorly understood. In this study, we have performed a genome-wide investigation of human noncoding RNAs for cell regulatory functions in brain tissue. By analysing ENCODE regulatory features, associations with FANTOM5 tissue-specific enhancers, as well as tissue-specific expression profiles, we have identified 17,743 noncoding RNAs comprising at least one nervous system-related expression Quantitative TraitLoci (eQTL) polymorphism that is associated with protein coding genes. Of these, 908 brain-enriched noncoding RNAs (comprising 907 long noncoding RNAs and 1 pseudogene) also overlap with chromatin states characterised as enhancers. Based 2 on these criteria, we referred to such noncoding RNAs with putative enhancer activity as brain 'enhancer-ncRNAs'. To investigate their impact in neurodevelopmental disorders, we integrated GWAS SNPs and Copy Number Variation (CNV) data and found that 265 enhancer-ncRNAs were either mutated (CNV deletion or duplication) or contain at least one GWAS SNPs in the context of such conditions. Of these, the eQTLassociated gene for 82 enhancer-ncRNAs did not overlap with either GWAS SNPs or CNVs. However, in 23 of these 82 enhancer-ncRNAs, eQTL interaction was explained solely by the presence of each of these noncoding RNAs, suggesting in such contexts that mutations to neurodevelopment gene enhancers disrupt ncRNA interaction. We also cross-referenced our data with the DECIPHER database of clinical phenotypes to find that mutations to 34 of the 82 enhancer-ncRNAs are significantly associated with phenotypes including behavioural abnormality, and cognitive impairment. Taken together, we provide evidence for a distinct set of brain-enriched ncRNAs that influence genomic enhancers during neurodevelopment, suggesting enhancer mutations may be relevant to the functions for such ncRNAs in neurodevelopmental disorders.

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Section: Resultsmentioning

confidence: 99%

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders

Asgari

Heng

Lovell

et al. 2020

Preprint

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“…To gain a further understanding of the genes that our candidate ncRNAs are interacting with, we analyzed two publicly available Hi-C datasets from HMEC obtained from the Rao et al study [45]. Here, we used MHiC [46] and . CC-BY-NC-ND 4.0 International license available under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”

Section: Chromosome Conformation Capture Data Shows a Potential Regulatory Role For Bc-associated Non-coding Rnasmentioning

confidence: 99%

“…In our study, we used two replications related to the HMEC [45]. We used MHiC [46] and Hi-C Pro [62] with the default parameters for analyzing and aligning Hi-C data in 5kb fragment size. We then used MaxHiC [47] as a background correction model to identify significant Hi-C interactions for getting true cisinteraction.…”

Section: Hi-c Data Analysismentioning

confidence: 99%

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Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer

Rezaie

Bayati

Tahaei

et al. 2021

Preprint

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De novo somatic point mutations identified in breast cancer are predominantly non-coding and typically attributed to altered regulatory elements such as enhancers and promoters. However, while the non-coding RNAs (ncRNAs) form a large portion of the mammalian genome, their biological functions are mostly poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we reanalyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancers. We identify 929 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs in breast cancer samples significantly enrich for active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 929 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other diseases. Using breast tissue related Hi-C data we then show that 87% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role for candidate ncRNA genes in activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (http://ncrna.ictic.sharif.edu), to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used in the analysis of somatic mutations in all cancers.

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“…The length of each fragment used in the dataset is 5kb. We used a recently developed tool MHiC [22] for mapping, filtering and interaction calling of Hi-C data. FASTQ paired-end reads were aligned to the mm9 genome and filtered through the HiC-Pro [15] pipeline developed.…”

Section: Datasetmentioning

confidence: 99%

A Multi-Object Simulated Annealing Approach to Identify Likely Functional Genomic Pairs

Hosseinpoor¹,

Parvïn²

2021

Preprint

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Metaheuristic algorithms have been frequently using to tackle optimization problems, however such algorithms in the analysis of health-related data is not commonly used as developing metaheuristic algorithms that work well on health-related data is a difficult task due to complexity of the health data in particular genomics and epigenetics data. One of the important tasks in genomics is to predict genomic elements that are incorporating together to regulate a disease-related genes. Predicting such elements are important as they can be used to develop a personalized cure. In this study, we present for the first time, a multi-object simulated annealing algorithm to identify enhancer-promoter like interactions from Hi-C (chromosome conformation capture) data. These regulatory elements can potentially play vital roles as promoters and/or enhancers in appearance and exacerbation of the regulation of gene.s To evaluate the efficiency of the proposed method, we applied our proposed method and traditional methods on the Hi-C data from mice and compared together. Our results show that the interacting elements identified by our new method are more likely to be functional. The source code of the method is publicly available.

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MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data

Cited by 17 publications

References 11 publications

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders

Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer

A Multi-Object Simulated Annealing Approach to Identify Likely Functional Genomic Pairs

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