Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus

Maulik et al. BMC Genetics (2018) 19:9 DOI 10.1186/s12863-017-0574-7 RESEARCH ARTICLE Open Access Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus Ujjwal Maulik1* , Sagnik Sen1 , Saurav Mallik1 and Sanghamitra Bandyopadhyay2 Abstract Background: Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection. Results: First of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis. Thereafter, we utilize weighted topological overlap matrix (TOM) measure and average linkage clustering consecutively on these genesets for intraand inter-species study.We identify co-methylated and multi-stage co-methylated gene modules by using dynamic tree cut, for intra-and inter-species cases, respectively. Each module is represented by individual color in the dendrogram. Gene Ontology and KEGG pathway based analysis are then performed to identify biological functionalities of the identified modules. Finally, top ten regulator TFs and targeter miRNAs that are associated with the maximum number of gene modules, are determined for both intra-and inter-species analysis. Conclusions: The novel TFs and miRNAs obtained from the analysis are: MYST3 and ZNF771 as TFs (for human intra-species analysis), BAZ2B, RCOR3 and ATF1 as TFs (for rhesus intra-species analysis), and mml-miR-768-3p and mml-miR-561 as miRs (for rhesus intra-species analysis); and MYST3 and ZNF771 as miRs(for inter-species study). Furthermore, the genes/TFs/miRNAs that are already found to be liable for several brain-related dreadful diseases as well as rare neglected diseases (e.g., wolf Hirschhorn syndrome, Joubarts Syndrome, Huntington’s disease, Simian Immunodeficiency Virus(SIV) mediated enchaphilits, Parkinsons Disease, Bipolar disorder and Schizophenia etc.) are mentioned. Keywords: Multiple cytosine variants, Differentially 5hmC-methylated genes, Intra-species co-methylated gene-modules, Differentially multi-stage methylated genes, Inter-species multi-stage co-methylated gene-modules, Weighted TOM and dynamic tree cut, Top regulator transcription factors, Top targeter miRNAs *Correspondence: Department of Computer Science and Engineering, Jadavpur University, 700032 Kolkata, India Full list of author information is available at the end of the article 1 © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Maulik et al. BMC Genetics (2018) 19:9 Background DNA methylation placed at the 5th position of cytosine (viz., 5mC or 5-methylcytosine) [1–3] is one of the most important epigenetic factors which plays a significant role in genome regulation, host-defending, and inactivation of X-chromosome ([4–7]). 5-methylcytosine (5mC) is predominantly observed in CpG dinucleotides of the mammalian genome. It is well-known that individual CpGs which are occupied in different parts of the genome, are differentially methylated depending on the category of tissue/cell and development-phase. DNA methylation is catalysed by several enzymes (viz., DNA methyltransferases (DNMTs):- DNMT1, DNMT3A, DNMT3B and DNMT3L) [8, 9]. Furthermore, transcriptional status of gene and the density of GC affect the status of DNA methylation e.g., the maximum parts of CpG islands (symbolized as CGIs) which contain a closely compacted CpG content, are basically hypo-methylated; whereas the remaining portions of the genome including dispersed CpGs in the regions of gene-coding, and the heterochromatin regions, having repetitive CpGs are hyper-methylated in general. Interestingly, it is still under debate that how genome-wide methylation is differentially regulated in the different discrete loci, and how it has been working dynamically in separate cell-categories at the development-stage. However, DNA methylation decreases the gene expression level in general, and therefore plays an crucial task in gene-silencing [1, 2, 10, 11]. Oxidative product of 5mC is 5-hydroxymethylcytosine (5hmC). The 5hmC mark was discovered approximately six decades ago in T-even bacteriophage [12]. Later it has been identified in vertebrate-brain and various other tissues (as mentioned in [13–15]). The 5hmC is found in the embryonic stem cells of mouse at high-level. Although level deteriorates after differentiation of the embryonic stem cells (according to [16, 17]), but increased again in terminally differentiated cells (viz., Purkinje neurons) (according to [13]). Currently, 5hmC is observed in zygotes of bovines, mice and rabbits, and it is collected specifically at paternal pro-nucleus concurring with reduction of 5mC ([18, 19]). The members of several translocation (TET) protein-family mediates the 5hmC. Here, each protein consists of a C-terminal oxidase region. An effective chemical methodology is recently proposed in order to capture and label the 5hmC which shows the map of first distribution for the 5hmC in a brain genome of mouse (i.e., mammal), and the enrichment of it in the highly transcribed genes. Hence, the involvement of 5hmC in the specified gene-bodies during differentiation and maturation of neufirons notifies that the 5hmC is temporally and spatially distributed on brain tissue at the time of the brain development. Conversion of 5mC to 5hmC is responsible for passive DNA methylation. 5hmC is divided in three categories in terms of functions, Page 2 of 22 5hmC-A, 5hmC-B and 5hmC-C. Among them 5hmC-A are mostly protecting DNA replication whereas 5hmC-C can affect the functional annotations of DNA binding proteins. Differential methylation is stated to have significant differences in methylation values of a gene across the group of cancer (diseased/experimental) samples and the group of normal (control) samples. Statistical test is a technique of statistical inference which is applied for measuring the differential methylation between two groups (populations). Differential methylation analysis is carried out for determining wh (...truncated)