Distinct Set Of Transcription Factors Research Articles

Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression.

Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.

Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease†.

The placenta is a dynamic organ that must perform a remarkable variety of functions during its relatively short existence in order to support a developing fetus. These functions include nutrient delivery, gas exchange, waste removal, hormone production, and immune barrier protection. Proper placenta development and function are critical for healthy pregnancy outcomes, but the underlying genomic regulatory events that control this process remain largely unknown. We hypothesized that mapping sites of transcriptional enhancer activity and associated changes in gene expression across gestation in human placenta tissue would identify genomic loci and predicted transcription factor activity related to critical placenta functions. We used a suite of genomic assays [i.e., RNA-sequencing (RNA-seq), Precision run-on-sequencing (PRO-seq), and Chromatin immunoprecipitation-sequencing (ChIP-seq)] and computational pipelines to identify a set of >20000 enhancers that are active at various time points in gestation. Changes in the activity of these enhancers correlate with changes in gene expression. In addition, some of these enhancers encode risk for adverse pregnancy outcomes. We further show that integrating enhancer activity, transcription factor motif analysis, and transcription factor expression can identify distinct sets of transcription factors predicted to be more active either in early pregnancy or at term. Knockdown of selected identified transcription factors in a trophoblast stem cell culture model altered the expression of key placental marker genes. These observations provide a framework for future mechanistic studies of individual enhancer-transcription factor-target gene interactions and have the potential to inform genetic risk prediction for adverse pregnancy outcomes.

Towards molecular mechanisms for pathogenic Th17 cell differentiation in ocular autoimmunity

Abstract CD4+ T helper (Th) cells play critical roles in coordinating proper immune responses by differentiating into effector subtypes specialized against different types of pathogens, while dysregulated Th cells can drive autoimmune disease by triggering inappropriate immune responses. Pathogenic Th17 (pTh17) cells, which combine behaviors of classic Th1 and Th17 effector cells by producing both interferon-gamma (IFNg) and interleukin-17A (IL17A), have been implicated in autoimmune diseases. Our goal is to map regulatory networks and identify novel regulators underlying pTh17 differentiation and activation using the murine model experimental autoimmune uveitis (EAU), in which ocular autoimmunity is driven by pTh17 cells. To track pTh17 differentiation, we bred a double reporter mouse with IL17A-cre/tdTomato-flox tracer and IFNg-YFP. We sorted both Tomato+YFP+ and Tomato+YFP- CD4+ T cells from eyes and spleens after EAU induction for single-cell RNA-seq. Clustering of single-cell transcriptomes revealed distinct transcriptomes between eyes and spleen. In the eye, we identified clusters similar to pTh17 and non-pathogenic (np)Th17 populations defined in a myelin autoimmunity model. The pTh17 cluster contained both double positive and Tomato single positive cells, suggesting a heterogeneous pathogenic population. In contrast, the npTh17 cluster only contained single positives. Differential gene expression analysis showed that pathogenic and non-pathogenic clusters utilize distinct sets of transcription factors. We are further characterizing epigenetic differences between pTh17 and npTh17 to better understand how distinct regulatory networks shape pTh17 differentiation. Supported by the NEI Intramural Research Program fund (ZIAEY000569-01)

IRF8 deficiency induces the transcriptional, functional, and epigenetic reprogramming of cDC1 into the cDC2 lineage

Conventional dendritic cells (cDCs) consist of two major functionally and phenotypically distinct subsets, cDC1 and cDC2, whose development is dependent on distinct sets of transcription factors. Interferon regulatory factor 8 (IRF8) is required at multiple stages of cDC1 development, but its role in committed cDC1 remains unclear. Here, we used Xcr1-cre to delete Irf8 in committed cDC1 and demonstrate that Irf8 is required for maintaining the identity of cDC1. In the absence of Irf8, committed cDC1 acquired the transcriptional, functional, and chromatin accessibility properties of cDC2. This conversion was independent of Irf4 and was associated with the decreased accessibility of putative IRF8, Batf3, and composite AP-1-IRF (AICE)-binding elements, together with increased accessibility of cDC2-associated transcription-factor-binding elements. Thus, IRF8 expression by committed cDC1 is required for preventing their conversion into cDC2-like cells.

Integration of Spatial and Temporal Patterning in the Invertebrate and Vertebrate Nervous System.

The nervous system is one of the most sophisticated animal tissues, consisting of thousands of interconnected cell types. How the nervous system develops its diversity from a few neural stem cells remains a challenging question. Spatial and temporal patterning mechanisms provide an efficient model through which diversity can be generated. The molecular mechanism of spatiotemporal patterning has been studied extensively in Drosophila melanogaster, where distinct sets of transcription factors define the spatial domains and temporal windows that give rise to different cell types. Similarly, in vertebrates, spatial domains defined by transcription factors produce different types of neurons in the brain and neural tube. At the same time, different cortical neuronal types are generated within the same cell lineage with a specific birth order. However, we still do not understand how the orthogonal information of spatial and temporal patterning is integrated into the progenitor and post-mitotic cells to combinatorially give rise to different neurons. In this review, after introducing spatial and temporal patterning in Drosophila and mice, we discuss possible mechanisms that neural progenitors may use to integrate spatial and temporal information. We finally review the functional implications of spatial and temporal patterning and conclude envisaging how small alterations of these mechanisms can lead to the evolution of new neuronal cell types.

Gene Regulatory Circuits in Innate and Adaptive Immune Cells.

Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry.

Developmental single-cell transcriptomics of hypothalamic POMC neurons reveal the genetic trajectories of multiple neuropeptidergic phenotypes.

Proopiomelanocortin (POMC) neurons of the hypothalamic arcuate nucleus are essential to regulate food intake and energy balance. However, the ontogenetic transcriptional programs that specify the identity and functioning of these neurons are poorly understood. Here, we use single-cell RNA-sequencing (scRNA-seq) to define the transcriptomes characterizing Pomc-expressing cells in the developing hypothalamus and translating ribosome affinity purification with RNA-sequencing (TRAP-seq) to analyze the subsequent translatomes of mature POMC neurons. Our data showed that Pomc-expressing neurons give rise to multiple developmental pathways expressing different levels of Pomc and unique combinations of transcription factors. The predominant cluster, featured by high levels of Pomc and Prdm12 transcripts, represents the canonical arcuate POMC neurons. Additional cell clusters expressing medium or low levels of Pomc mature into different neuronal phenotypes featured by distinct sets of transcription factors, neuropeptides, processing enzymes, cell surface, and nuclear receptors. We conclude that the genetic programs specifying the identity and differentiation of arcuate POMC neurons are diverse and generate a heterogeneous repertoire of neuronal phenotypes early in development that continue to mature postnatally.

StrongestPath: a Cytoscape application for protein\u2013protein interaction analysis

BackgroundStrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein–protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can also identify any activating or inhibitory regulatory paths between two distinct sets of transcription factors and target genes. This application can be used on the built-in human and mouse PPI or signaling databases, or any user-provided database for some organism.ResultsOur results on 12 signaling pathways from the NetPath database demonstrate that the application can be used for indicating proteins which may play significant roles in a pathway by finding the strongest path(s) in the PPI or signaling network.ConclusionEasy access to multiple public large databases, generating output in a short time, addressing some key challenges in one platform, and providing a user-friendly graphical interface make StrongestPath an extremely useful application.

Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.

Gene expression is controlled by regulatory elements within accessible chromatin. Although most regulatory elements are cell type-specific, a subset is accessible in nearly all the 517 human and 94 mouse cell and tissue types assayed by the ENCODE consortium. We systematically analyzed 9000 human and 8000 mouse ubiquitously-accessible candidate cis-regulatory elements (cCREs) with promoter-like signatures (PLSs) from ENCODE, which we denote ubi-PLSs. These are more CpG-rich than non-ubi-PLSs and correspond to genes with ubiquitously high transcription, including a majority of cell-essential genes. ubi-PLSs are enriched with motifs of ubiquitously-expressed transcription factors and preferentially bound by transcriptional cofactors regulating ubiquitously-expressed genes. They are highly conserved between human and mouse at the synteny level but exhibit frequent turnover of motif sites; accordingly, ubi-PLSs show increased variation at their centers compared with flanking regions among the ∼186 thousand human genomes sequenced by the TOPMed project. Finally, ubi-PLSs are enriched in genes implicated in Mendelian diseases, especially diseases broadly impacting most cell types, such as deficiencies in mitochondrial functions. Thus, a set of roughly 9000 mammalian promoters are actively maintained in an accessible state across cell types by a distinct set of transcription factors and cofactors to ensure the transcriptional programs of cell-essential genes.

<i>Irf8</i> Deficiency Induces Functional, Transcriptional and Epigenetic Reprogramming of cDC1 into the cDC2 Lineage

Conventional dendritic cells (cDC) consist of two functionally and phenotypically distinct subsets, cDC1 and cDC2, whose development is dependent on distinct sets of transcription factors. Interferon regulatory factor 8 (IRF8) is required at multiple stages of cDC1 development, but its role in mature cDC1 remains unclear. Here we used XCR1-cre to delete Irf8 in committed cDC1 and demonstrate that Irf8 is required for maintaining the identity of cDC1 but not their survival. In the absence of Irf8, committed cDC1 (“ex-cDC1”) acquired the transcriptional, functional and chromatin accessibility properties of cDC2. This conversion was independent of Irf4 and was associated with decreased accessibility of putative IRF8, Batf3 and composite AP-1-IRF (AICE) binding elements, together with increased accessibility of cDC2 associated transcription factor binding elements. Thus, IRF8 expression by committed cDC1 is required for preventing their conversion into cDC2.

Article of Significant Interest in This Issue

The transcription factors C/EBPβ and C/EBPδ are transcriptionally induced soon after the treatment of preadipocytes with an adipogenic cocktail. In turn C/EBPβ and C/EBPδ promote the expression of the master adipocyte transcription factors peroxisome proliferator-activated receptor gamma and C/EBPα. However, the factors responsible for induction of C/EBPβ and C/EBPδ have remained incompletely understood. Lee et al. (e00209-20) show that the MLL3/MLL4/PTIP-associated protein PAGR1 cooperates with CREB and the glucocorticoid receptor to regulate the induction of C/EBPβ and C/EBPδ during the early phase of adipogenesis. This study presents an updated model in which components of the MLL3/MLL4 complex promote adipocyte differentiation by regulating the expression of distinct sets of transcription factors.

Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis

Development requires highly coordinated changes in chromatin accessibility in order for proper gene regulationto occur. Here, we identify factors associated with major, discrete changes in chromatin accessibility during butterfly wing metamorphosis. By combining mRNA sequencing (mRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and machine learning analysis of motifs, we show that distinct sets of transcription factors are predictive of chromatin opening at different developmental stages. Our data suggest an important role for nuclear hormone receptors early in metamorphosis, whereas PAS-domain transcription factors are strongly associated with later chromatin opening. Chromatin immunoprecipitation sequencing (ChIP-seq) validation of select candidate factors showed spineless binding to be a major predictor of opening chromatin. Surprisingly, binding of ecdysone receptor (EcR), a candidate accessibility factor in Drosophila, was not predictive of opening but instead marked persistent sites. This work characterizes the chromatin dynamics of insect wing metamorphosis, identifies candidate chromatin remodeling factors in insects,and presents a genome assembly of the model butterfly Junonia coenia.

Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells.

Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data. According to the origins of variation in DNA methylation, we determined the genomic loci associated with allelic-specific methylation or asymmetric DNA methylation, and explored a beta mixture model to infer the genomic loci exhibiting cell-subset specific methylation (CSM). We observed that the putative CSM loci in ESCs are significantly enriched in CpG island (CGI) shelves and regions with histone marks for promoter and enhancer, and the genes hosting putative CSM loci show wide-ranging expression among ESCs. More interestingly, the putative CSM loci may be clustered into co-methylated modules enriching the binding motifs of distinct sets of transcription factors. Taken together, our study provided a novel tool to explore single-cell methylome and transcriptome to reveal the underlying transcriptional regulatory networks associated with epigenetic heterogeneity of ESCs.

Niche signals and transcription factors involved in tissue-resident macrophage development

Tissue-resident macrophages form an essential part of the first line of defense in all tissues of the body. Next to their immunological role, they play an important role in maintaining tissue homeostasis. Recently, it was shown that they are primarily of embryonic origin. During embryogenesis, precursors originating in the yolk sac and fetal liver colonize the embryonal tissues where they develop into mature tissue-resident macrophages. Their development is governed by two distinct sets of transcription factors. First, in the pre-macrophage stage, a core macrophage program is established by lineage-determining transcription factors. Under the influence of tissue-specific signals, this core program is refined by signal-dependent transcription factors. This nurturing by the niche allows the macrophages to perform tissue-specific functions. In the last 15 years, some of these niche signals and transcription factors have been identified. However, detailed insight in the exact mechanism of development is still lacking.

Bioinformatics review of alcohol exposed neuronal stem cells and transcription factor consensus sequences in cell cycle progression genes.

Previous studies from microarray analysis of neuronal stem cells exposed to moderate levels of alcohol suggested that alterations in proliferation and induced apoptosis may well be associated with a distinct set of transcription factors and associated consensus sequences in key gene sets responsible for G1/S phase progression and DNA synthesis. The objective of the study was to gather existing information on the Fox1, E2F1, DP-1, DP-2, DP-3, AP-1, and SP-1 transcription factors and examine their interaction with the promoter regions of genes involved in cell cycle progression through a bioinformatics approach. To complete this review, data was compiled using the Unipro UGENE program. Using this program, the promoter regions of genes of interest were aligned with the known DNA consensus sequences targeted by the transcription factors. Based on the alignments – or lack thereof – conclusions were drawn as to which transcription factors exert influence on controlling proper cell cycle progression. Data showed interactions among several of the transcription factors with the multiple regions in the promoter regions of almost all the examined genes. Based on the discovered consensus sequences and their influence on the expression rates of genes necessary for cell cycle progression, this study provides plausible evidence of transcription factors worth targeting for controlling specific genes in cell cycle progression.

Erratum: Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells.

Tissue-resident memory T cells (TRM cells) in the airways mediate protection against respiratory infection. We characterized TRM cells expressing integrin αE (CD103) that reside within the epithelial barrier of human lungs. These cells had specialized profiles of chemokine receptors and adhesion molecules, consistent with their unique localization. Lung TRM cells were poised for rapid responsiveness by constitutive expression of deployment-ready mRNA encoding effector molecules, but they also expressed many inhibitory regulators, suggestive of programmed restraint. A distinct set of transcription factors was active in CD103+ TRM cells, including Notch. Genetic and pharmacological experiments with mice revealed that Notch activity was required for the maintenance of CD103+ TRM cells. We have thus identified specialized programs underlying the residence, persistence, vigilance and tight control of human lung TRM cells.

Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells.

Tissue-resident memory T cells (TRM cells) in the airways mediate protection against respiratory infection. We characterized TRM cells expressing integrin αE (CD103) that reside within the epithelial barrier of human lungs. These cells had specialized profiles of chemokine receptors and adhesion molecules, consistent with their unique localization. Lung TRM cells were poised for rapid responsiveness by constitutive expression of deployment-ready mRNA encoding effector molecules, but they also expressed many inhibitory regulators, suggestive of programmed restraint. A distinct set of transcription factors was active in CD103+ TRM cells, including Notch. Genetic and pharmacological experiments with mice revealed that Notch activity was required for the maintenance of CD103+ TRM cells. We have thus identified specialized programs underlying the residence, persistence, vigilance and tight control of human lung TRM cells.

Loss of tumorigenic potential upon transdifferentiation from keratinocytic into melanocytic lineage.

Lineage-specific transcription factors determine the cell fate during development. Direct conversion of several cell types into other lineages has been achieved by the overexpression of specific transcription factors. Even cancer cells have been demonstrated to be amenable to transdifferentiation. Here, we identified a distinct set of transcription factors, which are sufficient to transform cells of the keratinocytic lineage to melanocyte-like cells. Melanocyte marker expression was induced and melanosome formation was observed in non-tumorigenic keratinocytes (HaCaT) and tumorigenic squamous cell carcinoma (MET-4) cells. Moreover, reduced proliferation, cell metabolism, invasion and migration were measured in vitro in transdifferentiated MT-MET-4 cells. A loss of tumorigenic potential of squamous cell carcinoma cells could be due to the upregulation of the melanocyte differentiation associated gene IL-24. Our data show that cells from the keratinocytic lineage can be transdifferented into the melanocytic lineage and provide a proof of principle for a potential new therapeutic strategy.

Mitochondria operate as signaling platforms in yeast aging

Mitochondria are vital to physiology and health of eukaryotic organisms across phyla. These organelles generate the majority of cellular ATP and create biosynthetic intermediates for amino acids, nucleotides and lipids [1]. Mitochondria can also operate as signaling platforms and structural scaffolds for coordinating diverse cellular responses to changes in a variety of physiological conditions [2, 3]. Therefore, the functional state of mitochondria is crucial for a plethora of cellular processes, including cell growth, division, differentiation, homeostasis, metabolism, stress response, signaling, immune response, survival and death [1 - 4]. Because mitochondrial functionality gradually declines with age in evolutionarily distant organisms, such age-related deterioration of mitochondrial function is regarded as the universal hallmark of cellular and organismal aging [5]. The budding yeast Saccharomyces cerevisiae, a unicellular eukaryote, has been intensively used as a model organism for uncovering mechanisms linking mitochondrial functionality and cellular aging [3]. Our recent studies have revealed how a geroprotective chemical compound delays yeast chronological aging by causing an age-related remodeling of mitochondrial lipidome [6], how such remodeling elicits changes to mitochondrial morphology and functionality [6], and how such changes enable mitochondria to operate as signaling platforms that exploit a distinct set of transcription factors to choreograph a longevity-extending transcriptional program for many nuclear genes [7]. We found that exogenously added lithocholic bile acid (LCA), which is known to slow the chronological aging of S. cerevisiae, enters yeast cell, amasses within a double membrane delimiting mitochondria and resides primarily in the inner mitochondrial membrane [6]. After being confined to mitochondrial membranes, LCA elicits specific changes in the concentrations of mitochondrial membrane phospholipids; these changes occur in an age-related fashion and are believed to be due to a characteristic remodeling of pathways for phospholipid synthesis and movement within both mitochondrial membranes [6]. The resulting major changes in mitochondrial membrane lipidome cause a substantial enlargement of mitochondria, decrease the number of these organelles, significantly increase the total length on mitochondrial cristae, and reduce the extent of connectivity between these cristae and the inner mitochondrial membrane [6]. These extensive alterations in mitochondrial abundance and morphology incite a distinct pattern of changes in the age-related chronology of such key longevity-defining processes as mitochondrial respiration, membrane potential maintenance, ATP synthesis and reactive oxygen species homeostasis [6]. Such specific changes to the age-related chronology of mitochondrial functionality allow mitochondria to function as signaling platforms that coordinate a stepwise establishment of a distinct transcriptional program for many nuclear genes [7]. The observed age-related rewiring of transcriptional patterns is choreographed by a distinct set of transcription factors [7]. These transcription factors respond to different aspects of altered mitochondrial functionality in yeast cells exposed to LCA; they include the following regulators of transcription: 1) the Rtg1, Rtg2 and Rtg3 protein components of the mitochondrial retrograde signaling pathway; 2) the Sfp1 protein component of the mitochondrial back-signaling pathway; 3) the Aft1 transcription factor modulated by the concentrations of iron-sulfur clusters, which function as inorganic cofactors of numerous mitochondrial, nuclear and cytosolic proteins; 4) a transcription factor involved in the unfolded protein response pathway of mitochondria-to-nucleus communications; this pathway is elicited in response to reduced concentrations of the mitochondrial protease Yme1 and the mitochondrial peptide exporter Mdl1; and 5) the transcription factors Yap1, Msn2/Msn4, Skn7 and Hog1, all modulated by mitochondrially generated reactive oxygen species [7]. Based on these observations, we proposed a model for how LCA-driven changes in mitochondrial proteome and functionality early and late in life of chronologically aging yeast coordinate a stepwise development of an aging-delaying cellular pattern and its maintenance throughout lifespan [7]. In sum, we demonstrated that the geroprotective chemical compound LCA can delay the onset and slow the progression of chronological aging in yeast by causing an age-related remodeling of mitochondrial lipidome. Our findings revealed that such remodeling of mitochondrial lipidome alters mitochondrial morphology and functionality, thereby enabling mito-chondria to act as signaling platforms that can 1) choreograph a longevity-extending transcriptional program for many nuclear genes governed by a distinct set of transcription factors; and 2) orchestrate a gradual establishment and long-term maintenance of a longevity-extending cellular pattern. Thus, targeting the discovered role of mitochondria as signaling platforms in yeast aging has potential as a novel therapeutic strategy for slowing aging, improving health, attenuating age-related pathologies and delaying the onset of age-related diseases in humans.

Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation.

BackgroundDNA methylation plays an important role in regulating gene expression during many biological processes. However, the mechanism of DNA-methylation-dependent gene regulation is not fully understood. Here, we explore two possible DNA methylation regulatory mechanisms with opposite modes of gene expression regulation.ResultsBy comparing the genome-wide methylation and expression patterns in different tissues, we find that majority of tissue-specific differentially methylated regions (T-DMRs) are negatively correlated with expression of their associated genes (negative T-DMRs), consistent with the classical dogma that DNA methylation suppresses gene expression; however, a significant portion of T-DMRs are positively correlated with gene expression (positive T-DMRs). We observe that the positive T-DMRs have similar genomic location as negative T-DMRs, except that the positive T-DMRs are more enriched in the promoter regions. Both positive and negative T-DMRs are enriched in DNase I hypersensitivity sites (DHSs), suggesting that both are likely to be functional. The CpG sites of both positive and negative T-DMRs are also more evolutionarily conserved than the genomic background. Interestingly, the putative target genes of the positive T-DMR are enriched for negative regulators such as transcriptional repressors, suggesting a novel mode of indirect DNA methylation inhibition of expression through transcriptional repressors. Likewise, two distinct sets of DNA sequence motifs exist for positive and negative T-DMRs, suggesting that two distinct sets of transcription factors (TFs) are involved in positive and negative regulation mediated by DNA methylation.ConclusionsWe find both negative and positive association between T-DMRs and gene expression, which implies the existence of two different mechanisms of DNA methylation-dependent gene regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1271-4) contains supplementary material, which is available to authorized users.