Browsing by Author "Jjingo, Daudi"

Now showing 1 - 9 of 9
  • Thumbnail Image
    Item
    Compound Cis-Regulatory Elements With Both Boundary and Enhancer Sequences in the Human Genome
    (Oxford University Press, 2013-10) Jjingo, Daudi; Wang, Jianrong; Conley, Andrew B.; Lunyak, Victoria V.; Jordan, I. King
    Motivation: It has been suggested that presumably distinct classes of genomic regulatory elements may actually share common sets of features and mechanisms. However, there has been no genome-wide assessment of the prevalence of this phenomenon. Results: To evaluate this possibility, we performed a bioinformatics screen for the existence of compound regulatory elements in the human genome. We identified numerous such collocated boundary and enhancer elements from human CD4þ T cells. We report evidence that such compound regulatory elements possess unique chromatin features and facilitate cell type-specific functions related to inflammation and immune response in CD4+ T cells.
  • Thumbnail Image
    Item
    Computational identification of transposable elements in the mouse genome
    (2007) Jjingo, Daudi; Makalowski, Wojciech
    Repeat sequences cover about 39 percent of the mouse genome and completion of sequencing of the mouse genome [1] has enabled extensive research on the role of repeat sequences in mammalian genomics. This research covers the identification of Transposable elements (TEs) within the mouse transcriptome, based on available sequence information on mouse cDNAs (complementary DNAs) from GenBank [28]. The transcripts are screened for repeats using RepeatMasker [23], whose results are sieved to retain only Interspersed repeats (IRS). Using various bioinformatics software tools as well as tailor made programming, the research establishes: (i) the absolute location coordinates of the TEs on the transcript. (ii) The location of the IRs with respect to the 5’UTR, CDS and 3’UTR sequence features. (iii) The quality of alignment of the TE’s consensus sequence on the transcripts where they exist, (iv) the frequencies and distributions of the TEs on the cDNAs, (v) descriptions of the types and roles of transcripts containing TEs. This information has been collated and stored in a relational database (MTEDB) at http://warta.bio.psu.edu/htt_doc/M TEDB/homepage.htm).
  • Thumbnail Image
    Item
    Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression
    (Oxford University Press, 2011-02-28) Jjingo, Daudi; Huda, Ahsan; Gundapuneni, Madhumati; Mariño-Ramǐrez, Leonardo; Jordan, I. King
    Independent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot be considered independently. We evaluated the TE environment of human genes and GL jointly in an attempt to tease apart their relative effects. TE gene fractions and GL were compared with the overall level of gene expression and the breadth of expression across tissues. GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, confirming the selection hypothesis that attributes the compactness of highly expressed genes to selection for economy of transcription. However, TE gene fractions overall, and for the L1 family in particular, show stronger anti-correlations with expression level than GL, indicating that GL may not be the most important target of selection for transcriptional economy. These results suggest a specific mechanism, removal of TEs, by which highly expressed genes are selectively tuned for efficiency. MIR elements are the only family of TEs with gene fractions that show a positive correlation with tissue-specific expression, suggesting that they may provide regulatory sequences that help to control human gene expression. Consistent with this notion, MIR fractions are relatively enriched close to transcription start sites and associated with expression in specific sets of related tissues. Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation.
  • Thumbnail Image
    Item
    Effects of Repetitive DNA and Epigenetics on Human Genome Regulation
    (Georgia Institute of Technology, 2013-07) Jjingo, Daudi
    The highly developed and specialized anatomical and physiological characteristics observed for eukaryotes in general and mammals in particular are underwritten by an elaborate and intricate process of genome regulation. This precise control of the location, timing and amplitude of gene expression is achieved by a variety of genetic and epigenetic tools and mechanisms. Such tools include cis- and trans- transcriptional regulation, epigenetic marks and chromosomal conformation in the nucleus [78, 79]. While all these regulatory mechanisms have been extensively studied, our understanding of the complex and diverse associations between various epigenetic marks and genetic elements with genome regulatory systems has remained incomplete. However, the last few years have seen a profound development in two areas that have significantly improved the depth and breadth to which their functions and relationships can be understood; 1) Next generation sequencing (NGS) and 2) its application in the genome-wide profiling of multiple DNA elements and functional factors. These include suites of histone modifications, transcription factors, DNA methylations and DNAse hypersensitive sites in various mammalian tissues by the ENCODE consortium and other research laboratories. The objective of this thesis has been to apply bioinformatic computational and statistical tools to analyze and interpret various recent high throughput datasets from a combination of Next generation sequencing and Chromatin immune precipitation (ChIP-seq ) experiments. These datasets have been analyzed to further our understanding of the dynamics of gene regulation in humans particularly as it relates to repetitive DNA, cis-regulation and DNA methylation. The thesis thus resides at the intersection of three major areas in the overarching domain of human genome regulation; transposable elements, cis-regulatory elements and epigenetics. It explores how those three aspects of regulation relate with gene expression and the functional implications of those interactions. From this analysis of high throughput datasets, the thesis provides new insights into; 1) the relationship between the transposable element environment of human genes and their expression, 2) the role of mammalian-wide interspersed repeats (MIRs) in the function of human enhancers and enhancement of tissue-specific functions, 3) the existence and function of composite cis-regulatory elements and 4) the dynamics and relationship between human gene-body DNA methylation and gene expression. The specific advances of my research in the field of human genome regulation are summarized as follows: Research advance 1: With both TE fractions and GL being highly correlated to gene length, this study evaluated the two parameters together and teased apart their relative contributions to the gene expression parameters of tissue-specificity and expression levels. By showing that GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, this study elicited evidence for the selection hypothesis [23] that attributes the compactness of highly expressed genes to selection for economy of transcription as opposed to the genomic design hypothesis [135]. In fact, TE fractions of human genes were shown to be more anti-correlated to gene expression levels, suggesting that TEs, rather than GL might be more important targets of selection for transcriptional economy. Finally, MIRs were found to be the only TEs that positively associate with tissue-specific gene expression. Relevance of TEs environment for gene expression was confirmed and distinct mechanisms by which they may contribute to genome regulation were adduced. Research advance 2: Mammalian-wide interspersed repeats (MIRs), previously shown to be related to tissue-specific gene expression [61], are shown to execute this function primarily through enhancers. This study found MIRs to be significantly enriched within enhancers and reports many novel MIR-derived enhancers. Indeed, the density of enhancer-MIRs around genes is shown to be significantly related to both their level of expression, their tissue specificity and to be involved in tissue-specific cellular functions. MIRs within enhancers are shown to possess significantly higher numbers of transcriptional factor binding sites (TFBSs) relative to the genomic background, a finding that might explain their co-option into enhancers and thus their longstanding conservation and wide distribution in the mammalian clade. Research advance 3: This research adduced evidence that confirmed previous postulations that distinctions between different classes of cis-regulatory elements may not be definitive and that different elements might share regulatory features and mechanisms. Taking boundary elements and enhancers within the human CD4+ T cells as examples, we identified 174 composite cis-regulatory elements, for which both enhancers and boundary elements are co-located. These composite cis-regulatory elements possess unique chromatin environments and regulatory features and are revealed to facilitate cell-type specific functions. Research advance 4: This research used the approach of a meta-analysis of new high throughput chromatin, methylation and gene expression datasets to address aspects of the long standing DNA methylation paradox [63]. Contrary to previous knowledge [2, 4, 56, 83, 88, 108], it is shown that the relationship between gene-body methylation and gene expression levels is not linear but actually non-monotonic (bell-shaped). These results confirm that gene-body DNA methylation does serve to repress spurious intragenic transcription. However, they also illustrate that role to be only epiphenomenal, with gene-body methylation levels being predominantly determined by the accessibility of the DNA to methylating enzyme complexes rather than by an evolutionary adaptation to minimize the spurious intragenic transcription.
  • Thumbnail Image
    Item
    Flow-Dependent Epigenetic DNA Methylation Regulates Endothelial Gene Expression and Atherosclerosis
    (American Society for Clinical Investigation, 2014) Dunn, Jessilyn; Qiu, Haiwei; Kim, Soyeon; Jjingo, Daudi; Hoffman, Ryan; Kim, Chan Woo; Jang, Inhwan; Son, Dong Ju; Kim, Daniel; Pan, Chenyi; Fan, Yuhong; Jordan, I. King; Jo, Hanjoong
    In atherosclerosis, plaques preferentially develop in arterial regions of disturbed blood flow (d-flow), which alters endothelial gene expression and function. Here, we determined that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase–dependent (DNMT-dependent) manner. Induction of d-flow by partial carotid ligation surgery in a murine model induced DNMT1 in arterial endothelium. In cultured endothelial cells, DNMT1 was enhanced by oscillatory shear stress (OS), and reduction of DNMT with either the inhibitor 5-aza-2′-deoxycytidine (5Aza) or siRNA markedly reduced OS-induced endothelial inflammation. Moreover, administration of 5Aza reduced lesion formation in 2 mouse models of atherosclerosis. Using both reduced representation bisulfite sequencing (RRBS) and microarray, we determined that d-flow in the carotid artery resulted in hyper-methylation within the promoters of 11 mechanosensitive genes and that 5Aza treatment restored normal methylation patterns. Of the identified genes, HoxA5 and Klf3 encode transcription factors that contain cAMP response elements, suggesting that the methylation status of these loci could serve as a mechanosensitive master switch in gene expression. Together, our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.
  • Thumbnail Image
    Item
    Mammalian-Wide Interspersed Repeat (MIR)-Derived Enhancers and the Regulation of Human Gene Expression
    (BioMed Central, 2014) Jjingo, Daudi; Conley, Andrew B.; Wang, Jianrong; Mariño-Ramírez, Leonardo; Lunyak, Victoria V.; Jordan, I. King
    Background: Mammalian-wide interspersed repeats (MIRs) are the most ancient family of transposable elements (TEs) in the human genome. The deep conservation of MIRs initially suggested the possibility that they had been exapted to play functional roles for their host genomes. MIRs also happen to be the only TEs whose presence in-and-around human genes is positively correlated to tissue-specific gene expression. Similar associations of enhancer prevalence within genes and tissue-specific expression, along with MIRs’ previous implication as providing regulatory sequences, suggested a possible link between MIRs and enhancers. Results: To test the possibility that MIRs contribute functional enhancers to the human genome, we evaluated the relationship between MIRs and human tissue-specific enhancers in terms of genomic location, chromatin environment, regulatory function, and mechanistic attributes. This analysis revealed MIRs to be highly concentrated in enhancers of the K562 and HeLa human cell-types. Significantly more enhancers were found to be linked to MIRs than would be expected by chance, and putative MIR-derived enhancers are characterized by a chromatin environment highly similar to that of canonical enhancers. MIR-derived enhancers show strong associations with gene expression levels, tissue-specific gene expression and tissue-specific cellular functions, including a number of biological processes related to erythropoiesis. MIR-derived enhancers were found to be a rich source of transcription factor binding sites, underscoring one possible mechanistic route for the element sequences co-option as enhancers. There is also tentative evidence to suggest that MIR-enhancer function is related to the transcriptional activity of non-coding RNAs. Conclusions: Taken together, these data reveal enhancers to be an important cis-regulatory platform from which MIRs can exercise a regulatory function in the human genome and help to resolve a long-standing conundrum as to the reason for MIRs’ deep evolutionary conservation.
  • Thumbnail Image
    Item
    On the Presence and Role of Human Gene-Body DNA Methylation
    (International Multidisciplinary Publishing Academy for Computational Technologies, 2012-05-09) Jjingo, Daudi; Conley, Andrew B.; Yi, Soojin V.; Lunyak, Victoria V.; Jordan, I. King
    DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly, the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes initiate the most intragenic transcription, which is inconsistent with the previously held notion that gene-body methylation serves to repress spurious intragenic transcription to allow for efficient transcriptional elongation. These observations lead us to propose a model to explain the presence of human gene-body methylation. This model holds that the repression of intragenic transcription by gene-body methylation is largely epiphenomenal, and suggests that gene-body methylation levels are predominantly shaped via the accessibility of the DNA to methylating enzyme complexes.
  • Thumbnail Image
    Item
    Prediction of transposable element derived enhancers using chromatin modification profiles
    (PLoS ONE (Public Library of Science), 2011-11-07) Huda, Ahsan; Tyagi, Eishita; Marino-Ramırez, Leonardo; Bowen, Nathan J.; Jjingo, Daudi; King Jordan, I.
    Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.
  • Thumbnail Image
    Item
    Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
    (PLoS ONE (Public Library of Science), 2013-11-11) Lopes, Fabrício R.; Jjingo, Daudi; R. M. da Silva, Carlos; Andrade, Alan C.; Marraccini, Pierre; Teixeira, Joaõ B.; Carazzolle, Marcelo F.; A. G. Pereira, Gonçalo; Pereira, Luiz Filipe P.; Vanzela, André L. L.; Wang, Lu; Jordan, I. King; Carareto, Claudia M. A.
    Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences.