Transposable elements as a potent source of diverse
            <i>cis</i>
            -regulatory sequences in mammalian genomes

Sundaram, Vasavi; Wysocka, Joanna

doi:10.1098/rstb.2019.0347

Cited by 163 publications

(176 citation statements)

References 108 publications

(157 reference statements)

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“…Previous reports have shown that orphan genes generally have lower expression levels but higher tissue-specific expression compared to phylogenetically conserved genes (Levine et al , 2006; Donoghue et al , 2011; Wu, Irwin and Zhang, 2011). Several hypotheses have been proposed to explain the regulation of these younger genes that lead to tissue-specific and/or stage-specific expression, including transposon insertion upstream of the transcription start-site, shared regulatory elements with older genes (possibly by gene overlap), association with a bidirectional promoter, or by being located within an intron (Maksakova and Mager, 2005; Toll-Riera et al , 2008; Arendsee, Li and Wurtele, 2014; Sundaram and Wysocka, 2020). We explored the cis-regulatory elements in the putative promoter regions of these genes below.…”

Section: Resultsmentioning

confidence: 99%

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Arachchilage

Mullet

Marshall‐Colón

2020

Preprint

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The genetic engineering of value-added traits such as the accumulation of bioproducts 21 in high biomass C4 grass stems is one promising strategy to make plant-derived biofuels more 22 economical for industrial use. A first step toward achieving this goal is to identify stem-specific 23 promoters that can drive the expression of genes of interest with good temporal and spatial 24 specificity. However, a comprehensive characterization of the spatial-temporal regulatory 25 elements of stem tissue-specific promoters for C4 grasses has not been reported. Therefore, we 26 performed an in-silico analysis on Sorghum bicolor cv BTx623 transcriptomes from multiple 27 tissues over development to identify stem-expressed genes. The analysis identified 10 genes that 28 are "Always-On-Stem-Specific," 59 genes that are "Temporally-Stem-Specific during early 29 development," and 21 genes that are "Temporally-Stem-Specific during late development." 30 Promoter analysis revealed common and/or unique cis-regulatory elements in promoters of genes within each of the three categories. Subsequent gene regulatory network (GRN) analysis revealed 32 that different transcriptional regulatory programs are responsible for the temporal activation of the 33 stem-expressed genes. The analysis of temporal stem GRNs between sweet (cv Della) and grain 34 (cv BTx623) sorghum varieties revealed genetic variation that could influence the regulatory 35 landscape. This study provides new insights about sorghum stem biology, and information for 36 future genetic engineering efforts to fine-tune the spatial-temporal expression of transgenes in C4 37 grass stems. 38 39 40 High biomass grasses, such as sorghum (Sorghum bicolor), miscanthus (Miscanthus x 41 giganteus), switchgrass (Panicum virgatum), and sugarcane (Saccharum sp.), offer an abundant 42 and renewable source of biomass for biofuels production (McLaughlin and Kszos, 2005; Rooney 43 et al.

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Section: Resultsmentioning

confidence: 99%

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Arachchilage

Mullet

Marshall‐Colón

2020

Preprint

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“…These studies supported the longstanding hypothesis that TE domestication is important in eukaryotic genome evolution and that some TEs play integral roles in regulating gene expression. However, most of these studies were focused on Class I TEs in animal and human systems (Sundaram and Wysocka, 2020). In this study, we identified a new mechanism by whichClass II TEs can influence gene regulation in maize.…”

Section: Discussionmentioning

confidence: 93%

Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition

Peterson

Zuo

2020

Preprint

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Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status and generating small RNAs. In this study, we demonstrated that Ac/fAc transposable elements are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of Class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events which involve the termini of two different, nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations and Composite Insertions (CIs). We identified over 50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is effected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate Composite Insertions that can control gene expression.

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“…Transposable elements (TEs) have been shown to influence gene regulation via participation in genome folding and generation of regulatory elements, with expansions of TEs influencing evolution of gene expression across species (Sundaram and Wysocka, 2020) . Specific TEs have previously been shown to be enriched within LADs, and LADs are postulated to be a key element in multiple mechanisms that many species have evolved to silence and limit accessibility to highly repetitive DNA and other TEs (Hollister and Gaut, 2009;Meuleman et al, 2013) .…”

Section: T1-and T2-lads Have Distinct Genomic Featuresmentioning

confidence: 99%

An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype

Keough

Shah

Gjoni

et al. 2020

Preprint

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Three-dimensional genome organization, specifically organization of heterochromatin at the nuclear periphery, coordinates cell type-specific gene regulation. While defining various histone modifications and chromatin-associated proteins in multiple cell types has provided important insights into epigenetic regulation of gene expression and cellular identity, peripheral heterochromatin has not been mapped comprehensively and relatively few examples have emerged detailing the role of peripheral heterochromatin in cellular identity, cell fate choices, and/or organogenesis. In this study, we define nuclear peripheral heterochromatin organization signatures based on association with LAMIN B1 and/or dimethylation of lysine 9 on H3 (H3K9me2) across thirteen human cell types encompassing pluripotent stem cells, intermediate progenitors and differentiated cells from all three germ layers. Genomic analyses across this atlas reveal that lamin-associated chromatin is organized into at least two different compartments, defined by differences in genome coverage, chromatin accessibility, residence of transposable elements, replication timing domains, and gene complements. Our datasets reveal that only a small subset of lamin-associated chromatin domains are cell type invariant, underscoring the complexity of peripheral heterochromatin organization. Moreover, by integrating peripheral chromatin maps with transcriptional data, we find evidence of cooperative shifts between chromatin structure and gene expression associated with each cell type. This atlas of peripheral chromatin provides the largest resource to date for peripheral chromatin organization and a deeper appreciation for how this organization may impact the establishment and maintenance of cellular identity.

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Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

Cited by 163 publications

References 108 publications

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition

An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype

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