Dfam: a database of repetitive DNA based on profile hidden Markov models

Wheeler, Travis J.; Clements, Jody; Eddy, Sean R.; Hubley, Robert; Jones, Thomas A.; Jurka, Jerzy; Smit, Arian F. A.; Finn, Robert D.

doi:10.1093/nar/gks1265

Cited by 261 publications

(248 citation statements)

References 12 publications

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“…REP522, originally called a telomeric satellite, is a largely palindromic, unclassified interspersed repeat of $1.8 Kb in size (28). We observed that out of 72 promoters overlapping REP522, 25 were upregulated in cancer (odds ratio, 62.05).…”

Section: Bidirectional Transcription From Rep522 Satellite Repeat Is mentioning

confidence: 87%

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Kaczkowski¹,

Tanaka

Kawaji

et al. 2016

Cancer Research

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Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genomewide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression.Cancer Res; 76(2); 216-26. Ó2015 AACR.

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Section: Bidirectional Transcription From Rep522 Satellite Repeat Is mentioning

confidence: 87%

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Kaczkowski¹,

Tanaka

Kawaji

et al. 2016

Cancer Research

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“…To determine the signaling domains in the DosM sequence, we identified the limits of the MCPsignal (PF00015) Pfam (41) protein domain model with HMMER3 (42). To determine the heptad class of each domain, we used hidden Markov models provided previously (28,43).…”

Section: Methodsmentioning

confidence: 99%

Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM

Briegel

Ortega

Mann

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.chemotaxis | chemoreceptor arrays | Vibrio cholerae | electron cryotomography | microscopy M ost motile bacteria move toward favorable environments through a process called chemotaxis. The molecular basis of this behavior is best understood in Escherichia coli, where transmembrane methyl-accepting chemotaxis proteins (MCPs, or chemoreceptors) form large arrays at the cell pole. The chemoreceptors bind attractants or repellents in the periplasm (1-3) and relay signals to histidine kinases (CheA) in the cytoplasm (4). When activated, CheA first autophosphorylates and then transfers the phosphoryl group to the response regulators CheY and CheB. Phosphorylated CheY binds to the flagellar motor, changing the direction of flagellar rotation. This allows the cells to switch from swimming forward smoothly (so-called "runs") to tumbling randomly. Changes in the duration and frequency of run and tumble phases drive a biased random walk that moves the cells toward favorable environments (5). The other response regulator, CheB, is a methylesterase, which, in conjunction with the constitutively active methyltransferase CheR, tunes the sensitivity of the system by changing the methylation state of the chemoreceptors (6-8).Although there is only one chemotaxis system in E. coli, most chemotactic bacterial and archaeal species have multiple systems (9). For instance, Rhodobacter sphaeroides has three chemotaxis systems encoded in three distinct clusters of genes, one of which (CheOp2) encodes two receptors without predicted transmembrane domains, TlpT and TlpC (10). Analysis of fluorescently tagged TlpT and TlpC revealed that they localize in foci around midcell. The foci split before cell division and are segregated to the midcell position within the future daughter cells. The chromosome-associated ParA-like ATPase PpfA controls the localization and segregation of the foci through an interaction with the N terminus of TlpT in a ParB-like manner (11).Using electron cryotomography (ECT), we discovered that these cytoplasmic foci in R. sphaerodes are ordered arrays of chemore...

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“…To be specific, 2.8 % of DNA transposons, 8.3 % of LTR retrotransposons, and 33.7 % of non-LTR retrotransposons (16.9 % of LINE, 10.6 % of Alu, 0.2 % of SVA, 6 % of others) exist in human genome (Cordaux and Batzer 2009). Recently, computer program RepeatMasker has been updated, and it has provided classification of TEs in most of the living things (Carbone et al 2014;Jurka et al 2005;Smit et al 2010;Walker et al 2012;Wheeler et al 2012). Table 1 is supporting the information of TEs distribution in human and diverse primates.…”

Section: Transposable Element Distribution Of Human and Various Primatesmentioning

confidence: 99%

Composition and evolutionary importance of transposable elements in humans and primates

Lee

Kim

2014

Genes Genom

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Transposable elements (TEs) have skill of altering the position inside the genome and these TEs are widespread in both of plants and animals. They are separated into class I called retrotransposons, and class II called DNA transposons. According to the previous studies, not only TEs are related with disease, they are key factor of human and primate evolution. From this review, we discussed about the impact of transposable element, its role in the genome of human and primates and how TE distribution is differ from them. Additionally, we described how TEs contributed on primate evolution by its unique role. This review could be great use for further studies in relation to evolution mechanism and various diseases.

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Dfam: a database of repetitive DNA based on profile hidden Markov models

Cited by 261 publications

References 12 publications

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM

Composition and evolutionary importance of transposable elements in humans and primates

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