ENCODE whole-genome data in the UCSC genome browser (2011 update)

Raney, Brian J.; Cline, Melissa; Rosenbloom, Kate R.; Dreszer, Timothy R.; Learned, Katrina; Barber, Galt P.; Meyer, Laurence R.; Sloan, Cricket A.; Malladi, Venkat S.; Roskin, Krishna M.; Suh, Bernard; Hinrichs, Angie S.; Clawson, Hiram; Zweig, Ann S.; Kirkup, Vanessa M.; Fujita, Pauline A.; Rhead, Brooke; Smith, Kayla; Pohl, Andy; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James

doi:10.1093/nar/gkq1017

Cited by 169 publications

(163 citation statements)

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“…To interrogate whether Arid3a plays a regulatory role in IFN-a signaling, we analyzed chromatin-immunoprecipitation sequencing (ChIP-seq) data from the human hematopoietic line K562. 41 Assessment of ARID3A binding to select IFN/Stat1-related loci revealed scant binding to IFN-a cytokine genes (data not shown), suggesting that decreased IFN-a transcription observed in the Arid3a KO embryo is indirect ( Figure 6A). However, ARID3A occupied the genomic loci of IFN-aR1, IRF1, and STAT1 at positions marked by euchromatic histone modifications (H3K4m3 and H3K4m1) (Figure 6C-E).…”

Section: Arid3a and Stat1 Co-occupy Promoters Of Ifn Effector Genesmentioning

confidence: 97%

Interferon-α signaling promotes embryonic HSC maturation

Kim

Canver

Rhee

et al. 2016

Blood

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In the developing mouse embryo, the first hematopoietic stem cells (HSCs) arise in the aorta-gonad-mesonephros (AGM) and mature as they transit through the fetal liver (FL). Compared with FL and adult HSCs, AGM HSCs have reduced repopulation potential in irradiated adult transplant recipients but mechanisms underlying this deficiency in AGM HSCs are poorly understood. By co-expression gene network analysis, we deduced that AGM HSCs show lower levels of interferon-a (IFN-a)/Jak-Stat1-associated gene expression than FL HSCs. Treatment of AGM HSCs with IFN-a enhanced long-term hematopoietic engraftment and donor chimerism. Conversely, IFN-a receptor-deficient AGMs (Ifnar1 2/2 ), had significantly reduced donor chimerism. We identify adenine-thymine-rich interactive domain-3a (Arid3a), a factor essential for FL and B lymphopoiesis, as a key transcriptional co-regulator of IFN-a/Stat1 signaling. Arid3a occupies the genomic loci of Stat1 as well as several IFN-a effector genes, acting to regulate their expression. Accordingly, Arid3a 2/2 AGM HSCs had significantly reduced transplant potential, which was rescued by IFN-a treatment. Our results implicate the inflammatory IFN-a/ Jak-Stat pathway in the developmental maturation of embryonic HSCs, whose manipulation may lead to increased potency of reprogrammed HSCs for transplantation. (Blood. 2016;128(2):204-216)

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Section: Arid3a and Stat1 Co-occupy Promoters Of Ifn Effector Genesmentioning

confidence: 97%

Interferon-α signaling promotes embryonic HSC maturation

Kim

Canver

Rhee

et al. 2016

Blood

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“…All sequences that overlap (even partially) a tRNA gene were considered. The chromosomal location of each tRNA gene was based on the data of the UCSC Genome Browser (Raney et al 2010).…”

Section: Encodementioning

confidence: 99%

Conservation of the relative tRNA composition in healthy and cancerous tissues

Mahlab

Tuller²,

Linial³

2012

RNA

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Elongation in protein translation is strongly dependent on the availability of mature transfer RNAs (tRNAs). The relative concentrations of the tRNA isoacceptors determine the translation efficiency in unicellular organisms. However, the degree of correspondence of codons and the relevant tRNA isoacceptors serves as an estimator for translation efficiency in all organisms. In this study, we focus on the translational capacity of the human proteome. We show that the correspondence between the codon usage and tRNAs can be improved by combining experimental measurements with the genomic copy number of isoacceptor groups. We show that there are technologies of tRNA measurements that are useful for our analysis. However, fragments of tRNAs do not agree with translational capacity. It was shown that there is a significant increase in the absolute levels of tRNA genes in cancerous cells in comparison to healthy cells. However, we find that the relative composition of tRNA isoacceptors in healthy, cancerous, or transformed cells remains almost identical. This result may indicate that maintaining the relative tRNA composition in cancerous cells is advantageous via its stabilizing of the effectiveness of translation.

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“…ChIP in combination with tiled microarray analysis (ChIP-ChIP) or high-throughput sequencing (ChIP-seq) has been extensively used to study the genomic distributions of hundreds of proteins [33]. While many important insights have been gained through ChIP-chip and ChIP-seq, there are limitations.…”

Section: Technologies For Base-pair Resolution Epigenomic Mappingmentioning

confidence: 99%