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GenomicsA system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters
Our system recapitulates expected characteristics of the well characterized H3.3 histone variant, and show that we gain additional information by using a kinetic approach. Additionaly, our results on the less-studied MacroH2A2 variant revealed differential dynamic profiles of this M-bM-^@M-^\repress...
ORGANISM(S): Mus musculus 
2014-08-08 | E-GEOD-57665 | biostudies-arrayexpress
GenomicsA key role for Mbd3 in 5-hydroxymethylcytosine-dependent gene regulation in embryonic stem cells
Numerous chromatin regulators are required for embryonic stem (ES) cell self-renewal and pluripotency, but few have been studied in detail. Here, we examine the roles of several chromatin regulators whose loss affects the pluripotent state of ES cells. We find that Mbd3 and Brg1 antagonistically reg...
ORGANISM(S): Mus musculus 
2011-12-01 | E-GEOD-31690 | biostudies-arrayexpress
GenomicsHigh-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm
Mammalian embryonic stem (ES) cells and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-bind...
ORGANISM(S): Mus musculus 
2014-07-08 | E-GEOD-58101 | biostudies-arrayexpress
TranscriptomicsAAV vector-mediated in vivo miRNA antagonism for studying miRNA function and treating dyslipidemia
Understanding the function of individual miRNA species in mice would require the production of hundreds of loss-of-function strains. To accelerate analysis of miRNA biology in mammals, we combined recombinant adeno-associated virus (rAAV) vectors with miRNA ‘Tough Decoys’ (TuDs) to inhibit specific ...
ORGANISM(S): Mus musculus 
2011-12-10 | E-GEOD-25971 | biostudies-arrayexpress
GenomicsHdac6 regulates Tip60-p400 function in stem cells (sequencing)
The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The m...
ORGANISM(S): Mus musculus 
2013-11-20 | E-GEOD-42209 | biostudies-arrayexpress
TranscriptomicsDicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals
Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs...
ORGANISM(S): Mus musculus 
2012-12-07 | E-GEOD-37443 | biostudies-arrayexpress
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