Results 1 - 10
of
12
A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell 125
, 2006
"... The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by ex ..."
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The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci. We identified a specific modification pattern, termed ‘‘bivalent domains,’ ’ consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation. Bivalent domains tend to coincide with TF genes expressed at low levels. We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation. We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells. These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency.
Widely variable endogenous retroviral methylation levels in
, 2007
"... human placenta ..."
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Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana
, 2004
"... Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-re ..."
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Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-related SINE S1 founder copy in Arabidopsis thaliana. The main population is composed of poly(A)-ending (pa) SINE RNAs,while two minor populations correspond tofulllength (fl) or poly(A) minus [small cytoplasmic (sc)] SINE RNAs. Part of the poly(A) minus RNAs is modified by 3 0-terminal addition of C or CA nucleotides. All three RNA populations accumulate in the cytoplasm. Using a mutagenesis approach, we show that the poly(A) region and the 3 0 end unique region, present at the founder locus, are both important for the maturation and the steady-state accumulation of the different S1 RNA populations. The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate.
Article Classifying Genomic Sequences by Sequence Feature Analysis
"... Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence fea-tures, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classif ie ..."
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Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence fea-tures, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classif ied the upstream, exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could clas-sify the functional regions of genome based on sequence feature and discriminant analysis.
Certified by............................................................................................................................................
, 2009
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unknown title
, 2012
"... doi:10.1093/nar/gks1458 Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator ..."
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doi:10.1093/nar/gks1458 Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator
unknown title
, 2007
"... Widely variable endogenous retroviral methylation levels in human placenta ..."
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Widely variable endogenous retroviral methylation levels in human placenta
unknown title
, 2007
"... Widely variable endogenous retroviral methylation levels in human placenta ..."
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Widely variable endogenous retroviral methylation levels in human placenta
i DNA METHYLATION AND PROMOTER SEQUENCE ANALYSIS OF COLON CANCER GENES
, 2008
"... Aberrant DNA methylation in the genome is associated with human cancers. Tumor cells can undergo an overall loss of DNA methylation in non-coding repetitive regions (including the Alu elements) and at the same time maintain hypermethylation in the CpG islands in promoter region of multiple genes. We ..."
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Aberrant DNA methylation in the genome is associated with human cancers. Tumor cells can undergo an overall loss of DNA methylation in non-coding repetitive regions (including the Alu elements) and at the same time maintain hypermethylation in the CpG islands in promoter region of multiple genes. We are interested in understanding the pattern of DNA methylation in the promoters of genes that may mediate the tumor genesis in colon cells. Recent literature survey suggested that about two dozens of genes, when mutated or undergone changes in DNA methylation, can directly promote the development of colon cancers. We downloaded the promoter sequences of these possible colon cancer causing genes from the Human Genome Browser for bioinformatics analysis and investigation of the sequence features on their Alu elements, transcription factor binding sites, and CpG islands. Our results suggest that sequence conservation of the flanking transcription factor binding sites plays an important role in protecting their flanking CpG islands from hypermethylation. In addition, colon cancer genes may harbor a lower density Alu element when compared to control random genes.
