Transcriptional Regulation of Early Transposon Elements, an Active Family of Mouse Long Terminal Repeat Retrotransposons

Maksakova, Irina A.; Mager, Dixie L.

doi:10.1128/jvi.79.22.13865-13874.2005

Cited by 50 publications

(58 citation statements)

References 65 publications

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“…2B). This peak is due solely to a Dicer-independent short RNA that is antisense to the primer-binding site of the early transposon repeat, an endogenous retrovirus abundantly expressed in the early mouse embryo and ES cells (28). The proportions of repetitive sequences overlapping SINE and simple repeats were significantly lower in the Dicer Ϫ/Ϫ compared with the Dicer ϩ/ϩ library (Fig.…”

Section: Analysis Of Repeat-overlapping Novel Readsmentioning

confidence: 96%

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

Calabrese

Seila

Yeo

et al. 2007

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

301

269

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Short RNA expression was analyzed from Dicer -positive and Dicer -knockout mouse embroyonic stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the miRNA pathway in ES cells may be to shape their distinct cell cycle. Forty-six previously uncharacterized miRNAs were identified, most of which are expressed at low levels and are less conserved than the set of known miRNAs. Low-abundance short RNAs matching all classes of repetitive elements were present in cells lacking Dicer , although the production of some SINE- and simple repeat-associated short RNAs appeared to be Dicer-dependent. These and other Dicer-dependent sequences resembled miRNAs. At a depth of sequencing that approaches the total number of 5′ phosphorylated short RNAs per cell, miRNAs appeared to be Dicer's only substrate. The results presented suggest a model in which repeat-associated miRNAs serve as host defenses against repetitive elements, a function canonically ascribed to other classes of short RNA.

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Section: Analysis Of Repeat-overlapping Novel Readsmentioning

confidence: 96%

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

Calabrese

Seila

Yeo

et al. 2007

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

301

269

View full text Add to dashboard Cite

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“…Nuclear extraction, probe labeling and the gel shift assay were preformed as described (30). Protein concentration was determined using the Qubit Quantitation Platform (Invitrogen).…”

Section: Electrophoretic Mobility Shift Assay (Emsa)mentioning

confidence: 99%

Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1

Xiang

Argiropoulos

et al. 2010

Experimental Hematology

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Objective-MEIS1 is a Hox cofactor known for its role in development and strongly linked to normal and leukemic hematopoiesis. Although previous studies have focused on identifying protein partners of MEIS1 and its transcriptionaly regulated targets, little is known about the upstream transcriptional regulators of this tightly regulated gene. Understanding the regulation of MEIS1 is important toward the understanding of normal hematopoiesis and leukemogenesis.Materials and Methods-Here we describe our studies focusing on the evolutionary conserved putative MEIS1 promoter region. Phylogenetic sequence analysis followed and reporter assays in MEIS1 expressing (K562) and non-expressing (HL60) leukemic cell line models were used to identify key regulatory regions and potential transcription factor binding sites within the candidate promoter region followed by functional and expression studies of one identified regulator in both cell lines and primary human cord blood and leukemia samples. Results-The chromatin status of MEIS1 promoter region is associated with MEIS1 expression.Truncation and mutation studies coupled with reporter assays revealed that a conserved ETS family member binding site located 289bp upstream of the annotated human MEIS1 transcription start site (AHTSS) is required for promoter activity. Of the three ETS family members tested, only ELF1 was enriched on the MEIS1 promoter as assessed by both electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) experiments in K562. This finding was confirmed in MEIS1 expressing primary human samples. Moreover, siRNA -mediated knockdown of ELF1 in K562 cells was associated with a decreased MEIS1 expression.Conclusions-We conclude that the ETS transcription factor ELF1 is an important positive regulator of MEIS1 expression.

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“…Western Blot-Nuclear extraction was performed as described before (20). Protein concentration was determined using the NanoDrop ND-1000 (Thermo Scientific).…”

Section: Methodsmentioning

confidence: 99%

“…Nuclear extraction, probe labeling, and the gel shift assay were performed as described before (20). Seven g of protein was used per binding reaction (protein concentration was determined using the NanoDrop ND-1000 (Thermo Scientific)).…”

Section: Methodsmentioning

confidence: 99%