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User name	Sebastian Eilebrecht
Email	eilebrecht@ihes.fr
Phone / Fax number	+491755662397 /
Location	IHES (Systems Epigenomics Group) - 35, route de Chartres - 91440 Bures sur Yvette, France

Scientific description

The small nuclear 7SK RNA negatively controls transcription by inactivating positive transcription elongation factor b (P-TEFb) and is an integral component of TAT-dependent and independent HIV-1 transcription initiation complexes. 7SK RNA has recently been shown to also directly control HMGA1 transcription activity. HMGA1 is a master regulator of gene expression and its deregulation is associated with virtually any type of human cancer. The degree of HMGA1 overexpression thereby correlates with tumor malignancy and metastatic potential. 7SK snRNA directly interacts through its loop 2 (7SK L2) with the first A/T DNA binding hook of HMGA1. We have developed several 7SK L2 RNA chimera with the Epstein Barr Virus expressed RNA 2 (EBER2) to target HMGA1 function in transcription regulation. The efficiency of interfering with HMGA1 transcription activity by the chimeric 7SK L2 â€” EBER2 fusions by large exceeds the efficiency of 7SK wild-type RNA due to the stronger EBER2 promoter activity. Furthermore, the 7SK L2 â€” EBER2 chimera do not interfere with P-TEFb controlled transcription elongation or the formation of 7SK sn/hnRNPs.  The comparison of the effects of wild-type 7SK RNA on cellular transcriptome dynamics with those induced by the two 7SK L2 mutants as well as the changes in gene expression following inhibition of HMGA1 allow the identification and characterization of HMGA1-dependent and independent effects of 7SK snRNA. We furthermore also present evidence for P-TEFb and HMGA1-independent 7SK RNA L2 regulatory activity.

Technical description

For microarray analyses, RNA amplification, labeling, hybridization and detection were performed following the protocols supplied by Applied Biosystems using the corresponding kits (Applied Biosystems, ProdNo: 4339628 and 4336875). The data obtained were analyzed as described previously (10, 41,46-49).
The statistical analysis of the transcriptome data has been described previously (10, 41). Gene ontology enrichment analyses were also described previously (41, 49). The signalosome network inference will be described in detail elsewhere (BÃ©cavin et al. in preparation), and the network representation tool used was Cytoscape (51).

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References

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/21282977

RNA Biol. 2011 Jan 1;8(1). [Epub ahead of print]
HMGA1-dependent and independent 7SK RNA gene regulatory activity.

Eilebrecht S, BÃ©cavin C, LÃ©ger H, Benecke BJ, Benecke A.

Institut des Hautes Ã‰tudes Scientifiques & CNRS USR3078; Bures sur Yvette, France.