Identification of specific sequence motifs in the upstream region of 242 human miRNA genes.

@article{citeulike:1297776, abstract = {We have identified novel over-represented and conserved motifs in the upstream regions of human and mouse miRNA stem-loop sequences by means of a new bioinformatic processing regimen. We observed sequence conservation -500bp upstream in 189 human and mouse miRNAs declining with increasing distance from their putative miRNA stem-loop origin. We also found relatively GC-rich regions having more than 50\% of guanine+cytosine (G+C) content at about -30 and -170bp relative to human miRNA stem-loop sequence origin. To further identify specific sequence motifs that might be involved in the transcriptional regulation of miRNA precursors, we first searched 500bp upstream sequences of 194 non-redundant human miRNA stem-loop sequences for frequently occurring motifs 5-15bp long. We then found the comparable occurrences of the 20 most frequent motifs in the 2000bp upstream regions of 242 human and 290 mouse miRNAs. The significantly reduced frequency of occurrence of all 20 motifs in the regions 2000bp upstream of 23,570 human RefSeq genes demonstrated that these motifs were specific to the upstream miRNA sequences. The most frequently observed motif M1 (GTGCTTMTAGTGCAG), with a MEME E-value of 3.8e-57 was distributed within 500bp upstream of stem-loop sequences and was also miRNA-specific. We suggest that these over-represented motif sites are good candidates for experimentally testing miRNA expression as well as possible interaction with regulatory factors.}, address = {Graduate School of Engineering, The University of Tokushima, 2-1 Minamijosanjima, Tokushima City, Tokushima 770-8506, Japan.}, author = {Inouchi, Atsushi and Shinohara, Shuichi and Inoue, Hiroshi and Kita, Kenji and Itakura, Mitsuo }, citeulike-article-id = {1297776}, doi = {http://dx.doi.org/10.1016/j.compbiolchem.2007.03.011}, issn = {1476-9271}, journal = {Comput Biol Chem}, keywords = {human, mirna, promoter}, month = {March}, posted-at = {2007-05-22 09:39:33}, priority = {5}, title = {Identification of specific sequence motifs in the upstream region of 242 human miRNA genes.}, url = {http://dx.doi.org/10.1016/j.compbiolchem.2007.03.011}, year = {2007} }

TY - JOUR ID - citeulike:1297776 L3 - citeulike-article-id:1297776 TI - Identification of specific sequence motifs in the upstream region of 242 human miRNA genes. JF - Comput Biol Chem AD - Graduate School of Engineering, The University of Tokushima, 2-1 Minamijosanjima, Tokushima City, Tokushima 770-8506, Japan. SN - 1476-9271 N2 - We have identified novel over-represented and conserved motifs in the upstream regions of human and mouse miRNA stem-loop sequences by means of a new bioinformatic processing regimen. We observed sequence conservation -500bp upstream in 189 human and mouse miRNAs declining with increasing distance from their putative miRNA stem-loop origin. We also found relatively GC-rich regions having more than 50% of guanine+cytosine (G+C) content at about -30 and -170bp relative to human miRNA stem-loop sequence origin. To further identify specific sequence motifs that might be involved in the transcriptional regulation of miRNA precursors, we first searched 500bp upstream sequences of 194 non-redundant human miRNA stem-loop sequences for frequently occurring motifs 5-15bp long. We then found the comparable occurrences of the 20 most frequent motifs in the 2000bp upstream regions of 242 human and 290 mouse miRNAs. The significantly reduced frequency of occurrence of all 20 motifs in the regions 2000bp upstream of 23,570 human RefSeq genes demonstrated that these motifs were specific to the upstream miRNA sequences. The most frequently observed motif M1 (GTGCTTMTAGTGCAG), with a MEME E-value of 3.8e-57 was distributed within 500bp upstream of stem-loop sequences and was also miRNA-specific. We suggest that these over-represented motif sites are good candidates for experimentally testing miRNA expression as well as possible interaction with regulatory factors. KW - human KW - mirna KW - promoter AU - Inouchi, Atsushi AU - Shinohara, Shuichi AU - Inoue, Hiroshi AU - Kita, Kenji AU - Itakura, Mitsuo PY - 2007/03/31/ UR - http://dx.doi.org/10.1016/j.compbiolchem.2007.03.011 ER -