DOG 1.0: illustrator of protein domain structures

Ren, Jian; Wen, Longping; Gao, Xiaolan; Jin, Changjie; Xue, Yu; Yao, Xuebiao

doi:10.1038/cr.2009.6

Cited by 548 publications

(373 citation statements)

References 10 publications

Supporting

Mentioning

357

Contrasting

Order By: Relevance

“…The mechanism underlying this result is intricate. The structure of the UHRF2 protein has been identified by X-ray crystallographic and nuclear magnetic resonance (NMR) analyses (Ren et al, 2009). As previously noted, UHRF2 contains five functional domains.…”

Section: Discussionmentioning

confidence: 96%

UHRF2 mRNA Expression is Low in Malignant Glioma but Silencing Inhibits the Growth of U251 Glioma Cells in vitro

Zhang²,

Su³

et al. 2012

Asian Pacific Journal of Cancer Prevention

View full text Add to dashboard Cite

UHRF2 is a member of the ubiquitin plant homeo domain RING finger family, which has been proven to be frequently up-regulated in colorectal cancer cells and play a role as an oncogene in breast cancer cells. However, the role of UHRF2 in glioma cells remains unclear. In this study, we performed real-time quantitative PCR on 32 pathologically confirmed glioma samples (grade I, 4 cases; grade II, 11 cases; grade III, 10 cases; and grade IV, 7 cases; according to the 2007 WHO classification system) and four glioma cell lines (A172, U251, U373, and U87). The expression of UHRF2 mRNA was significantly lower in the grade III and grade IV groups compared with the noncancerous brain tissue group, whereas its expression was high in A172, U251, and U373 glioma cell lines. An in vitro assay was performed to investigate the functions of UHRF2. Using a lentivirus-based RNA interference (RNAi) approach, we down-regulated UHRF2 expression in the U251 glioma cell line. This downregulation led to the inhibition of cell proliferation, an increase in cell apoptosis, and a change of cell cycle distribution, in which S stage cells decreased and G2/M stage cells increased. Our results suggest that UHRF2 may be closely related to tumorigenesis and the development of gliomas.

show abstract

Section: Discussionmentioning

confidence: 96%

UHRF2 mRNA Expression is Low in Malignant Glioma but Silencing Inhibits the Growth of U251 Glioma Cells in vitro

Zhang²,

Su³

et al. 2012

Asian Pacific Journal of Cancer Prevention

View full text Add to dashboard Cite

show abstract

“…All the figures were created with PyMOL, and the charge distribution on the E71GSF surface was calculated by APBS (39). The domain architecture was prepared by DOG (40).…”

Section: Methodsmentioning

confidence: 99%

Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation

Qin

Hao

Tian

et al. 2014

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background:The molecular basis for catalysis by human glycyl-tRNA synthetase (hGlyRS) is unclear. Results: hGlyRS-tRNA complex structures are reported, and the molecular details for enzymatic recognition are elucidated. Conclusion: hGlyRS catalysis involves multiple conformational changes, and insertions 1 and 3 may facilitate tRNA binding. Significance: Understanding the catalytic pathway also provides insights into the role of hGlyRS in disease.

show abstract

“…BP-like genes were Bra000638 in B. rapa, Thhalv10028724m.g in T. halophila, Carubv10002748m.g in C. rubella, and 489727 in A. lyrata. The protein domains of FRF and FRS factors were analyzed with InterPro (http://www.ebi.ac.uk/interpro/; Hunter et al, 2012) and drawn using Domain Graph, version 2.0.1 (http://dog.biocuckoo.org/index.php; Ren et al, 2009).…”

Section: Phylogenetic Analysis and Protein Sequence Analysismentioning

confidence: 99%

Transcriptional, Posttranscriptional, and Posttranslational Regulation of SHOOT MERISTEMLESS Gene Expression in Arabidopsis Determines Gene Function in the Shoot Apex

et al. 2014

View full text Add to dashboard Cite

The activity of SHOOT MERISTEMLESS (STM) is required for the functioning of the shoot apical meristem (SAM). STM is expressed in the SAM but is down-regulated at the site of leaf initiation. STM is also required for the formation of compound leaves. However, how the activity of STM is regulated at the transcriptional, posttranscriptional, and posttranslational levels is poorly understood. We previously found two conserved noncoding sequences in the promoters of STM-like genes across angiosperms, the K-box and the RB-box. Here, we characterize the function of the RB-box in Arabidopsis (Arabidopsis thaliana). The RB-box, along with the K-box, regulates the expression of STM in leaf sinuses, which are areas on the leaf blade with meristematic potential. The RB-box also contributes to restrict STM expression to the SAM. We identified FAR1-RELATED SEQUENCES-RELATED FACTOR1 (FRF1) as a binding factor to the RB-box region. FRF1 is an uncharacterized member of a subfamily of four truncated proteins related to the FAR1-RELATED SEQUENCES factors. Internal deletion analysis of the STM promoter identified a region required to repress the expression of STM in hypocotyls. Expression of STM in leaf primordia under the control of the JAGGED promoter produced plants with partially undifferentiated leaves. We further found that the ELK domain has a role in the posttranslational regulation of STM by affecting the nuclear localization of STM.

show abstract

DOG 1.0: illustrator of protein domain structures

Cited by 548 publications

References 10 publications

UHRF2 mRNA Expression is Low in Malignant Glioma but Silencing Inhibits the Growth of U251 Glioma Cells in vitro

UHRF2 mRNA Expression is Low in Malignant Glioma but Silencing Inhibits the Growth of U251 Glioma Cells in vitro

Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation

Transcriptional, Posttranscriptional, and Posttranslational Regulation of SHOOT MERISTEMLESS Gene Expression in Arabidopsis Determines Gene Function in the Shoot Apex

Contact Info

Product

Resources

About