siRNA Selection Server: an automated siRNA oligonucleotide prediction server

Yuan, Bingbing; Latek, Robert; Hoßbach, Markus; Tuschl, Thomas; Lewitter, Fran

doi:10.1093/nar/gkh366

Cited by 286 publications

(188 citation statements)

References 14 publications

(8 reference statements)

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“…For this purpose, the cell monolayers were fixed for 10 min with 4% buffered formaldehyde followed by 20 min methanol (À201C) for cell permeabilization. Primary antibodies used in this study are polyclonal anti-insulin (C. Van Schravendijk, VUB, Brussels), 36,37 polyclonal anti-rat C-peptide-I (O.D. Madsen, Hagedorn Research Institute, Gentofte, Denmark), 38 polyclonal anti-Pdx1 (O.D.…”

Section: Immunocytochemistrymentioning

confidence: 99%

See 1 more Smart Citation

Ngn3 expression during postnatal in vitro beta cell neogenesis induced by the JAK/STAT pathway

Baeyens¹,

Bonné²,

German³

et al. 2006

Cell Death Differ

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The basic helix-loop-helix protein Neurogenin3 specifies precursor cells of the endocrine pancreas during embryonic development, and is thought to be absent postnatally. We have studied Ngn3 expression during in vitro generation of beta-cells from adult rat exocrine pancreas tissue treated with epidermal growth factor and leukaemia inhibitory factor. This treatment induced a transient expression of both Ngn3 and its upstream activator hepatocyte nuclear factor 6. Inhibition of EGF and LIF signalling by pharmacological antagonists of the JAK2/STAT3 pathway, or knockdown of Ngn3 by RNA interference prevented the generation of new insulin-positive cells. This study demonstrates that in vitro growth factor stimulation can induce recapitulation of an embryonic endocrine differentiation pathway in adult dedifferentiated exocrine cells. This could prove to be important for understanding the mechanism of beta-cell regeneration and for therapeutic ex vivo neogenesis of beta cells. Keywords: neurogenin3; transdifferentiation; beta cell; pancreas; diabetes Abbreviations: CK20, cytokeratin 20; EGF, epidermal growth factor; eGFP, enhanced green fluorescent protein; Hnf6, hepatocyte nuclear factor 6; JAK2, Janus kinase 2; LIF, leukaemia inhibitory factor; Ngn3, neurogenin 3; Pdx1, pancreatic and duodenal homeobox 1; STAT3, signal transducer and activator of transcription 3 IntroductionThere is currently a lot of interest in the development of a treatment for diabetes that is based on beta-cell replacement or regeneration. Beta-cells could be (re-)generated by stimulation of beta-cell replication and/or (trans-)differentiation of stem/progenitor cells. It has been demonstrated that, during adult life, beta-cell maintenance and compensatory growth in mice results primarily from proliferation of the pre-existing beta cells. 1 However, numerous reports of alternative sources of beta-cell 'neogenesis' in response to severe tissue injury have been described. [2][3][4][5][6] The pancreas is composed of exocrine tissue, comprising acinar and duct cells, and of endocrine tissue that contains beta-, alpha-, delta-and pancreatic polypeptide cells. A possible source of progenitor cells is the acinar cell population that is the most abundant in adult pancreas and is known to retain a remarkable plasticity both in vivo and in vitro. 7-9 Isolated acinar cells can undergo dedifferentiation in vitro whereby they lose their zymogen granules and gain a duct-like phenotype including expression of the duct cell marker cytokeratin20. 8,10 External stimuli can induce a phenotypical switch in these cells towards a hepatocyte-like phenotype. 7 We have recently developed a model for in vitro beta-cell neogenesis based upon growth factor stimulation of dedifferentiated acinar pancreatic cells. 11 The molecular regulation of this transdifferentiation from acinar to beta cells is unknown at present. Although it is known that during pancreatic regeneration the exocrine population can dedifferentiate towards an embryonic-like state in vivo, 12 in v...

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Section: Immunocytochemistrymentioning

confidence: 99%

“…37 Corresponding oligo DNA molecules (Eurogentec) were cloned in the BglII and HindIII sites of the pSuper.basic vector (Oligoengine). Insert-containing clones were PCR-selected and sequenced.…”

Section: Immunocytochemistrymentioning

confidence: 99%

Ngn3 expression during postnatal in vitro beta cell neogenesis induced by the JAK/STAT pathway

Baeyens¹,

Bonné²,

German³

et al. 2006

Cell Death Differ

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“…We used siRNA selection program to predict candidate siRNA on the LIR ( Figure 5). 33 There are perhaps more candidates if the inverted exons were taken Inverted GSTM exons in the intron of GSTM5 gene Y Wang and FCC Leung into consideration. The hypothetical siRNA obtained from the intronic LIR will find the target on mature mRNAs of GSTM1, GSTM4 and GSTM5 genes, and finally result in the digestion of mRNAs.…”

Section: Discussionmentioning

confidence: 99%

Acquisition of inverted GSTM exons by an intron of primate GSTM5 gene

Wang

Leung

2009

J Hum Genet

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The human GSTM gene family is composed of five gene members, GSTM1-5, and plays an important role in detoxification. In this study, the human GSTM5 gene was found to have a long inverted repeat (LIR) in intron 5. The LIR is able to form a stem-loop structure with a 31-bp stem and a 9-nt loop. The intronic LIR was also identified in other primates but not in non-primates. The human and chimpanzee LIRs had undergone compensating mutations that make the stem loop more stable, suggesting a functional role for the LIR. Sequence homology showed that the LIR was actually a part of inverted exons acquired by the intron. Results of phylogenetic analysis indicate that the inverted exons were derived from exon 5 of GSTM4 and exon 5 of GSTM1. The intronic LIR and inverted GSTM exons can probably introduce complexity in the expression of GSTM gene family.

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“…The sequences for human KDR/VEGFR-2 siRNA (http:// ncbi.nlm.nih.gov/nuccore; accession number NM_002253) were designed as previously reported 12 …”

Section: Rna Interferencementioning

confidence: 99%