LIVIVO - Search results -

Search results

Result 1 - 10 of total 14

Search options

Article ; Online: Osteonectin downregulates E-cadherin, induces osteopontin and focal adhesion kinase activity stimulating an invasive melanoma phenotype.

Smit, Darren J / Gardiner, Brooke B / Sturm, Richard A

2007 Volume 121, Issue 12, Page(s) 2653–2660

Abstract: Osteonectin is recognised as a marker of metastasis progression in melanoma and has been implicated in the transition from radial to vertical growth phase. A Tetracycline-inducible system was used to regulate Osteonectin protein levels in melanoma cell ... ...

Abstract	Osteonectin is recognised as a marker of metastasis progression in melanoma and has been implicated in the transition from radial to vertical growth phase. A Tetracycline-inducible system was used to regulate Osteonectin protein levels in melanoma cell lines to examine the morphological, biochemical and invasive changes that accompany its altered expression. Assay of protein and phosphorylation changes showed a downregulation of E-cadherin, upregulation of Osteopontin and a corresponding increase in phosphorylation of Focal Adhesion Kinase on Tyr(397) and Tyr(576) concomitant with Osteonectin induction. Melanoma cells overexpressing Osteonectin displayed increased invasive potential, whereas ablation of Osteonectin gene transcription using siRNA suppressed the invasive potential of these cells and resulted in the upregulation of E-cadherin. The recently described interaction of Osteonectin with Integrin Linked Kinase leading to modulation of its activity suggests a mechanism relevant to the loss of E-cadherin and cell adhesion that occurs during melanoma progression. These results indicate a central role for Osteonectin in the regulation of gene expression changes driving the progression of melanoma toward metastasis.
MeSH term(s)	Cadherins/metabolism ; Cell Line, Tumor ; Cells, Cultured ; Down-Regulation ; Enzyme Induction ; Focal Adhesion Protein-Tyrosine Kinases/biosynthesis ; Focal Adhesion Protein-Tyrosine Kinases/metabolism ; Humans ; Melanocytes/metabolism ; Melanoma/metabolism ; Melanoma/pathology ; Neoplasm Invasiveness ; Osteonectin/genetics ; Osteonectin/metabolism ; Osteopontin/metabolism ; Phenotype ; RNA, Small Interfering/metabolism ; Transcription, Genetic ; Up-Regulation
Chemical Substances	Cadherins ; Osteonectin ; RNA, Small Interfering ; Osteopontin (106441-73-0) ; Focal Adhesion Protein-Tyrosine Kinases (EC 2.7.10.2)
Language	English
Publishing date	2007-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.23039
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 478: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 576: Show issues

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾

Article ; Online: Compound heterozygous mutations in RIPPLY2 associated with vertebral segmentation defects.

McInerney-Leo, Aideen M / Sparrow, Duncan B / Harris, Jessica E / Gardiner, Brooke B / Marshall, Mhairi S / O'Reilly, Victoria C / Shi, Hongjun / Brown, Matthew A / Leo, Paul J / Zankl, Andreas / Dunwoodie, Sally L / Duncan, Emma L

Human molecular genetics

2015 Volume 24, Issue 5, Page(s) 1234–1242

Abstract: Segmentation defects of the vertebrae (SDV) are caused by aberrant somite formation during embryogenesis and result in irregular formation of the vertebrae and ribs. The Notch signal transduction pathway plays a critical role in somite formation and ... ...

Abstract	Segmentation defects of the vertebrae (SDV) are caused by aberrant somite formation during embryogenesis and result in irregular formation of the vertebrae and ribs. The Notch signal transduction pathway plays a critical role in somite formation and patterning in model vertebrates. In humans, mutations in several genes involved in the Notch pathway are associated with SDV, with both autosomal recessive (MESP2, DLL3, LFNG, HES7) and autosomal dominant (TBX6) inheritance. However, many individuals with SDV do not carry mutations in these genes. Using whole-exome capture and massive parallel sequencing, we identified compound heterozygous mutations in RIPPLY2 in two brothers with multiple regional SDV, with appropriate familial segregation. One novel mutation (c.A238T:p.Arg80*) introduces a premature stop codon. In transiently transfected C2C12 mouse myoblasts, the RIPPLY2 mutant protein demonstrated impaired transcriptional repression activity compared with wild-type RIPPLY2 despite similar levels of expression. The other mutation (c.240-4T>G), with minor allele frequency <0.002, lies in the highly conserved splice site consensus sequence 5' to the terminal exon. Ripply2 has a well-established role in somitogenesis and vertebral column formation, interacting at both gene and protein levels with SDV-associated Mesp2 and Tbx6. We conclude that compound heterozygous mutations in RIPPLY2 are associated with SDV, a new gene for this condition.
MeSH term(s)	Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Bone Diseases, Developmental/genetics ; Cells, Cultured ; Codon, Nonsense ; DNA Mutational Analysis ; Disease Models, Animal ; Exome ; Exons ; Female ; Gene Frequency ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mutant Proteins/genetics ; Mutation ; Pedigree ; Quantitative Trait, Heritable ; RNA Splicing ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Somites/metabolism ; Spine/pathology ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Codon, Nonsense ; Mesp2 protein, mouse ; Mutant Proteins ; Repressor Proteins ; Ripply2 protein, mouse ; Tbx6 protein, mouse ; Transcription Factors
Language	English
Publishing date	2015-03-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddu534
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3469: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-free BMP4 culture

Burke Les J / Gardiner Brooke B / Bruce Stephen J / Gongora M Milena / Grimmond Sean M / Perkins Andrew C

BMC Genomics, Vol 8, Iss 1, p

2007 Volume 365

Abstract: Abstract Background Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or ... ...

Abstract	Abstract Background Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this process is intrinsic to ES cells once the stem cell program has been inactivated. The aims of this study were to determine the transcriptional programs associated with the stem cell state and to characterize mesoderm differentiation between serum and serum-free culture. Results ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found. Conclusion Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.
Keywords	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
Subject code	571
Language	English
Publishing date	2007-10-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture.

Bruce, Stephen J / Gardiner, Brooke B / Burke, Les J / Gongora, M Milena / Grimmond, Sean M / Perkins, Andrew C

BMC genomics

2007 Volume 8, Page(s) 365

Abstract: Background: Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this ...

Abstract	Background: Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this process is intrinsic to ES cells once the stem cell program has been inactivated. The aims of this study were to determine the transcriptional programs associated with the stem cell state and to characterize mesoderm differentiation between serum and serum-free culture. Results: ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found. Conclusion: Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.
MeSH term(s)	Amino Acid Sequence ; Animals ; Base Sequence ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Proteins/pharmacology ; Cell Culture Techniques/methods ; Cell Differentiation/drug effects ; Cell Differentiation/genetics ; Cluster Analysis ; Culture Media, Serum-Free/pharmacology ; Embryonic Stem Cells/drug effects ; Embryonic Stem Cells/metabolism ; Embryonic Stem Cells/physiology ; Erythropoiesis/drug effects ; Erythropoiesis/genetics ; Gene Expression Profiling ; Mesoderm/metabolism ; Mesoderm/physiology ; Mice ; Molecular Sequence Data ; Myocytes, Cardiac/metabolism ; Myocytes, Cardiac/physiology ; Oligonucleotide Array Sequence Analysis ; Time Factors ; Transcription, Genetic
Chemical Substances	Bmp4 protein, mouse ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Proteins ; Culture Media, Serum-Free
Language	English
Publishing date	2007-10-10
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-8-365
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells.

Tallack, Michael R / Whitington, Tom / Yuen, Wai Shan / Wainwright, Elanor N / Keys, Janelle R / Gardiner, Brooke B / Nourbakhsh, Ehsan / Cloonan, Nicole / Grimmond, Sean M / Bailey, Timothy L / Perkins, Andrew C

Genome research

2010 Volume 20, Issue 8, Page(s) 1052–1063

Abstract: KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors. To determine the local cis-regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse. ... ...

Abstract	KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors. To determine the local cis-regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse. We found at least 945 sites in the genome of E14.5 fetal liver erythroid cells which are occupied by endogenous KLF1. Many of these recovered sites reside in erythroid gene promoters such as Hbb-b1, but the majority are distant to any known gene. Our data suggests KLF1 directly regulates most aspects of terminal erythroid differentiation including production of alpha- and beta-globin protein chains, heme biosynthesis, coordination of proliferation and anti-apoptotic pathways, and construction of the red cell membrane and cytoskeleton by functioning primarily as a transcriptional activator. Additionally, we suggest new mechanisms for KLF1 cooperation with other transcription factors, in particular the erythroid transcription factor GATA1, to maintain homeostasis in the erythroid compartment.
MeSH term(s)	Animals ; Apoptosis/genetics ; Base Sequence ; Cytoskeleton/genetics ; Erythrocyte Membrane/genetics ; Erythroid Cells/metabolism ; Erythropoiesis/genetics ; GATA1 Transcription Factor/genetics ; GATA1 Transcription Factor/metabolism ; Gene Expression ; Globins/biosynthesis ; Globins/genetics ; Heme/biosynthesis ; Heme/genetics ; Kruppel-Like Transcription Factors/genetics ; Mice ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Promoter Regions, Genetic
Chemical Substances	GATA1 Transcription Factor ; Gata1 protein, mouse ; Kruppel-Like Transcription Factors ; erythroid Kruppel-like factor ; Heme (42VZT0U6YR) ; Globins (9004-22-2)
Language	English
Publishing date	2010-05-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.106575.110
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.

Mercer, Tim R / Dinger, Marcel E / Bracken, Cameron P / Kolle, Gabriel / Szubert, Jan M / Korbie, Darren J / Askarian-Amiri, Marjan E / Gardiner, Brooke B / Goodall, Gregory J / Grimmond, Sean M / Mattick, John S

Genome research

2010 Volume 20, Issue 12, Page(s) 1639–1650

Abstract: The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo ...

Abstract	The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.
MeSH term(s)	Epigenesis, Genetic/genetics ; Eukaryota/genetics ; Gene Expression Profiling ; Genetic Variation ; Peptide Hydrolases/metabolism ; RNA Processing, Post-Transcriptional/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Sequence Analysis, RNA
Chemical Substances	RNA, Messenger ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2010-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.112128.110
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling.

Thiagarajan, Rathi D / Cloonan, Nicole / Gardiner, Brooke B / Mercer, Tim R / Kolle, Gabriel / Nourbakhsh, Ehsan / Wani, Shivangi / Tang, Dave / Krishnan, Keerthana / Georgas, Kylie M / Rumballe, Bree A / Chiu, Han S / Steen, Jason A / Mattick, John S / Little, Melissa H / Grimmond, Sean M

BMC genomics

2011 Volume 12, Page(s) 441

Abstract: Background: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These ... ...

Abstract	Background: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results: To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion: The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.
MeSH term(s)	Alternative Splicing ; Animals ; Exons ; High-Throughput Nucleotide Sequencing/methods ; Kidney/embryology ; Kidney/metabolism ; Mice ; MicroRNAs/genetics ; Organogenesis ; RNA, Antisense/genetics ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; Transcription, Genetic ; Transcriptome
Chemical Substances	MicroRNAs ; RNA, Antisense ; RNA, Messenger
Language	English
Publishing date	2011-09-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-12-441
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Rumballe Bree A / Georgas Kylie M / Krishnan Keerthana / Tang Dave / Wani Shivangi / Nourbakhsh Ehsan / Kolle Gabriel / Mercer Tim R / Gardiner Brooke B / Cloonan Nicole / Thiagarajan Rathi D / Chiu Han S / Steen Jason A / Mattick John S / Little Melissa H / Grimmond Sean M

BMC Genomics, Vol 12, Iss 1, p

2011 Volume 441

Abstract: Abstract Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. ... ...

Abstract	Abstract Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.
Keywords	RNA-Seq ; kidney development ; microarray ; Six2 ; Wt1 ; sense-antisense transcripts ; alternative splicing ; mesenchymal-epithelial transition ; miR-214 ; microRNA ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
Subject code	616
Language	English
Publishing date	2011-09-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Osteonectin/SPARC induction by ectopic beta(3) integrin in human radial growth phase primary melanoma cells.

Sturm, Richard A / Satyamoorthy, Kapaeth / Meier, Freidegund / Gardiner, Brooke B / Smit, Darren J / Vaidya, Bhavesh / Herlyn, Meenhard

Cancer research

2002 Volume 62, Issue 1, Page(s) 226–232

Abstract: Expression of the beta(3) integrin subunit in melanoma in situ has been found to correlate with tumor thickness, the ability to invade and metastasize, and poor prognosis. Transition from the radial growth phase (RGP) to the vertical growth phase (VGP) ... ...

Abstract	Expression of the beta(3) integrin subunit in melanoma in situ has been found to correlate with tumor thickness, the ability to invade and metastasize, and poor prognosis. Transition from the radial growth phase (RGP) to the vertical growth phase (VGP) is a critical step in melanoma progression and survival and is distinguished by the expression of beta(3) integrin. The molecular pathways that operate in melanoma cells associated with invasion and metastasis were examined by ectopic induction of the beta(3) integrin subunit in RGP SBcl2 and WM1552C melanoma cells, which converts these cells to a VGP phenotype. We used cDNA representational difference analysis subtractive hybridization between beta(3)-positive and -negative melanoma cells to assess gene expression profile changes accompanying RGP to VGP transition. Fourteen fragments from known genes including osteonectin (also known as SPARC and BM-40) were identified after three rounds of representational difference analysis. Induction of osteonectin was confirmed by Northern and Western blot analysis and immunohistochemistry and correlated in organotypic cultures with the beta(3)-induced progression from RGP to VGP melanoma. Expression of osteonectin was also associated with reduced adhesion to vitronectin, but not to fibronectin. Osteonectin expression was not blocked when melanoma cells were cultured with anti-alpha(v)beta(3) LM609 mAb, mitogen-activated protein kinase, or protein kinase C inhibitors, indicating that other signaling pathway(s) operate through alpha(v)beta(3) integrin during conversion from RGP to VGP.
MeSH term(s)	Antigens, CD/biosynthesis ; Antigens, CD/physiology ; Cell Adhesion/physiology ; Disease Progression ; Gene Expression Regulation, Neoplastic ; Humans ; Integrin beta3 ; Melanoma/genetics ; Melanoma/metabolism ; Melanoma/pathology ; Neoplasm Invasiveness ; Osteonectin/biosynthesis ; Osteonectin/genetics ; Platelet Membrane Glycoproteins/biosynthesis ; Platelet Membrane Glycoproteins/physiology ; Receptors, Vitronectin/biosynthesis ; Receptors, Vitronectin/physiology ; Skin/pathology ; Transduction, Genetic ; Tumor Cells, Cultured
Chemical Substances	Antigens, CD ; Integrin beta3 ; Osteonectin ; Platelet Membrane Glycoproteins ; Receptors, Vitronectin
Language	English
Publishing date	2002-01-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uh III Zs.135/5: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.

Dinger, Marcel E / Amaral, Paulo P / Mercer, Tim R / Pang, Ken C / Bruce, Stephen J / Gardiner, Brooke B / Askarian-Amiri, Marjan E / Ru, Kelin / Soldà, Giulia / Simons, Cas / Sunkin, Susan M / Crowe, Mark L / Grimmond, Sean M / Perkins, Andrew C / Mattick, John S

Genome research

2008 Volume 18, Issue 9, Page(s) 1433–1445

Abstract: The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost exclusively on protein-coding transcripts. However, recent ... ...

Abstract	The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost exclusively on protein-coding transcripts. However, recent transcriptome analyses show that the mammalian genome contains thousands of long noncoding RNAs (ncRNAs), many of which appear to be expressed in a developmentally regulated manner. The functions of these remain untested. To identify ncRNAs involved in ES cell biology, we used a custom-designed microarray to examine the expression profiles of mouse ES cells differentiating as embryoid bodies (EBs) over a 16-d time course. We identified 945 ncRNAs expressed during EB differentiation, of which 174 were differentially expressed, many correlating with pluripotency or specific differentiation events. Candidate ncRNAs were identified for further characterization by an integrated examination of expression profiles, genomic context, chromatin state, and promoter analysis. Many ncRNAs showed coordinated expression with genomically associated developmental genes, such as Dlx1, Dlx4, Gata6, and Ecsit. We examined two novel developmentally regulated ncRNAs, Evx1as and Hoxb5/6as, which are derived from homeotic loci and share similar expression patterns and localization in mouse embryos with their associated protein-coding genes. Using chromatin immunoprecipitation, we provide evidence that both ncRNAs are associated with trimethylated H3K4 histones and histone methyltransferase MLL1, suggesting a role in epigenetic regulation of homeotic loci during ES cell differentiation. Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery.
MeSH term(s)	Animals ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cell Differentiation ; Cell Lineage ; Chromatin/metabolism ; Embryo, Mammalian/metabolism ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Female ; Gene Expression Profiling ; Mice ; Pluripotent Stem Cells/cytology ; Pluripotent Stem Cells/metabolism ; Promoter Regions, Genetic ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism
Chemical Substances	Carrier Proteins ; Chromatin ; RNA, Untranslated
Language	English
Publishing date	2008-06-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.078378.108
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito