HIRA regulate Arabidopsis dedifferentiation process
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Frederic Berger
PROVIDER: E-GEOD-57044 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Plant development is characterised by the capacity to reprogram differentiated cells to initiate asexual reproduction and to produce new organs such as lateral roots. To test whether HIRA could be involved in aspects of developmental reprogramming we studied the effect of HIRA during de-differentiation
2014-10-01 | GSE57044 | GEO
Project description:HIRA regulate Arabidopsis dedifferentiation process
| PRJNA245311 | ENA
Project description:Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state into a M-bM-^@M-^Xstem cellM-bM-^@M-^Y-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. We showed that follicular granulosa cells (GC), which have distinct functions in vivo, can dedifferentiate during culture in vitro and acquire multipotency. We investigated the dedifferentiation of GC using global gene expression analyses. Total RNA was isolated from GCs to DFOG cells at 5 time points during dedifferentiation (cultured in 0day, 1day, 2day, 4day and 7day). Each timepoint was performed in triplicate (ie, biological replicates). Using Affymetrix porcine genome array, we performed microarray time course experiments to analyze gene expression profiles during GC dedifferentiation.
2012-11-21 | E-GEOD-18854 | biostudies-arrayexpress
Project description:Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state into a M-bM-^@M-^Xstem cellM-bM-^@M-^Y-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. We showed that mature adipocytes (MA) and follicular granulosa cells (GC), which have distinct functions in vivo, can dedifferentiate during culture in vitro and acquire multipotency. We investigated the dedifferentiation mechanism of MA and GC using global gene expression analyses. Using Affymetrix porcine genome array, we compared global gene expression profiles during dedifferentiation to search for particular biological functions in genes of which expression intensities were increased or decreased by MA and GC dedifferentiation.
2011-03-10 | E-GEOD-17264 | biostudies-arrayexpress
Project description:The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites. We used microarrays to detail the global programme of gene expression after knockdown of HIRA HeLa cells were nucleofacted with Dharmacon control siRNA and siRNA to HIRA and RNA was isolated 72 hours after transfection in four biological replicates
2013-04-18 | E-GEOD-45022 | biostudies-arrayexpress
Project description:The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites. We used microarrays to detail the global programme of gene expression after knockdown of HIRA
2013-04-18 | GSE45022 | GEO
Project description:The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites. Examination of 3 histone chaperone proteins in HeLa cells
2013-04-18 | E-GEOD-45024 | biostudies-arrayexpress
Project description:Hira has been implicated in replication-independent chromatin assembly. To determine the role of Hira in the regulation of embryonic stem (ES) cell gene expression, we used microarrays to analyze the global program of gene expression in Hira null versus WT undifferentiated ES cells.
2009-12-19 | GSE19542 | GEO
Project description:Autologous chondrocyte implantation (ACI) is an effective method to treat chronic articular cartilage injury in recent years, which requires a large number of human hyaline chondrocytes. Unfortunately, human hyaline chondrocytes often undergo dedifferentiation in vitro. Thus, it is important to elucidate the mechanism of dedifferentiation for the application of ACI technology. Long noncoding RNAs (lncRNA) play a regulatory role in gene expression in many pathological and physiological processes. However, the role of lncRNAs in human hyaline chondrocyte dedifferentiation remains unclear. The aim of this study was to investigate the expression profiles of lncRNAs in human hyaline chondrocyte dedifferentiation during in vitro culture. First, we cultured human hyaline chondrocytes in vitro and detected the expression of COL1A1, COL2A1, and SOX-9 in passage 1 (P1) and 5 (P5) chondrocytes using quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence, and western blotting. Then, we analyzed the expression profiles of lncRNAs and mRNAs in P1 and P5 chondrocytes by microarray analysis.
2020-02-25 | GSE145817 | GEO
Project description:The mammalian HIRA/UBN1/ASF1a complex is a histone chaperone complex that is conserved from yeast (Saccharomyces cerevisiae) to humans. This complex preferentially deposits the histone variant H3.3 into chromatin in a DNA replication-independent manner and is implicated in diverse chromatin regu- latory events from gene activation to heterochromatinization. In yeast, the orthologous complex consists of three Hir proteins (Hir1p, Hir2p, and Hir3p), Hpc2p, and Asf1p. Yeast Hir3p has weak homology to CABIN1, a fourth member of the human complex, suggesting that Hir3p and CABIN1 may be orthologs. Here we show that HIRA and CABIN1 interact at ectopic and endogenous levels of expression in cells, and we isolate the quaternary HIRA/UBN1/CABIN1/ASF1a (HUCA) complex, assembled from recombinant proteins. Mutational analyses support the view that HIRA acts as a scaffold to bring together UBN1, ASF1a, and CABIN1 into a quaternary complex. We show that, like HIRA, UBN1, and ASF1a, CABIN1 is involved in heterochromatinization of the genome of senescent human cells. Moreover, in proliferating cells, HIRA and CABIN1 regulate overlapping sets of genes, and these genes are enriched in the histone variant H3.3. In sum, these data demonstrate that CABIN1 is a functional member of the human HUCA complex and so is the likely ortholog of yeast Hir3p. We used microarrays to detail the global programme of gene expression after knockdown of HIRA and CABIN1 in 3 replicates HeLa cells were nucleofacted with Dharmacon control siRNA and siRNA to HIRA and CABIN1 and RNA was isolated 72 hours after transfection.
2013-03-20 | E-GEOD-45295 | biostudies-arrayexpress