Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification

Bakel, Harm van; Werven, Folkert J. van; Radonjić, Marijana; Brok, Mariël; Leenen, Dik van; Holstege, Frank C.P.; Timmers, H. Th. Marc

doi:10.1093/nar/gkm1144

Cited by 38 publications

(39 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Purified immunoprecipitated and whole-cell extract (input) DNAs were amplified using the double-round T7 RNA polymerase-based amplification method (van Bakel et al, 2008). Labeled DNA samples were hybridized to the Mouse Promoter ChIP-on-chip 244 K Microarray (G4495A#14716, 14717, Agilent Technologies), washed and scanned according to the mammalian ChIP-on-chip protocol (Agilent Technologies).…”

Section: Chip-on-chip and Chip-seqmentioning

confidence: 99%

RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

et al. 2015

View full text Add to dashboard Cite

Polycomb group (PcG) proteins play a pivotal role in silencing developmental genes and help to maintain various stem and precursor cells and regulate their differentiation. PcG factors also regulate dynamic and complex regional specification, particularly in mammals, but this activity is mechanistically not well understood. In this study, we focused on proximal-distal (PD) patterning of the mouse forelimb bud to elucidate how PcG factors contribute to a regional specification process that depends on developmental signals. Depletion of the RING1 proteins RING1A (RING1) and RING1B (RNF2), which are essential components of Polycomb repressive complex 1 (PRC1), led to severe defects in forelimb formation along the PD axis. We show that preferential defects in early distal specification in Ring1A/B-deficient forelimb buds accompany failures in the repression of proximal signal circuitry bound by RING1B, including Meis1/2, and the activation of distal signal circuitry in the prospective distal region. Additional deletion of Meis2 induced partial restoration of the distal gene expression and limb formation seen in the Ring1A/B-deficient mice, suggesting a crucial role for RING1-dependent repression of Meis2 and likely also Meis1 for distal specification. We suggest that the RING1-MEIS1/2 axis is regulated by early PD signals and contributes to the initiation or maintenance of the distal signal circuitry.

show abstract

Section: Chip-on-chip and Chip-seqmentioning

confidence: 99%

RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously. 19 Labeling, hybridization, and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (Version 9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.…”

Section: Chip-on-chip Experimentsmentioning

confidence: 99%

Role of SOX17 in hematopoietic development from human embryonic stem cells

Nakajima‐Takagi

Osawa

Oshima

et al. 2013

Blood

View full text Add to dashboard Cite

To search for genes that promote hematopoietic development from human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), we overexpressed several known hematopoietic regulator genes in hESC/iPSC-derived CD34 ؉ CD43 ؊ endothelial cells (ECs) enriched in hemogenic endothelium (HE). Among the genes tested, only Sox17, a gene encoding a transcription factor of the SOX family, promoted cell growth and supported expansion of CD34 ؉ CD43 ؉ CD45 ؊/low cells expressing the HE marker VE-cadherin. SOX17 was expressed at high levels in CD34 ؉ CD43 ؊ ECs compared with low levels in CD34 ؉ CD43 ؉ CD45 ؊ pre-hematopoietic progenitor cells (pre-HPCs) and CD34 ؉ CD43 ؉ CD45 ؉ HPCs. Sox17-overexpressing cells formed semiadherent cell aggregates and generated few hematopoietic progenies. However, they retained hemogenic potential and gave rise to hematopoietic progenies on inactivation of

show abstract

“…Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously. 18 Labeling, hybridization, and washing were carried out according to the Agilent mammalian ChIP-chip protocol (Version 9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.…”

Section: Chip-chip Experimentsmentioning

confidence: 99%

Genome-wide analysis of target genes regulated by HoxB4 in hematopoietic stem and progenitor cells developing from embryonic stem cells

Oshima

Endoh

Endo³

et al. 2011

Blood

View full text Add to dashboard Cite

Forced expression of the transcription factor HoxB4 has been shown to enhance the self-renewal capacity of mouse bone marrow hematopoietic stem cells (HSCs) and confer a long-term repopulating capacity to yolk sac and embryonic stem (ES) cell-derived hematopoietic precursors. The fact that ES cell-derived precursors do not repopulate bone marrow without HoxB4 underscores an important role for HoxB4 in the maturation of ES-derived hematopoietic precursors into long-term repopulating HSCs. However, the precise molecular mechanism underlying this process is barely understood. In this study, we performed a genome-wide analysis of HoxB4 using ES cell-derived hematopoietic stem/progenitor cells. The results revealed many of the genes essential for HSC development to be direct targets of HoxB4, such as Runx1, Scl/Tal1, Gata2, and Gfi1. The expression profiling also showed that HoxB4 indirectly affects the expression of several important genes, such as Lmo2, Erg, Meis1, Pbx1, Nov, AhR, and Hemgn. HoxB4 tended to activate the transcription, but the downregulation of a significant portion of direct targets suggested its function to be context-dependent. These findings indicate that HoxB4 reprograms a set of key regulator genes to facilitate the maturation of developing HSCs into repopulating cells. Our list of HoxB4 targets also provides novel candidate regulators for HSCs. (Blood. 2011;117(15):e142-e150)

show abstract

Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification

Cited by 38 publications

References 18 publications

RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

Role of SOX17 in hematopoietic development from human embryonic stem cells

Genome-wide analysis of target genes regulated by HoxB4 in hematopoietic stem and progenitor cells developing from embryonic stem cells

Contact Info

Product

Resources

About