... of the multifaceted, context-dependent functions of SOX2 as a master regulator of stem cell activities. ChIP-seq Chromatin binding Pioneer factor SOX2 Stem cell regulation Vetenskapsrådet http://dx.doi.org/10.13039/501100004359 2021-03083 Swedish Cancer Foundation http://dx.doi.org...

... developing pancreas have not been examined. To address this knowledge gap, we performed PDX1 ChIP-seq and single-cell RNA-seq using fetal human pancreata. We integrated our datasets with published datasets and revealed the dynamics of PDX1 binding and potential cell lineage-specific PDX1-bound genes...

... target genes have remained largely elusive. Here, we identify the SMAD4 target genes in mouse limb buds using an epitope-tagged Smad4 allele for ChIP-seq analysis in combination with transcription profiling. This analysis shows that SMAD4 predominantly mediates BMP signal transduction during early limb...

... . Genome Res.   12 , 996 - 1006 . 10.1101/gr.229102 Kidder , B. L. , Hu , G. and Zhao , K. ( 2011 ). ChIP-Seq: technical considerations for obtaining high-quality data . Nat. Immunol.   12 , 918 - 922 . 10.1038/ni.2117 Kidder , B. L. , Hu , G. , Yu , Z.-X...

... in specific behavioral defects. To broaden evidence for Ars2 as a chromatin regulator in neural development, we generated Ars2 ChIP-seq data. Notably, Ars2 preferentially occupies DNA enhancers in NSCs, where it colocalizes broadly with NSC regulator SOX2. Ars2 association with chromatin is markedly reduced...

... and zygotic mutant for the Polycomb group gene ezh2 reveals major conserved and divergent mechanisms in epigenetic gene repression during vertebrate development. Polycomb Ezh2 Zebrafish ChIP-seq Transcriptomics Proteomics Nederlandse Organisatie voor Wetenschappelijk Onderzoek http...

... a large suite of effector genes that control the morphogenetic behaviors and biomineral-forming activities of skeletogenic cells. To better understand the gene regulatory control of skeletogenesis by Alx1, we used genome-wide ChIP-seq to identify Alx1-binding sites and direct gene targets. Our analysis...

... to identify new Npas4l target genes. The resulting Venn diagram includes the overexpression experiment, the transcriptome of npas4l mutants at the six-somite stage and the ChIP-Seq data, considering all genes whose TSS is found within a 100 kb window from at least one Npas4l-binding site. As the Venn...

... ). ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions . Nat. Rev. Genet.   13 , 840 - 852 . 10.1038/nrg3306 Grabole , N. , Tischler , J. , Hackett , J. A. , Kim , S. , Tang , F. , Leitch , H. G. , Magnúsdóttir , E...

... targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh-binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding...

... in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts...

... of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0 ), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. Highlighted article: Dual ChIP-seq and RNA-seq in vivo experiments show...

.... The transcription factors Sal-like 4 (SALL4) and promyelocytic leukemia zinc finger (PLZF; also known as ZBTB16) are known to be required for normal SSC function, but their targets are largely unknown. ChIP-seq in mouse THY1 + spermatogonia identified 4176 PLZF-bound and 2696 SALL4-bound genes, including 1149...

... differentiation and can act alone to specify the endoderm. Caenorhabditis   elegans Endoderm development Transcription GATA factor ELT-2 ChIP-Seq The C. elegans endoderm provides an experimentally accessible and relatively simple example of a transcriptional network that drives...

... is known about how SOX9 regulates heart valve formation or its transcriptional targets. Therefore, we mapped putative SOX9 binding sites by ChIP-Seq in E12.5 heart valves, a stage at which the valve mesenchyme is actively proliferating and initiating differentiation. Embryonic heart valves have been shown...

... was shown to function downstream of Foxa1 and Foxa2 to regulate differentiation from immature to mature midbrain dopaminergic neurons. Our genome-wide Foxa1-bound cis-regulatory sequences from ChIP-Seq and Foxa1/2 candidate target genes from RNA-Seq analyses of embryonic midbrain dopamine cells also provide...

...William T. Chiu; Rebekah Charney Le; Ira L. Blitz; Margaret B. Fish; Yi Li; Jacob Biesinger; Xiaohui Xie; Ken W. Y. Cho Nodal/TGFβ signaling regulates diverse biological responses. By combining RNA-seq on Foxh1 and Nodal signaling loss-of-function embryos with ChIP-seq of Foxh1 and Smad2/3, we...

...-helix transcription factors (TFs), Ascl1 and Ptf1a, have contrasting functions in specifying these neurons. To understand how Ascl1 and Ptf1a function in this process, we identified their direct transcriptional targets genome-wide in the embryonic mouse neural tube using ChIP-Seq and RNA-Seq. We show...