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Method: Single-cell-level spatial gene expression in the embryonic neural differentiation niche
- Yi Huang,
- Xiaoming Yu,
- Na Sun,
- Nan Qiao,
- Yaqiang Cao,
- Jerome D. Boyd-Kirkup,
- Qin Shen,
- and Jing-Dong J. Han
Genome Res. April 2015 25: 570-581; Published in Advance January 9, 2015, doi:10.1101/gr.181966.114
...the genes with negative AvgPCCs, and Smad5 and Gli2 have the most negative AvgPCC within these two pathways (Fig. 5A). Consistent with their regulatory role in coordinating the phase transition, BMP up-regulated genes (Methods) are significantly enriched in Cluster 1, 4, and 5, while SHH up-regulated genes...
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Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...used microarrays to detect significantly up-and down-regulated genes. We used BMP4 to induce astrocytic differentiation (Sun et al. 2011a), treatment with B27- and FGF2-containing medium to induce an early neuronal progenitor fate (Spiliotopoulos et al. 2009), and BMP4 + FGF2 to induce NS cell...
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Research: Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance
- Benjamin L. Kidder and
- Stephen Palmer
Genome Res. April 2010 20: 458-472; Published in Advance February 22, 2010, doi:10.1101/gr.101469.109
...the promoters of genes expressed highly in TS cells such as Bmp8b, Bmpr1a, Elf5, Klf5, Smad7, Rbpsuh, and Smo and genes expressed highly during placental development such as Cited2, Gata2, and Smad2 (Supplemental Table S2). To identify common targets of SMARCA4 in TS cells and ES cells, we compared genes bound...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...functionally related regulatory enhancers situated in the Fli1 , Hhex (also known as Hex ), and Smad6 gene loci ( Donaldson et al. 2005a , b ; Donaldson and Gottgens 2006 ; Pimanda et al. 2007a ), and are thus beginning to define key components of the transcriptional networks controlling HSCs ( Pimanda et al...
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Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
- Leeban Yusuf,
- Matthew C. Heatley,
- Joseph P.G. Palmer,
- Henry J. Barton,
- Christopher R. Cooney,
- and Toni I. Gossmann
Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
...with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a -wide scale over macroevolutionary time is feasible. Although the coding...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
...is uniformly high (but not above wildtype levels), leading to a mesodermal precursor fate (Schneider et al. 1991). In gastrulation defective (gd) mutant embryos gd7, Dl is not activated, resulting in uniformly high signaling activity of the fly BMP2/4 ortholog Decapentaplegic (Dpp) but below wildtype maximum...
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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...that is significantly enriched for functional annotation terms related to transcription regulation and embryonic morphogenesis (Fig. 4A “pluri,” Supplemental Fig. S10A; Supplemental Table S3). These genes included canonical pluripotency expressed genes such as DNMT3B, POU5F1, EYA1, PBX1, FOXH1, FOXK1, SMAD3, TFAP2A...
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Research: Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
- Håvard Aanes,
- Cecilia L. Winata,
- Chi Ho Lin,
- Jieqi P. Chen,
- Kandhadayar G. Srinivasan,
- Serene G.P. Lee,
- Adrian Y.M. Lim,
- Hajira Shreen Hajan,
- Philippe Collas,
- Guillaume Bourque,
- Zhiyuan Gong,
- Vladimir Korzh,
- Peter Aleström,
- and Sinnakaruppan Mathavan
Genome Res. August 2011 21: 1328-1338; Published in Advance May 9, 2011, doi:10.1101/gr.116012.110
...in organismal and anatomical structure development, cell movement, and cellular development (Supplemental Figs. S5E, S6; Supplemental File S2). IPA analysis revealed 11 transcripts involved in embryonic stem cell pluripotency (BMP4, FGF4, FGFR2, FZD2, FZD3, FZD9, GSK3B, SOX2, TGFBR1, WNT5B, SMAD1). Genes...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...demonstrated by multiple in vivo and in vitro genetic experiments. Homozygous Tal1- murine embryos die of anemia with failed yolk sac hematopoiesis (Robb et al. 1995; Shivdasani et al. 1995). Furthermore, no hematopoietic lineages were detectable from Tal1- embryonic stem cells after in vitro...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...progenitors and precursors temporarily rewire their transcriptome, up- and downregulating hundreds of genes to accelerate the production of mature RBCs. Effective regeneration requires communication between critical cytokine signals (e.g., BMP4) and cis-regulatory elements on chromatin which coordinate...

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