Contributors: Elizabeth M. Duncan, Alex D. Chitsazan, Chris W. Seidel, Alejandro Sánchez Alvarado

Date: 2015-01-01

ChIP-seq from dissociated whole-worm tissue; Drosophila S2 chromatin was...ChIP-seq starting from FACS-isolated Smed cell populations; Drosophila...of ChIP-seq starting from FACS-isolated Smed cell populations; Drosophila...Drosophila (dSet1, dTrx) and human (hSet1, hMLL1, hMLL2). (B) Timeline...Schematic of ChIP-seq from dissociated whole-worm tissue; Drosophila S2... those of Drosophila (dSet1, dTrx) and human (hSet1, hMLL1, hMLL2). (B ... Histone H3 lysine 4 trimethylation (H3K4me3) is known to correlate with both active and poised genomic loci, yet many questions remain regarding its functional roles in vivo. We identify functional genomic targets of two H3K4 methyltransferases, Set1 and MLL1/2, in both the stem cells and differentiated tissue of the planarian flatworm Schmidtea mediterranea. We show that, despite their common substrate, these enzymes target distinct genomic loci in vivo, which are distinguishable by the pattern each enzyme leaves on the chromatin template, i.e., the breadth of the H3K4me3 peak. Whereas Set1 targets are largely associated with the maintenance of the stem cell population, MLL1/2 targets are specifically enriched for genes involved in ciliogenesis. These data not only confirm that chromatin regulation is fundamental to planarian stem cell function but also provide evidence for post-embryonic functional specificity of H3K4me3 methyltransferases in vivo.

Contributors: Jana Friedrich, Sebastian Sorge, Fatmire Bujupi, Michael P. Eichenlaub, Natalie G. Schulz, Jochen Wittbrodt, Ingrid Lohmann

Date: 2016-02-02

Drosophila embryo with the MHE and MHD muscle precursors, the MN, and ...Drosophila Feeding Motor Unit...ChIP-Seq Experiments Are Classified According to Their Gene Ontology Annotations...Drosophila...a stage 16 Drosophila embryo with the MHE and MHD muscle precursors, the ... Feeding is an evolutionarily conserved and integral behavior that depends on the rhythmic activity of feeding muscles stimulated by specific motoneurons. However, critical molecular determinants underlying the development of the neuromuscular feeding unit are largely unknown. Here, we identify the Hox transcription factor Deformed (Dfd) as essential for feeding unit formation, from initial specification to the establishment of active synapses, by controlling stage-specific sets of target genes. Importantly, we found Dfd to control the expression of functional components of synapses, such as Ankyrin2-XL, a protein known to be critical for synaptic stability and connectivity. Furthermore, we uncovered Dfd as a potential regulator of synaptic specificity, as it represses expression of the synaptic cell adhesion molecule Connectin (Con). These results demonstrate that Dfd is critical for the establishment and maintenance of the neuromuscular unit required for feeding behavior, which might be shared by other group 4 Hox genes.

Contributors: Dmitri Papatsenko, Henia Darr, Ivan V. Kulakovskiy, Avinash Waghray, Vsevolod J. Makeev, Ben D. MacArthur, Ihor R. Lemischka

Date: 2015-01-01

ChIP-seq) data sources for three transcriptional regulators: Oct4, Sox2 ... Analyses of gene expression in single mouse embryonic stem cells (mESCs) cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM). In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN) reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP) data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB) suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

Contributors: Stefania Comes, Miriam Gagliardi, Nicola Laprano, Annalisa Fico, Amelia Cimmino, Andrea Palamidessi, Dario De Cesare, Sandro De Falco, Claudia Angelini, Giorgio Scita

Date: 2013-10-15

ChIP-seq data (p = 0.03; Fisher’s exact test; upper panel) and KEGG pathways...expression and ChIP-seq data (p = 0.03; Fisher’s exact test; upper panel...ChIP-seq data (p = 0.03; Fisher’s exact test; upper panel). KEGG pathway ... Metabolites are emerging as key mediators of crosstalk between metabolic flux, cellular signaling, and epigenetic regulation of cell fate. We found that the nonessential amino acid L-proline (L-Pro) acts as a signaling molecule that promotes the conversion of embryonic stem cells into mesenchymal-like, spindle-shaped, highly motile, invasive pluripotent stem cells. This embryonic-stem-cell-to-mesenchymal-like transition (esMT) is accompanied by a genome-wide remodeling of the H3K9 and H3K36 methylation status. Consistently, L-Pro-induced esMT is fully reversible either after L-Pro withdrawal or by addition of ascorbic acid (vitamin C), which in turn reduces H3K9 and H3K36 methylation, promoting a mesenchymal-like-to-embryonic-stem-cell transition (MesT). These findings suggest that L-Pro, which is produced by proteolytic remodeling of the extracellular matrix, may act as a microenvironmental cue to control stem cell behavior.

Contributors: Hung Ping Shih, Philip A. Seymour, Nisha A. Patel, Ruiyu Xie, Allen Wang, Patrick P. Liu, Gene W. Yeo, Mark A. Magnuson, Maike Sander

Date: 2015-10-13

ChIP-seq analysis of hESC-derived pancreatic progenitors. (B) Venn diagram...ChIP-seq binding profiles (reads per million) for PDX1, SOX9, and histone ... The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox9 as cooperative inducers of a gene regulatory network that distinguishes the pancreatic from the intestinal lineage. Genetic studies demonstrate dual and cooperative functions for Pdx1 and Sox9 in pancreatic lineage induction and repression of the intestinal lineage choice. Pdx1 and Sox9 bind to regulatory sequences near pancreatic and intestinal differentiation genes and jointly regulate their expression, revealing direct cooperative roles for Pdx1 and Sox9 in gene activation and repression. Our study identifies Pdx1 and Sox9 as important regulators of a transcription factor network that initiates pancreatic fate and sheds light on the gene regulatory circuitry that governs the development of distinct organs from multi-lineage-competent foregut progenitors.

Contributors: Shigeki Iwase, Emily Brookes, Saurabh Agarwal, Aimee I. Badeaux, Hikaru Ito, Christina N. Vallianatos, Giulio Srubek Tomassy, Tomas Kasza, Grace Lin, Andrew Thompson

Date: 2016-02-09

ChIP-seq and RNA-seq were performed on two biological replicates of WT...Transcription ChIP-seq and RNA-seq were performed on two biological replicates ... Mutations in a number of chromatin modifiers are associated with human neurological disorders. KDM5C, a histone H3 lysine 4 di- and tri-methyl (H3K4me2/3)-specific demethylase, is frequently mutated in X-linked intellectual disability (XLID) patients. Here, we report that disruption of the mouse Kdm5c gene recapitulates adaptive and cognitive abnormalities observed in XLID, including impaired social behavior, memory deficits, and aggression. Kdm5c-knockout brains exhibit abnormal dendritic arborization, spine anomalies, and altered transcriptomes. In neurons, Kdm5c is recruited to promoters that harbor CpG islands decorated with high levels of H3K4me3, where it fine-tunes H3K4me3 levels. Kdm5c predominantly represses these genes, which include members of key pathways that regulate the development and function of neuronal circuitries. In summary, our mouse behavioral data strongly suggest that KDM5C mutations are causal to XLID. Furthermore, our findings suggest that loss of KDM5C function may impact gene expression in multiple regulatory pathways relevant to the clinical phenotypes.