GEO DataSets

(Submitter supplied) Long-range gene regulation is rare in bacteria and is confined to the classical DNA looping model. Here, we use a combination of biophysical approaches, including X-ray crystallography and single-molecule analysis, to show that long-range gene silencing on the plasmid RK2, a source of multidrug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL34685

12 Samples

Download data: CSV

(Submitter supplied) Liquid crystal-like, low-dimensional and long-range ordered structures (LC) are found in human tissues including bones. The excellent mechanical and biological functions of natural bones entail the well-orchestrated nano-scale hydroxyapatite (HAp) crystals within collagen fibres matrix. However, the understanding of the self-assembling of HAp nanocrystals and formation of hierarchically ordered bone structure are still elusive. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

15 Samples

Download data: TXT

(Submitter supplied) The Bin/amphiphysin/Rvs (BAR) domain protein FAM92A1 is a multifunctional protein engaged in the regulation of mitochondrial ultrastructure and ciliogenesis. However, the physiological role of FAM92A1 in the brain, particularly in neurons with specialized membrane architecture, remains unexplored. Here, we demonstrate that FAM92A1 is prominently expressed in the brain and neurons during early mouse embryonic development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: TXT

(Submitter supplied) Fibroblast growth factors and their receptors (FGFRs) play important roles in multiple cellular processes. FGFR genetic alterations such as mutations, amplifications, and chromosomal translocations are prevalent in various cancer types, contributing to the initiation and progression of tumors by enhancing FGFR signaling. Identifying effective small molecule inhibitors that selectively target FGFR can advance cancers therapy driven by FGFR abnormalities. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: RESULTS, TXT

(Submitter supplied) Human airway basal cells (BC) are the stem/progenitor population of the airway epithelium, and play a central role in anchoring the epithelium to the basement membrane. The anatomic position of BC allows for potential paracrine signaling between BC and the underlying non-epithelial stromal cells. In support of this, we previously demonstrated endothelial cells (EC) support growth of BC during co-culture via vascular endothelial growth factor A (VEGFA)-mediated signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: FPKM_TRACKING

(Submitter supplied) MALAT1 lncRNA plays key roles in regulating transcription, splicing, and tumorigenesis. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3′ cytoplasmic mascRNA. mascRNA was proposed to fold into a tRNA-like secondary structure, but lacks eight conserved linking residues required by the canonical tRNA fold. Here, we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30173

12 Samples

Download data: XLSX

(Submitter supplied) The inability of the adult human heart to regenerate lost or damaged myocardial tissue has created one of the most pressing public health dilemmas due to the devastating impact of heart failure. Our group and others have outlined several regulators of cardiomyocyte mitosis that may impact the regenerative capacity of the adult myocardium in mammals. Recently, we reported that the transcription factors Meis1 and Hoxb13 regulate postnatal cardiomyocyte cell cycle arrest, where concomitant deletion of both genes induced cardiomyocyte proliferation and myocardial regeneration following ischemic injury. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TAB

(Submitter supplied) The inability of the adult human heart to regenerate lost or damaged myocardial tissue has created one of the most pressing public health dilemmas due to the devastating impact of heart failure. Our group and others have outlined several regulators of cardiomyocyte mitosis that may impact the regenerative capacity of the adult myocardium in mammals. Recently, we reported that the transcription factors Meis1 and Hoxb13 regulate postnatal cardiomyocyte cell cycle arrest, where concomitant deletion of both genes induced cardiomyocyte proliferation and myocardial regeneration following ischemic injury. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: BIGWIG, BROADPEAK

(Submitter supplied) DNA methyltransferases DNMT3A- and DNMT3B-mediated de novo DNA methylation critically regulates epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote macro-oligomer formation, leading to aberrant DNA methylation that in turn contributes to pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the hotspot mutation-induced functional mis-regulation of DNMT3A remains unclear. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

32 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methyltransferases DNMT3A- and DNMT3B-mediated de novo DNA methylation critically regulates epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote macro-oligomer formation, leading to aberrant DNA methylation that in turn contributes to pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the hotspot mutation-induced functional mis-regulation of DNMT3A remains unclear. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

15 Samples

Download data: BW, XLSX

(Submitter supplied) We describe the regulation, biogenesis and function of circDOCK1(2,27), a large, abundant EMT-regulated circular RNA whose formation is dependent on the epithelial-specific splicing regulator ESRP1. CircDOCK1(2,27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis along with CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2,27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

11 Samples

Download data: BED

(Submitter supplied) Aging, a risk factor for many diseases, is largely attributable to cell senescence and impaired mitochondrial function. Here, we used connectivity map (CMAP) to predict the anti-aging effects of drugs based on age-related transcriptomic signatures. We found the kinase inhibitor GW8510 can extend lifespan of yeast, and C57BL/6J or ICR mice by 92.18%, 31.9%, and 142.9%, respectively. Mechanistically, GW8510 can ameliorate cellular senescence by enhancing mitochondrial function, decreasing SA-β-gal staining, p21 and SASP marker expression, and rescues age-related histomorphological changes in mouse hippocampus, heart, kidney and liver. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) Histones are the primary building blocks of chromatin in eukaryotes and many archaea. Bacteria are thought to rely on an orthogonal set of proteins to organize their chromosomes. Several bacterial genomes do, however, encode proteins with putative histone fold domains. Whether these proteins adopt a bona fide histone fold, assemble into higher order complexes that bind DNA, and play a central role in bacterial nucleoid physiology is not known. more...

Organism:

Bdellovibrio bacteriovorus; Aquifex aeolicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25581 GPL28567

5 Samples

Download data: TXT

(Submitter supplied) Lysine residues in histones and other proteins can be modified by post-translational modifications (PTMs) that encode regulatory information. Acetylation and methylation of histone lysine residues are especially important for regulating chromatin and gene expression. Pathways involving these PTMs are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25244 GPL24676

68 Samples

Download data: BIGWIG, CSV, NARROWPEAK, TDF

(Submitter supplied) Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are important therapeutic targets in malignancy. Hormone binding triggers NR activation and their subsequent proteasomal degradation through unknown ligand-dependent ubiquitin ligase machinery. NR degradation is therapeutically relevant: the oncogenic PML-RARA fusion between PML and the retinoic acid receptor (RARA) drives acute promyelocytic leukemia and degradation of PML-RARA induced by all-trans-retinoic acid (ATRA) is required for anti-tumor activity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

24 Samples

Download data: BED, BW, CSV, NARROWPEAK

(Submitter supplied) The ASH1L lysine methyltransferase plays a critical role in development and is frequently dysregulated in cancer and neurodevelopmental diseases. ASH1L catalyzes mono- and dimethylation of histone H3K36 and contains a set of uncharacterized domains. Here, we report the structure-function relationships of the C-terminal cassette of ASH1L encompassing a bromodomain (BD), a PHD finger and a bromo-associated homology (BAH) domain and show that ASH1L co-localizes with H3K4me3 but not with H3K36me2 at transcription start sites genome-wide and is involved in embryonic stem cell differentiation and transcriptional regulation of differentiation marker genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: WIG

(Submitter supplied) The inhibitor of apoptosis protein (IAP) BIRC2 regulates fundamental cell death and survival signaling pathways. Aberrant activity of BIRC2 is associated with immunological diseases, inflammation, and cancer. Unlike other IAPs, BIRC2 can localize to and function in the nucleus through unknown mechanisms. Here, we show that BIRC2 accumulates in the nucleus via binding of its second and third BIR domains, BIRC2BIR2 and BIRC2BIR3, to histone H3 tail and report the crystal structure of the BIRC2BIR3:H3 complex. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism that underlies centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here we define the SNF2 ATPase ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes efficient deposition of core centromeric factors. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

6 Samples

Download data: BED

(Submitter supplied) Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism that underlies centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here we define the SNF2 ATPase ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes efficient deposition of core centromeric factors. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BED

(Submitter supplied) Double homeobox genes are unique to eutherian mammals, transiently expressed in early blastomere-stage embryos, and comprise 3 clades (DUXA, B, and C) evolved by homeodomain duplication and divergence from an ancestral single homeobox gene, sDUX, present in non-eutherian mammals and other vertebrates.  We test platypus sDUX and find that it drives cellular phenotypes identical to DUX4, the human DUXC gene, including cytotoxicity and inhibition of myogenic differentiation.  sDUX binds DNA as a head-to-head dimer, showing near overlap of protein core and DNA to the DUX4-DNA crystal structure.  DUXA and sDUX bind both palindromic and nonpalindromic TAAT/TGAT double homeodomain motifs against DUX4 preference for non-palindromic.  Although DUXA lacks transcriptional activation potential, we find significant similarities in transcriptional and chromatin profiles of sDUX with DUX4 and DUXA-VP64, including expression of ZGA genes and LTR elements.  Furthermore, DUXA binds to a significant fraction of DUX4 target sites and is able to counteract transcriptional activation of DUX4 on its targets, potentiating a feedback inhibitory loop, including in cells from patients with facioscapulohumeral muscular dystrophy (FSHD).  The DUX gene family therefore comprises cross-regulating members of opposing function, with implications for their roles in ZGA, FSHD, and cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301 GPL21697

58 Samples

Download data: BIGWIG, NARROWPEAK, RDATA, XLSX