GEO DataSets

(Submitter supplied) To investigate gene regulation by UHRF1, DNMT1, DNMT3B in THP-1 cells during differentiation, we established stable knockdown THP-1 cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) This methylation array was conducted to find out changes in genome-wide methylation pattern in THP-1 cells upon differentiation. Also, we tried to figure out the effects of knockdown of UHRF1, DNMT1 and DNMT3B in THP-1 cells in regulating genome-wide DNA methylation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

10 Samples

Download data: IDAT, TXT

(Submitter supplied) Accumulative studies indicate that DNA maintenance methylation by DNMT1 is initiated by binding of UHRF1 to replication fork. However, how UHRF1 gains access to chromatin in S phase is poorly understood. Here we report that LSH, a SNF2 family chromatin remodeler, facilitates DNA methylation in somatic cells primarily by promoting DNA methylation by DNMT1. We show that knockout of LSH in various somatic cells resulted in substantial reduction of DNA methylation, whereas knockout of DNMT3A and DNMT3B only moderately reduced the level of DNA methylation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL9052

8 Samples

Download data: DIFF, TXT

(Submitter supplied) During the progress of senescence, cells sequentially acquire diverse senescent phenotypes together with several gene reprogramming steps. It is still unclear what will be the key regulator in charge of collective gene expression changes at the initial senescent reprogramming. In this study, we show that suppression of DNA methyltransferase 1 (DNMT1)-mediated maintenance DNA methylation activity was an initial event developed prior to gain of senescent phenotypes by employing time-series gene expression profiles of two different senescence models of human diploid fibroblast (HDF), replicative senescence (RS; GSE41714) and H2O2-induced senescence (HS).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an essential epigenetic mark in mammals. It controls gene expression and genome stability. Global DNA methylation pattern is abnormal in cancers. Ubiquitin like with PHD and RING finger domains 1 (UHRF1) is a key epigenetic regulator that recruits and activates DNA methyltransferase 1 (DNMT1), the methylation maintenance enzyme. UHRF1 is a proven oncogene and its overexpression transforms cells in vitro and causes cancer in animal models. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an essential epigenetic mark in mammals. It controls gene expression and genome stability. Global DNA methylation pattern is abnormal in cancers. Ubiquitin like with PHD and RING finger domains 1 (UHRF1) is a key epigenetic regulator that recruits and activates DNA methyltransferase 1 (DNMT1), the methylation maintenance enzyme. UHRF1 is a proven oncogene and its overexpression transforms cells in vitro and causes cancer in animal models. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

62 Samples

Download data: TAB

(Submitter supplied) DNA methylation plays a critical role in development, particularly in silencing transposable elements. Conserved across mammals, the methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts 3a and 3b. Here we demonstrate that Dnmt1 displays clear de novo activity in vitro and in vivo and is specifically directed to IAP retrotransposons. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

4 related Platforms

90 Samples

Download data: BED, BW, CSV, XLSX

(Submitter supplied) Development of a multicellular organism uses the same genetic code to generate a broad diversity of cell types, which is instructed by extracellular cues and orchestrated by transcriptional activators and repressors. While transcription factors establish cell identities according to the central dogma, a number of enzymes, which index and regulate chromatin, appear to perform essential functions as well. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

54 Samples

Download data: BW, MTX, TSV

(Submitter supplied) The RING E3 ubiquitin ligase UHRF1 controls DNA methylation through its ability to target the maintenance DNA methyltransferase DNMT1 to newly replicated chromatin. DNMT1 recruitment relies on ubiquitylation of histone H3 by UHRF1, however, how UHRF1 deposits ubiquitin onto the histone is unknown. Here, we demonstrate that the ubiquitin-like domain (UBL) of UHRF1 is essential for RING-mediated H3 ubiquitylation. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16417

16 Samples

Download data: TXT

(Submitter supplied) The multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 for DNA methylation maintenance during DNA replication. Here, we show that MOF (Males absent On the First) is an acetyltransferase of UHRF1 to acetylate UHRF1 at Lys670 in the pre-RING linker region whereas HDAC1 is a deacetylase of UHRF1 at the same site. The MOF/HDAC1-mediated acetylation in UHRF1 is cell-cycle regulated and peaks at G1/S phase, in line with the function of UHRF1 in recruiting DNMT1 to maintain DNA methylation. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19057

7 Samples

Download data: TXT

(Submitter supplied) During spermatogenesis, mammalian spermatogonia undergo mitotic division, to maintain stem cell pool via self-renewal and generate differentiating progenitor cells for entry into meiotic prophase. During the perinatal stage, de novo DNA methylation occurring in pro-spermatogonia plays a key role to complete meiotic prophase and initiate meiotic division. In contrast, the role of the maintenance DNA methylation pathway for regulation of meiotic prophase, or meiotic division, in the adult is not well understood. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: TXT

(Submitter supplied) During spermatogenesis, mammalian spermatogonia undergo mitotic division, to maintain stem cell pool via self-renewal and generate differentiating progenitor cells for entry into meiotic prophase. During the perinatal stage, de novo DNA methylation occurring in pro-spermatogonia plays a key role to complete meiotic prophase and initiate meiotic division. In contrast, the role of the maintenance DNA methylation pathway for regulation of meiotic prophase, or meiotic division, in the adult is not well understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: CSV

(Submitter supplied) Maximizing DNA methyltransferase (DNMT’s) inhibition for cancer therapy requires defining the roles and interactions between these enzymes for maintaining the widespread DNA methylation abnormalities in cancer. Combining genetic and shRNA depletion in colon and other cancer cells reveals that DNMT1 is extremely dominant in this maintenance, with DNMT’s 3A and 3B playing minor roles, at all genomic loci including promoters and enhancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by array

Platforms:

GPL6480 GPL13534 GPL13497

48 Samples

Download data: TXT

(Submitter supplied) Maximizing DNA methyltransferase (DNMT’s) inhibition for cancer therapy requires defining the roles and interactions between these enzymes for maintaining the widespread DNA methylation abnormalities in cancer. Combining genetic and shRNA depletion in colon and other cancer cells reveals that DNMT1 is extremely dominant in this maintenance, with DNMT’s 3A and 3B playing minor roles, at all genomic loci including promoters and enhancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

8 Samples

Download data: TXT

(Submitter supplied) Maximizing DNA methyltransferase (DNMT’s) inhibition for cancer therapy requires defining the roles and interactions between these enzymes for maintaining the widespread DNA methylation abnormalities in cancer. Combining genetic and shRNA depletion in colon and other cancer cells reveals that DNMT1 is extremely dominant in this maintenance, with DNMT’s 3A and 3B playing minor roles, at all genomic loci including promoters and enhancers. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

33 Samples

Download data: TXT

(Submitter supplied) In HCT116 colorectal cancer cells, UHRF1 was knocked down by shRNA (puromycin) while simultaneously transduced with wildtype or mutant UHRF1 (blasticidin) or NDI1 (- control) followed by dual antibiotic selection. DNA was analyzed 11 days after viral transduction.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

4 Samples

Download data: IDAT

(Submitter supplied) Cytosine methylation (5mC) plays a key role in maintaining progenitor cell self-renewal and differentiation. Here, we analyzed the role of 5mC in kidney development by genome-wide methylation and expression profiling and by systematic genetic targeting of DNA methyltransferases (Dnmt) and Tet eleven hydroxylases (Tet). In mice, nephrons differentiate from Six2+ progenitor cells, therefore we created animals with genetic deletion of Dnmt 1, 3a, 3b, Tet1, or Tet2 in the Six2+ population (Six2Cre/Dnmt1flox/flox, Six2Cre/Dnmt3aflox/flox, Six2Cre/Dnmt3bflox/flox, Six2Cre/Tet2flox/flox or Tet1-/-). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6244 GPL16686

12 Samples

Download data: CEL

(Submitter supplied) Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MDA-MB-231S (sorted for high surface expression of CXCR4) and MDA-Bone-Un (Mouse bone metastasized MDA-MB-231 cells) human basal-like breast cancer cells cultured in 3D-Matrigel was performed. Changes in transcript levels of key microRNAs 29B1 and 29B2, miRLet7F1, miR519A1, MMP9, MMP1, FAM75D4, Interferons a7 and a17, Glycine receptor a3, CADM2 and claudin12

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL, TXT