title: ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation [ChiP-Seq and RNA-Seq]

status: Public on Aug 01 2018

first: Keith

summary: The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in modulating gene expression, is being increasingly appreciated. We investigated the interplay between ZBTB24, a zinc-finger protein belonging to the BTB-POZ family of transcription factors, and the de novo DNA methyltransferase DNMT3B. Both factors, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting they are mechanistically linked in some way, but almost nothing is known about ZBTB24. In this study, we identified genomic targets regulated by ZBTB24, and identified its recognition motif, binding to which leads to activation. Chromatin immunoprecipitation in model cell line systems revealed common genes bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function.

overall_design: Flag-tagged ZBTB24, DNMT3B, and tag-only stable ectopic lines were created and genomic sites bound by each factor was mapped using ChIP-seq. Loss of function approach was used to map the functional transcriptome and methylome regulated by ZBTB24 and DNMT3B.

first: Joyce

last: Thompson


title: 5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design

status: Public on May 07 2018

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

country: USA

institute: Washington University in St. Louis

summary: Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C generates high quality, high resolution maps of looping interactions genome-wide, but is intractable for high-throughput screening of loops across conditions due to the requirement of an enormous number of reads (>6 Billion) per library. Here, we describe 5C-ID, an updated version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ ChromosomeConformation-Capture (3C)) and ligation-mediated amplification performed with a new double alternating design. 5C-ID reduces spatial noise and enables higher resolution 3D genome folding maps than canonical 5C, allowing for a marked improvement in sensitivity and specificity of loop detection. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.

overall_design: Total of 7 samples of 5C using double alternating primers, including 1 sample from dilution 3C/5C and 6 samples from different genome copies of in situ 3C/5C

first: Ji

middle: H

last: Kim

first: Katelyn

middle: R

last: Titus

middle: E


title: M-Wnt claudin-low breast cancer model : metastatic derivatives

status: Public on May 10 2017

city: Chapel ill

first: Stephen

middle: D

last: Hursting

state: NC

address: 135 Dauer Drive

institute: University of North Carolina at Chapel Hill

summary: Analysis of lung and liver metastases derived from M-Wnt primary tumor. Results provide insight into genes associated with progression of triple negative breast cancer to metastatic disease.

overall_design: Two-condition experiment, M-Wnt (control) vs metM-Wnt(lung) or metM-Wnt (liver), M-Wnt 3 replicates, metM-Wnt(lung) 3 replicates, metM-Wnt (liver) 2 replicates

first: Ciara

last: O'Flanagan

first: Emily

middle: L

last: Rossi

first: Shannon

middle: B

last: McDonell

first: Xuewen

last: Chen

first: Yi-Hsuan

last: Tsai

first: Joel

middle: S

last: Parker

first: Jerry

last: Usary

first: Charles

middle: M

last: Perou


title: Age-related changes in gene expression patterns of immature and aged rat primordial follicles

status: Public on Jul 18 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Women are born with millions of primordial follicles which gradually decrease with increasing age and this irreversible supply of follicles completely exhausts at menopause. The fertility capacity of women diminishes in parallel with aging. The mechanisms for reproductive aging are not fully understood. In our recent work we observed a decline in BRCA1 mediated DNA repair in aging rat primordial follicles. To further understand the age-related molecular changes, we performed microarray gene expression analysis using total RNA extracted from immature (18–20 days) and aged (400–450 days) rat primordial follicles. The results of current microarray study revealed that there were 1011 (>1.5 fold, p<0.05) genes differentially expressed between two groups in which 422 genes were up-regulated and 589 genes were down-regulated in aged rat primordial follicles compared to immature. The gene ontology and pathway analysis of differentially expressed genes revealed a critical biological function such as cell cycle, oocyte meiosis, chromosomal stability, transcriptional activity, DNA replication and DNA repair were affected by age and this considerable difference in gene expression profiles may have adverse influence on oocyte quality. Our data provide information on the processes that may contribute to aging and age-related decline in fertility.

overall_design: In total of 6 samples, 3 replicate samples were from immature rat primordial follicles and 3 replicate samples were from aged rat primordial follicles. For each replicate sample, the primordial follicles isolated from multiple isolations (each time 10-20 rat ovaries) were finally pooled in order to get required quantity of RNA.

first: Vijayakumar

last: Govindaraj

first: Harshini

last: Krishnagiri

first: Payal

last: Chakraborty

first: Madavan

last: Vasudevan

first: A

middle: J

last: Rao


title: Εarly transcriptional effects of 17β-estradiol, 17β-estradiol-BSA and tamoxifen in human NSCLC cell lines A549 and H520

status: Public on Dec 22 2016

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

summary:
Assessment of different subcellular localizations (membrane, cytosol, nucleus) of estrogen receptors by multi-epitope protein expression in 200 NSCLC specimens and matched non-cancerous tissues and ESR-1 probe mapping meta-analysis of Affymetrix 2.0 plus data in 1398 NSCLC tumors and normal lung tissues and 39 NSCLC cell lines led us to the conclusion that ERα extranuclear variants are the main ERs in NSCLC. In order to further analyze these effects we treated A549 and H520 cell lines with 17β-estradiol, 17β-estradiol-BSA (plasma membrane impermeable conjugate) and tamoxifen for 3h, in order to investigate early transcriptional effects and responsiveness to estrogen agonists and antagonists.
The aim of this study was to demonstrate the functionality of NSCLC ERs and decipher which genes, canonical pathways and networks are affected by each treatment.

overall_design: Two NSCLC cell lines (HTB-182 and A549) were studied. As extranuclear ERs are particularly prone to trigger early transcriptional effects, 17β-estradiol-BSA was used to detect signals originating exclusively from plasma membrane bound ERs, and compare them with the signals generated by 17β-estradiol (acting in both intracellular and membrane bound ERs). Tamoxifen, an endocrine disruptor that can trigger mainly antagonist effects was used as an inhibitor. Therefore cells were either exposed to vehicle (ethanol) or 17-β estradiol, 17-β estradiol plus tamoxifen, 17-β estradiol-BSA, 17-β estradiol-BSA plus tamoxifen,

first: Elias

last: Castanas

first: Marilena

last: Kampa

first: Vasiliki

last: Pelekanou


title: YY1 and CTCF Orchestrate a 3D Chromatin Looping Switch during Early Neural Lineage Commitment

status: Public on May 22 2017

first: Jennifer

last: Phillips-Cremins

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3-D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naïve/primed pluripotency to multipotent primary neural progenitor cells (NPCs). Many pluripotency gene-enhancer interactions are anchored by CTCF and its occupancy is lost in parallel with loop decommissioning during differentiation. Conversely, CTCF binding sites in NPCs are largely pre-existing in pluripotent stem cells. Only a small number of CTCF sites arise de novo in NPCs. We identify another zinc finger protein, Yin Yang 1 (YY1), at the base of looping interactions between NPC-specific genes and enhancers. Putative NPC-specific enhancers exhibit strong YY1 signal when engaged in 3-D contacts and negligible YY1 signal when not in loops. Moreover, siRNA knockdown of YY1 specifically disrupts interactions between key NPC enhancers and their target genes. YY1-mediated interactions between NPC regulatory elements are often nested within constitutive loops anchored by CTCF.  Together, our results support a model in which YY1 acts as an architectural protein to connect developmentally regulated looping interactions; the location of YY1-mediated interactions may be demarcated in development by a pre-existing topological framework created by constitutive CTCF-mediated interactions.

overall_design:
Analysis of CTCF binding and higher-order chromatin architecture in mouse ES cells under 2i/LIF and serum/LIF conditions, and primary NPCs.
ChIP-Seq libraries and Chromosome-Conformation-Capture-Carbon-Copy (5C) libraries.

first: Jonathan

middle: A

last: Beagan

first: Michael

middle: T

last: Duong

first: Caroline

middle: V

last: Lachanski


title: APOL1 variant expression in mouse podocytes cause kidney disease

status: Public on Feb 15 2017

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: Next-generation sequencing (NGS) has become an important tool in molecular charactarization of animal models. APOL1 variants are associated with end stage renal disease in African Americans. We developed a mouse model with podocyte specific over expression of APOL1. Differential molecular signatures were identified between the groups by RNA-Sequencing on kidney.

overall_design: Total RNA of transgenic and control mice kidneys was isolated using RNeasy Mini Kit (Qiagen). RNA quality was assessed with the Agilent Bioanalyzer 2100 and RIN scores above 7 were used for cDNA production. Library was prepared and one microgram total RNA was used to isolate poly(A) purified mRNA using the Illumina TruSeq RNA Preparation Kit. We sequence our sample for single-end 100bp, and the annotated RNA counts (fastq) were calculated by Illumina’s CASAVA 1.8.2.

first: Pazit

last: Beckerman

first: Ae

last: Park

first: Katalin

last: Susztak


title: WDR-5 exhibits H3K4 methylation-independent activity during embryonic development in C. elegans

status: Public on Feb 08 2019

city: Manchester

first: Gino

middle: Bernard

last: Poulin

state: Greater Manchester

address: Dover Street

country: United Kingdom

institute: University of Manchester

summary:
Background:Histone H3 lysine 4 methylation (H3K4me) is generally associated with active transcription and bivalent chromatin, but can also contribute to repression. In metazoans, H3K4 methylation is catalysed by KMT2 methyltransferases assembled with the core scaffolding proteins WDR5, ASH2L, and RBBP5. RBBP5 mediates complex assembly and nucleosome binding, whilst WDR5 stabilises interactions to promote tri-methylation. However, WDR5 also exhibits additional ‘moonlighting’ functions, leaving its specific roles in H3K4 methylation and transcription regulation unclear. Using C. elegans embryos, spike-in ChIP-seq, and null alleles of wdr-5(-) and rbbp-5(-), we dissected the contributions of these scaffolds towards H3K4 mono-, di-, and tri-methylation as well as gene expression during C. elegans embryogenesis.
Results:We show that C. elegans RBBP-5 is essential for both mono- and multi-methylated H3K4 deposition. On the other hand, WDR-5 is primarily required for H3K4me3, but can influence H3K4me2 and H3K4me1 deposition either positively or negatively depending on the genomic feature involved. We additionally performed RNA-seq on these mutants and found that rbbp-5 deletion was largely tolerated with mis-regulation of ~ 700 genes, whereas the wdr-5 deletion led to widespread transcriptomic disruption (~ 3000 genes). We initially hypothesised that these broad changes were driven by the altered H3K4me1 and H3K4me2 landscapes in the wdr-5(-) mutant. However, transcriptomic profiling of the wdr-5(-); rbbp-5(-) double mutant, which lacks H3K4 methylation, revealed a high degree of similarity to the wdr-5(-) single mutant. This refuted our initial hypothesis and indicates that the changes in H3K4 methylation are unlikely to underlie the transcriptional effects of the wdr-5 deletion.
Conclusions:Our findings strongly indicate that WDR-5 profoundly shapes gene expression through mechanisms beyond H3K4 methylation. Distinguishing between H3K4me-dependent and independent functions of WDR-5 will further understanding of its roles in development and disease.

overall_design: Examination of 3 methyl marks (H3K4me1/me2/me3) into 3 genotypes (N2, wdr-5(-), rbbp-5(-)) in late C. elegans embryos

first: Paul

last: Labhart


title: ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation [Infinium]

status: Public on Jul 31 2018

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

first: Joyce

last: Thompson


title: Dynamic Reprogramming of DNA Methylation in SETD2-Deregulated Renal Cell Carcinoma

status: Public on Sep 30 2015

type: Methylation profiling by genome tiling array

summary: Clear cell renal cell carcinomas (ccRCCs) harbor frequent mutations in epigenetic modifiers including SETD2, the writer for H3K36me3. We profiles DNA methylation across cell line models of SETD2 inactivation and SETD2 mutated primary tumors as this epigenetic mark is linked to H3K36me3 and is a targetable mark for cancer therapy. SETD2 depleted cell line models (long-term and acute) exhibited a hypermethylation phenotype coinciding with ectopic gains in H3K36me3 centered across intergenic regions adjacent to low expression genes that became upregulated with dysregulation of the epigenome. Poised enhancers of developmental genes demonstrated enrichment for the hypermethylation phenotype. Deregulation of the epigenome observed in the cell line models was recapitulated in SETD2 mutated primary ccRCC, papillary renal cell carcinomas, and lung adenocarcinomas.

overall_design: 786-O parental ccRCC cell line was used to derive isogenic clones depleted of SETD2 through zinc-finger nuclease mediated knockout. NCCIT cells were transfected with siRNAs against SETD2. Genomic DNA was extracted and submitted for HumanMethylation 450 BeadChip Array processing.

first: Rochelle

last: Tiedemann

first: Ryan

last: Hlady

last: Hanavan

first: Douglas

middle: F

last: Lake

first: Raoul

last: Tibes

first: Jeong-Heon

last: Lee

first: Jeong-Hyeon

last: Choi

first: Thai

last: Ho


title: Hypoxia induces the dormant state in oocytes through expression of Foxo3

status: Public on May 28 2019

city: Fukuoka

first: So

last: Shimamoto

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku

department: Department of Developmental Stem Cell Biology

country: Japan

institute: Kyushu-university

summary: In mammals, most immature oocytes remain dormant in the primordial follicles in order to ensure the longevity of female reproductive life. A precise understanding of mechanisms underlying the dormancy is important for reproductive biology and medicine. In this study, by comparing mouse oogenesis in vivo and in vitro, the latter of which bypasses the primordial follicle stage, we defined the gene　expression profile representing the dormant state of oocytes. Overexpression of constitutively active FOXO3 partially reproduced the dormant state in vitro. Based on further gene expression analysis, we found that a hypoxic condition efficiently induced the dormant state in vitro. The effect of hypoxia was severely diminished by disruption of the Foxo3 gene and inhibition of hypoxia-inducible factors. Our findings provide insights into the importance of environmental conditions and their effectors for establishing the dormant state.

overall_design: Transcriptomes of oocytes isolated from in vivo ovaries at various stages or in vitro-reconstituted ovaries at various days of culture were determined by RNA-seq analysis. Transcriptomes of in vitro D21 oocytes derived from WT ESCs and Foxo3dNES Tg ESCs under a normoxic or hypoxic condition were also determined. Biologically triplicated (rep1-3) or duplicated (rep1-2) samples were analyzed.

first: Yohei

last: Nishimura

first: Go

last: Nagamatsu

first: Norio

last: Hamada

first: Haruka

last: Kita

first: Orie

last: Hikabe

first: Nobuhiko

last: Hamazaki

first: Katsuhiko

last: Hayashi


title: ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation

first: Keith

last: Robertson

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State During Somatic Cell Reprogramming

status: Public on May 05 2016

first: Jennifer

last: Phillips-Cremins

summary: The pluripotent genome is folded in a hierarchy of sophisticated topologies that markedly reconfigure during cell fate transitions. A critical unknown is whether chromatin folding is reversible and functionally linked to the re-establishment of pluripotency in somatic cell reprogramming. Here we integrate classic epigenetic marks with high-resolution architecture maps in embryonic stem (ES) cells, ES-derived neural progenitor cells (NPCs) and NPC-derived induced pluripotent stem (iPS) cells. Collectively we demonstrate that chromatin architecture is only partially reconfigured during somatic cell reprogramming and that pluripotent elements can retain architectural memory from their somatic cell of origin.

overall_design: Analysis of higher-order chromatin chromatin architecture and gene expression in mouse ES cells, primary NPCs and NPC-derived iPSCs.

first: Zachary

last: Plona

first: Jonathan

last: Beagan

first: Thomas

middle: G

last: Gilgenast

first: Jesi

last: Kim


title: Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [MBD-seq]

status: Public on Oct 20 2014

type: Methylation profiling by high throughput sequencing

summary: Global patterns of DNA methylation, mediated by the DNA methyltransferases (DNMTs), are disrupted in all cancers by mechanisms that remain largely unknown, hampering their development as therapeutic targets. Combinatorial acute depltion of all DNMTs in a pluripotent human tumor cell line, followed by epigenome and transcriptome analysis, revealed DNMT functions in unprecedented detail. DNMT3B occupancy regulates methylation during differentiation, while an unexpected interplay was discovered in which DNMT1 and DNMT3B antithetically regulate methylation and hydroxymethylation in gene bodies, a finding confirmed in other cell types. DNMT3B mediated nonCpG methylation, while DNMT3L influenced the activity of DNMT3B toward nonCpG versus CpG site methylation. Taken together, these data reveal new functional targets of each DNMT suggesting that isoform selective inhibition would be therapeutically advantageous.

overall_design: NCCIT cells were transfected with siRNAs against DNMT3B and a no-target control. Genomic DNA was extracted, and subsequently applied to affinity MBD-bound magnetic beads (Ribomed) to enrich methylated DNA sequences.

first: Rochelle

last: Tiedemann

first: Emily

last: Putiri

first: Jeong

last: Lee

first: Ryan

last: Hlady

first: Katsunobu

last: Kashiwagi

first: Tamas

last: Ordog

first: Zhiguo

last: Zhang

first: Chen

last: Liu


title: Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome


title: Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [gene expression]

overall_design: Affymetrix gene expression Human Gene 1.0 ST microarray of NCCIT human embryonic carcinoma cells (13 samples in duplicate).

last: Choi


title: Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [methylation]

summary: Global patterns of DNA methylation, mediated by the DNA methyltransferases (DNMTs), are disrupted in all cancers by mechanisms that remain largely unknown, hampering their development as therapeutic targets. Combinatorial acute depletion of all DNMTs in a pluripotent human tumor cell line, followed by epigenome and transcriptome analysis, revealed DNMT functions in unprecedented detail. DNMT3B occupancy regulates methylation during differentiation, while an unexpected interplay was discovered in which DNMT1 and DNMT3B antithetically regulate methylation and hydroxymethylation in gene bodies, a finding confirmed in other cell types. DNMT3B mediated nonCpG methylation, while DNMT3L influenced the activity of DNMT3B toward nonCpG versus CpG site methylation. Taken together, these data reveal new functional targets of each DNMT suggesting that isoform selective inhibition would be therapeutically advantageous.

overall_design: Overall, 27 samples were analyzed using the Infinium HumanMethylation450 BeadChip. 19 samples include NCCIT cells treated with various siRNAs targeting specific DNA methyltransferases. For the samples labeled biological replicate 1, NTC-1 serves as the control. Two additional biological replicates were analyzed for the siDNMT1, siDNMT3B, and si3B+3L condition; NTC-2 serves as the control for these samples. Six samples include HCT116 WT and various derivatives with alternative expression of DNMT1 and/or DNMT3B; WT serves as the control. Two samples include the undifferentiated (UD) and 7-day differentiated (DF) NCCIT cells; UD serves as the control.


title: Epigenetic signatures of alcohol abuse and hepatitis infection during hepatocarcinogenesis

status: Public on Sep 16 2014

summary: Hepatocellular carcinoma (HCC) is the second most common cause of cancer deaths worldwide. Altered DNA methylation landscapes are ubiquitous features of cancer. Interpretation of epigenetic aberrations in HCC is confounded by effects of multiple etiologic drivers and underlying cirrhosis in most cases. We globally profiled the DNA methylome of 34 normal livers and 122 primary liver disease tissues arising in the setting of chronic hepatitis B (HBV) or C (HCV) viral infection, alcoholism (EtOH), and other causes to examine how these environmental agents impact DNA methylation in a manner that contributes to liver disease. Our results demonstrate that each etiologic factor leaves unique and overlapping signatures on the DNA methylome. CpGs aberrantly methylated in cirrhosis-HCV and conserved in HCC were enriched for cancer driver genes, suggesting a pathogenic role for HCV-induced methylation changes. Additionally, large genomic regions displaying stepwise hypermethylation or hypomethylation during disease progression were identified. HCC-HCV/EtOH methylomes overlap highly with cryptogenic HCC, suggesting shared epigenetically deregulated pathways for hepatic carcinogenesis. Finally, overlapping methylation abnormalities between primary and cultured tumors unveil highly conserved epigenetic signatures in HCC. Taken together, this study characterizes progressive liver DNA methylome changes under exposure to detrimental environmental agents and illuminates possible biomarkers for early detection of HCC.

overall_design: 156 primary tissues and 25 cultured normal and HCC cell lines

first: William

last: Puszyk

first: Lewis

last: Roberts

first: Jeong-Hyeon


title: Impact of human MLL/COMPASS and Polycomb complexes on the DNA methylome [expression array]

status: Public on Jul 14 2014

first: Keith

last: Robertson

summary: The association of DNA CpG methylation (or its absence) with occupancy of histone post translational modifications has hinted at an underlying crosstalk between histone marks and DNA methylation in patterning the human methylome, an idea supported by corresponding alterations to both histone marks and DNA methylation during malignant transformation.  This study investigated the framework by which histone marks influence DNA methylation.  Using RNAi in a human pluripotent embryonic carcinoma cell line we depleted essential components of the histone modifying complexes that establish the posttranslational modifications H3K4me3, H3K27me3, and H2AK119ub, and we assayed the impact of the subsequent loss of these marks on the DNA methylome.  Absence of H2AK119ub resulted predominantly in hypomethylation across the genome.  Removal of H3K4me3 or, surprisingly, H3K27me3 caused CpG island hypermethylation at a subset of loci.  Intriguingly, many promoters were co-regulated by all three histone marks, becoming hypermethylated with loss of H3K4me3 or H3K27me3 and becoming hypomethylated with depletion of H2AK119ub, and many of these co-regulated loci were among those that are commonly, aberrantly hypermethylated in cancer.

overall_design: Affymetrix gene expression Human ST1.0 microarray of NCCIT human embryonic carcinoma cells (7 samples in duplicate).

first: Chunsheng


title: Impact of human MLL/COMPASS and Polycomb complexes on the DNA methylome [MBD-seq]

overall_design: Methylation profiling by affinity-based high throughput sequencing

first: Chunshen


title: Control of 5mC and 5hmC by TET dioxygenases in human embryonic carcinoma cells [Microarray]

status: Public on Jun 14 2014

summary: The TET family of dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), but their involvement in establishing normal 5mC patterns during mammalian development and their contributions to aberrant control of 5mC during cellular transformation remains largely unknown. We depleted TET1, TET2, and TET3 by siRNA in a pluripotent embryonic carcinoma cell model and examined the impact on genome-wide 5mC and 5hmC patterns.  TET1 depletion yielded widespread reduction of 5hmC, while depletion of TET2 and TET3 reduced 5hmC at a subset of TET1 targets suggesting functional co-dependence.  TET2 or TET3-depletion also caused increased 5hmC, suggesting they play a major role in 5hmC removal.  All TETs prevent hypermethylation throughout the genome, a finding dramatically illustrated in CpG island shores, where TET depletion resulted in prolific hypermethylation.  Surprisingly, TETs also promote methylation, as hypomethylation was associated with 5hmC reduction.  TET function was highly specific to chromatin environment:  5hmC maintenance by all TETs occurred at polycomb-marked chromatin and genes expressed at moderate levels; 5hmC removal by TET2 is associated with highly transcribed genes enriched for H3K4me3 and H3K36me3.  Importantly, genes prone to hypermethylation in cancer become depleted of 5hmC with TET deficiency, suggesting the TETs normally promote 5hmC at these loci, and all three TETs are required for 5hmC enrichment at enhancers, a condition necessary for expression of adjacent genes.  These results provide novel insight into the division of labor among TET proteins and reveal an important connection of TET activity with chromatin landscape and gene expression.

overall_design: Affymetrix gene expression Human ST1.0 microarray of NCCIT human embryonic carcinoma cells (4 samples in duplicate).


title: Control of 5mC and 5hmC by TET dioxygenases in human embryonic carcinoma cells [MBD-Seq]

overall_design: Methylation and hydroxymethylation profiling by affinity-based high throughput sequencing


title: Impact of human MLL/COMPASS and Polycomb complexes on the DNA methylome


title: NYGC ALS Consortium data

status: Public on Sep 20 2019

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary:
This SuperSeries is composed of the SubSeries listed below.

Consortium contacts:
Maria Pedersen: mpedersen@nygenome.org
Hemali Phatnani: hphatnani@nygenome.org
NYGC ALS Consortium: cgndhelp@nygenome.org

overall_design:
Refer to individual Series:
GSE116622
GSE124439
GSE153960


title: Control of 5mC and 5hmC by TET dioxygenases in human embryonic carcinoma cells