Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

Akalin, Altuna; Garrett-Bakelman, Francine E.; Kormáksson, Matthías; Busuttil, Jennifer; Zhang, Lu; Khrebtukova, Irina; Milne, Thomas A.; Huang, Yongsheng; Biswas, Debabrata; Hess, Jay L.; Allis, C. David; Roeder, Robert G.; Valk, Peter J.M.; Löwenberg, Bob; Delwel, Ruud; Fernandez, Hugo F.; Paietta, Elisabeth; Tallman, Martin S.; Schroth, Gary P.; Mason, Christopher E.; Melnick, Ari; Figueroa, María E.

doi:10.1371/journal.pgen.1002781

Cited by 280 publications

(325 citation statements)

References 51 publications

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“…Because piwi/piRNAs promote CpG methylation of retrotransposons, in particular LINE/LTR classes in the mouse germline (1, 2, 4) and the CREB2 promoter in Aplysia neurons (10), we investigated the consequences of the loss of the piRNA pathway on DNA methylation in the hippocampus and PFC. We interrogated DNA methylation status of CpGs at a base pair resolution across the genome using enhanced reduced representation bisulfite sequencing (ERRBS) (35). Consistent with a signature for piRNA pathway activity, we observed an overall DNA hypomethylation in the Mili −/− brain tissues, with 61.7% differentially methylated cytosines (DMCs) in hippocampi and 63.3% in PFC (Fig.…”

Section: Mili −/− Mice Exhibit Line1 Promoter Hypomethylation In Theimentioning

confidence: 63%

Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain

Nandi

Chandramohan

Fioriti

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Piwi-interacting RNAs (piRNAs), long thought to be restricted to germline, have recently been discovered in neurons of Aplysia, with a role in the epigenetic regulation of gene expression underlying long-term memory. We here ask whether piwi/piRNAs are also expressed and have functional roles in the mammalian brain. Large-scale RNA sequencing and subsequent analysis of protein expression revealed the presence in brain of several piRNA biogenesis factors including a mouse piwi (Mili), as well as small RNAs, albeit at low levels, resembling conserved piRNAs in mouse testes [primarily LINE1 (long interspersed nuclear element1) retrotransposon-derived]. Despite the seeming low expression of these putative piRNAs, single-base pair CpG methylation analyses across the genome of Mili/piRNA-deficient (Mili −/− ) mice demonstrate that brain genomic DNA is preferentially hypomethylated within intergenic areas and LINE1 promoter areas of the genome. Furthermore, Mili mutant mice exhibit behavioral deficits such as hyperactivity and reduced anxiety. These results suggest that putative piRNAs exist in mammalian brain, and similar to the role of piRNAs in testes, they may be involved in the silencing of retrotransposons, which in brain have critical roles in contributing to genomic heterogeneity underlying adaptation, stress response, and brain pathology. We also describe the presence of another class of small RNAs in the brain, with features of endogenous siRNAs, which may have taken over the role of invertebrate piRNAs in their capacity to target both transposons, as well as protein-coding genes. Thus, RNA interference through gene and retrotransposon silencing previously encountered in Aplysia may also have potential roles in the mammalian brain.piwi-interacting RNA | transposon | DNA methylation | behavior | endogenous siRNA P iwi-interacting RNAs (piRNAs) are 26-to 32-nt small noncoding RNAs that associate with the piwi clade of the Argonaute family of proteins and whose primary functions in mammals are associated with the silencing of transposons in the germline through de novo DNA methylation (1-4). Transposons constitute 44% of the human genome and could when active contribute to genetic heterogeneity, to alteration of behavior during adaptation, and to responses to stress. Somatic retrotransposition and its associated insertional mutagenesis have particularly important implications for brain disorders and are often associated with schizophrenia, Rett syndrome, and neurodegenerative disorders (5-7). The LINE1 (long interspersed nuclear element1) family of retrotransposons in particular is active in human and mouse hippocampus (8, 9).Although it has long been thought that piRNA expression and function are restricted to the germline, our laboratory and others have previously found that the piRNA pathway is functional in invertebrate neurons as well (10, 11). Aplysia neurons, in particular, have a strikingly abundant expression of piRNAs (contributing to at least 5% of the total noncoding RNA population); they in turn hav...

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Section: Mili −/− Mice Exhibit Line1 Promoter Hypomethylation In Theimentioning

confidence: 63%

Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain

Nandi

Chandramohan

Fioriti

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Compared to normal bone marrow controls and AML patients without IDH1m and IDH2m, these groups featured dominant cytosine hypermethylation patterns [25]. The hypermethylation signature was confirmed in studies of AML patients using Illlumina arrays [1] as well as enhanced reduced representation bisulfite sequencing (ERRBS) [26,27]. Mouse models expressing IDH1m recapitulated the hypermethylation signatures.…”

Section: Mutant Isocitrate Dehydrogenase Enzymes In Malignant Disordersmentioning

confidence: 91%

“…Thus, 2-HG inhibition of TET2 activity could result in aberrant gain of 5mC at both PU.1 and WT1 target gene promoters resulting in gene transcription repression. Interestingly, 5mC patterning in IDHm AML specimens was enriched for disruption of PU.1 binding sites, as well as other hematopoietic regulators such as GATA1 and GATA2 perhaps indicating an additional mechanism through which IDH1 and IDH2 mutations could antagonize transcription factors [25][26][27].…”

Section: Potential Mechanisms Of Aberrant Gene Expression In Idh1 and Imentioning

confidence: 99%

Mutant IDH : A Targetable Driver of Leukemic Phenotypes Linking Metabolism, Epigenetics and Transcriptional Regulation

Garrett-Bakelman

Melnick

2016

Epigenomics

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Aberrant epigenomic programming is a hallmark of acute myeloid leukemia. This is partially due to somatic mutations that perturb cytosine methylation, histone posttranslational modifications and transcription factors. Remarkably, mutations in the IDH1 and IDH2 genes perturb the epigenome through all three of these mechanisms. Mutant IDH enzymes produce high levels of the oncometabolite (R)-2-hydroxyglutarate that competitively inhibits dioxygenase enzymes that modify methylcytosine to hydroxymethylcytosine and histone tail methylation. The development of IDH mutant specific inhibitors may now enable the therapeutic reprogramming of both layers of the epigenome spontaneously to revert the malignant phenotype of these leukemias and improve clinical outcome for acute myeloid leukemia patients with IDH mutations.

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“…However, coverage over other genome elements like CpG island shores and some enhancer elements is limited (Gu et al 2011). With refinements to the method, enhanced RRBS (ERRBS) coverage in some of the less CG dense regions was improved (Akalin et al 2012b;Garrett-Bakelman et al 2015). The primary limitation to these methods is the dependence on the location of restriction sites in the genome and inability to tune coverage to regions of interest.…”

Section: Reduced Representation Bisulfite Sequencing-rrbs/errbsmentioning

confidence: 99%

Analysis of DNA modifications in aging research

et al. 2018

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As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through nextgeneration sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-theart for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.

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Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

Cited by 280 publications

References 51 publications

Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain

Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain

Mutant IDH : A Targetable Driver of Leukemic Phenotypes Linking Metabolism, Epigenetics and Transcriptional Regulation

Analysis of DNA modifications in aging research

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