The JMJD2 members of histone demethylase revisited

Tan, Haidong; Wu, Si‐Guo; Wang, Jinxia; Zhao, Zongbao K.

doi:10.1007/s11033-007-9121-3

Cited by 16 publications

(15 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Histone demethylases, such as members of the Jumonji family, revert histone methylation (24). In neural crest development, JmjD2A (also known as KDM4A) regulates neural crest specification (18).…”

Section: Discussionmentioning

confidence: 99%

DNA methyltransferase 3B regulates duration of neural crest production via repression of Sox10

Strobl-Mazzulla

Simões-Costa

et al. 2014

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

View full text Add to dashboard Cite

Neural crest stem cells arise within the central nervous system but then undergo an epithelial-to-mesenchymal transition to migrate away and contribute to the peripheral nervous system and craniofacial skeleton. Here we show that DNA methyltransferase 3B (DNMT3B) is responsible for the loss of competence of dorsal neural tube cells to generate emigrating neural crest cells. DNMT3B knockdown results in up-regulation of neural crest markers, prolonged neural crest emigration, and subsequent precocious neuronal differentiation of the trigeminal ganglion. We find that DNMT3B binds to the promoter of Sox10, known to be important for neural crest emigration and lineage acquisition. Bisulfite sequencing further reveals methylation of the Sox10 promoter region upon cessation of emigration in normal embryos, whereas this mark is reduced after DNMT3B loss. Taken together, these results reveal the importance of DNA methylation in regulating the ability of neural tube cells to produce neural crest cells and the timing of peripheral neuron differentiation.

show abstract

Section: Discussionmentioning

confidence: 99%

DNA methyltransferase 3B regulates duration of neural crest production via repression of Sox10

Strobl-Mazzulla

Simões-Costa

et al. 2014

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

View full text Add to dashboard Cite

show abstract

“…These demethylases remove tri-methyl groups from lysine residues. The function of these enzymes has been analyzed mainly during the early stages of development, with the JmjD2 sub-family involved in the demethylation of various lysine residues in undifferentiated and differentiated embryonic stem cells [58]. Concerning regulation of posterior development in animals, JMJD3 counterbalances the activity of PcG group proteins with respect to the state of lysine 27 of histone H3 [59].…”

Section: Perspectivesmentioning

confidence: 99%

Perfect timing: Epigenetic regulation of the circadian clock

Ripperger

Merrow

2011

FEBS Letters

View full text Add to dashboard Cite

a b s t r a c tIn mammals, higher order chromatin structures are critical for downsizing the genome (packaging) so that the nucleus can be small. The adjustable density of chromatin also regulates gene expression, thus this post-genetic molecular mechanism is one of the routes by which phenotype is shaped. Phenotypes that arise without a concomitant mutation of the underlying genome are termed epigenetic phenomena. Here we discuss epigenetic phenomena from histone and DNA modification as it pertains to the dynamic regulatory processes of the circadian clock. Epigenetic phenomena certainly explain some regulatory aspects of the mammalian circadian oscillator. Ó 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Some basic considerations concerning epigenetics and the circadian clockGenetic information is encoded in a relatively simple fashion. An average protein of between 50 and 100 kDa requires between 1.35 and 2.7 Â 10 3 nucleotides (nt). If we accept current estimates of circa 30,000 genes in the mammalian genome, then approximately 5 Â 10 7 nt could represent real protein coding information.This is only about 1-2 percent of the entire amount of DNA present in a cell. This observation invites two simple hypotheses: the extra DNA must be somehow used for shaping the expression of the genome (else it would not survive evolution since so much extra-genic DNA is energy-expensive to build and maintain) and the vast amount of DNA necessitates an efficient packaging mechanism for considerations of both size and organization. The latter point is facilitated by the formation of nucleosomes, which are DNA wrapped around histone octamers [1]. These can then form higher order structures enabling further compaction of DNA [2][3][4]. Most of the mammalian genome is packaged as heterochromatin, which is very dense, but regions that are transcriptionally active are less dense and are referred to as euchromatin. As a simple correlation, the tighter the packaging of the local chromatin structure, the less probable it is that transcription and gene expression will occur. The information on the local chromatin structure can be inherited to the next generation of cells. Thus, the local chromatin structure can exert epigenetic regulation, i.e., it modifies gene expression and consequently specific phenotypes in a heritable fashion without mutation of the DNA sequence. In mammals, the information reflecting the local chromatin structure is embedded in at least two distinct ways: (i) methylation of specific residues of the local histones [3,5], which are evenly distributed to the newly synthesized DNA during DNA replication, or (ii) methylation of specific cytosine residues in the DNA whose patterns can be enzymatically copied [6,7]. Hence, both kinds of marks can be easily copied to the newly synthesized DNA strands and transferred as such to subsequent generations. Note that temporal regulation of epigenetic modifications was initially not taken into consideration, as these marks wer...

show abstract

“…Among these modifications, important downstream effects on chromatin functionalities are proposed to occur upon methylation of specific lysine residues in histone proteins H3 and H4 [2][3][4][5]. Previously, methylation reaction on histone proteins have been thought to be irreversible and removal of the methylation has only been obtained by switching of the elder histone protein with a new molecule [6][7][8]. Recent studies, on the contrary, showed that methylation removal from the lysine residues are not irreversible [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…It has been proposed that, enzymes member of JMJD2 family are closely related with human cancers, thus promising as cancer targets [6,[12][13][14]. Among the members of JMJD2 family, the JMJD2A enzyme is indicated to be involved in human prostate cancer via binding to the Androgen receptor (AR) and Retinoblastoma protein (Rb) thus interfering the functionalities of these proteins [12,15].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Computational analysis of the binding free energy of H3K9me3 peptide to the tandem tudor domains of JMJD2A

Ozboyaci

Keskin

Erman

et al. 2010

2010 5th International Symposium on Health Informatics and Bioinformatics

View full text Add to dashboard Cite

JMJD2A is a histone lysine demethylase enzyme which plays a prominent role in the development of prostate and esophageal squamous cancers. Consisting of a JmjC, a JmjN, two PHD and two tandem tudor domains, JMJD2A recognizes and binds to four different methylated histone peptides: H3K4me3, H4K20me3, H4K20me2 and H3K9me3, via its tudor domains. Of the four histone peptides, only recognition of the H3K4me3 and H4K20me3 by JMJD2A-tudor has been identified. In this study, we investigated the recognition of trimethylated H3K9 by the tandem tudor domains of JMJD2A. Using the molecular dynamics simulations, we performed normal mode and molecular mechanics -Poisson Boltzmann / generalized born -surface area (MM-PB/GB-SA) analysis to find the entropic and enthalpic contributions to binding free energy respectively. We showed that binding of the ligand is mainly driven by favorable van der Waals interactions made after complexation. Our findings suggest that, upon complex formation, H3K9me3 peptide adopts a similar binding mode and the same orientation with H3K4me3 peptide.

show abstract

The JMJD2 members of histone demethylase revisited

Cited by 16 publications

References 43 publications

DNA methyltransferase 3B regulates duration of neural crest production via repression of Sox10

DNA methyltransferase 3B regulates duration of neural crest production via repression of Sox10

Perfect timing: Epigenetic regulation of the circadian clock

Computational analysis of the binding free energy of H3K9me3 peptide to the tandem tudor domains of JMJD2A

Contact Info

Product

Resources

About