Recent Papers

PAPERS PRESENTED IN EPIGENETICS JOURNAL CLUB

Fall 2016:

MTHFD1 Controls DNA methylation in Arabidopsis: http://www.nature.com/articles/ncomms11640.pdf

Spring 2016:

H. Strickfaden et al. Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation.  J Biol. Chem. 291(4):1789-802; 2016.

M. Dieuleveult et al.  Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells.  Nature 530(7588):113-6; 2016

M. Yu et al.  RNA polymerase II–associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II.  Science 350(6266):1383-6; 2015

Y. Matsumura et al. H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation.  Molec Cell 60:584; 2015.

D. Zhao et al.  SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination.  Nature 529:48; 2016.

 

Fall 2015:

Q. Zhang et al. Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6.  Nature 525(7569):389-93; 2015.

Y. Wei et al. Enriched Environment-induced Maternal Weight Loss Reprograms Metabolic Gene Expression in Mouse Offspring.  J Biol. Chem. 290:4604-19; 2015.

S. Duttke et al.  Human promoters are intrinsically directional.  Molec. Cell  57:674; 2015.

F. Lai et al.  Integrator mediates the biogenesis of enhancer RNAs.  Nature 525:399; 2015.

J. Zhu et al. Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth.  Nature 525(7568):206-11; 2015.

Rotem et al.  Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.  Nature Biotech. 33:1165; 2015.

 

Spring 2015:

V. Mutskov et al. Early Life Physical Activity Reverses Metabolic and Foxo1 Epigenetic Misregulation Induced by Gestational Sleep Disturbance.  Am J Physiol Regul Integr Comp Physiol 308(5):R419-30; 2015

V. Liyanage et al. Ethanol deregulates Mecp2/MeCP2 in differentiating neural stem cells via interplay between 5-methylcytosine and 5-hydroxymethylcytosine at the Mecp2 regulatory elements. Exp Neurol. 265:102; 2015.

F. Neri et al. Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.  Cell Reps. 10:674; 2015.

Yearim et al. HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing. Cell Reps.  10:1122; 2015.

Moussaieff et al. Glycolysis-Mediated Changes in Acetyl-CoA and Histone Acetylation Control the Early Differentiation of Embryonic Stem Cells.  Cell Metab.  21:392; 2015.

J. Guo et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.  Nature Neurosci. 17:215; 2014.

LJ Core et al.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.  Nat Genet. 46(12):1311-20; 2014.

 

Fall 2014:

L. Wen et al.  Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.  Genome Biol. 15:R49; 2014.

H. Wu et al.  Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers.  PLoS Genet 10(9):e1004610; 2014.

N.P. Blackledge et al.  Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation.  Cell 157(6):1445-59; 2014.

H. Guo et al. The DNA methylation landscape of human early embryos.  Nature 511:606; 2014.

Smith et al.  DNA methylation dynamics of the human preimplantation embryo.  Nature 511:611; 2014.

P. Batista et al. m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells.  Cell Stem Cell 15(6):707-19; 2014.

K. Schaukowitch et al. Enhancer RNA Facilitates NELF Release from Immediate Early Genes.  Molec Cell 56:29;2014.

V. Hovestadt et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing.  Nature 510:537; 2014.

L. Gaydos et al. H3K27me and PRC2 transmit a memory of repression across generations and during development.  Science 345:1515; 2014.

 

Spring 2014:

S. Kaneko et al. Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin. Molec Cell  53:290; 2014.

R. Massart et al.  The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes.  Transl. Psychiatry 4:3347; 2014.

G. Andrey et al.  A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs.  Science 340(6137): 1234167; 2013.

Di Ruscio et al.  DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 503:371; 2013.

R. Ostuni et al.  Latent enhancers activated by stimulation in differentiated cells. Cell 152:157; 2013.

F. Neri et al.  Dnmt3L antagonizes DNA methylation at bivalent promoters and favors DNA methylation at gene bodies in ESCs. Cell 155:121; 2013.

D. Colak et al.  Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome.  Science 343:1002; 2014.

J. Loven et al.  Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome.  Cell 153:320; 2013.

X. Wang et al.  Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome.  Nature 505:117; 2014.

S. Cortijo et al.  Mapping the Epigenetic Basis of Complex Traits.  Science 343:1145; 2014.

L. Wang et al.  CARM1 Methylates Chromatin Remodeling Factor BAF155 to Enhance Tumor Progression and Metastasis.  Cancer Cell 25:21; 2014.

S. Horvath.  DNA methylation age of human tissues and cell types. Genome Biol. 14:R115; 2013.

 

Fall 2013:

R. Lister et al.  Global Epigenomic Reconfiguration During Mammalian Brain Development.  Science 341 (6146):1237905; 2013.

MJ Ziller et al.  Charting a dynamic DNA methylation landscape of the human genome.  Nature 500(7463):477-81; 2013.

W. Whyte et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes. Cell 153:307; 2013.

J. Engreitz et al.  The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Science 341(6147):1237973; 2013.

CS Park et al.  Genome-wide analysis of H4K5 acetylation associated with fear memory in mice.  BMC Genomics 14:539; 2013.

C. Lorthongpanich et al.  Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos.  Science 341:1110; 2013.

FM Vassoler et al.  Epigenetic inheritance of a cocaine-resistance phenotype.  Nature Neurosci.  (1):42-7; 2013.