Cited by 577Genetics and Neurodevelopmental DisordersEpigenetics and DNA MethylationGenomics and Chromatin Dynamics

The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

Open access

Gabel, Harrison W., Kinde, Benyam, Stroud, Hume, Gilbert, Caitlin S., Harmin, David A., Kastan, Nathaniel R., Hemberg, Martin, Ebert, Daniel H., Greenberg, Michael E.·2015·Nature

DOI 10.1038/nature14319PMC PMC4480648

Open this paper in CoChat — free account

Abstract

Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that has been proposed to function as a transcriptional repressor, but despite numerous mouse studies examining neuronal gene expression in Mecp2 mutants, no clear model has emerged for how MeCP2 protein regulates transcription. Here we identify a genome-wide length-dependent increase in gene expression in MeCP2 mutant mouse models and human RTT brains. We present evidence that MeCP2 represses gene expression by binding to methylated CA sites within long genes, and that in neurons lacking MeCP2, decreasing the expression of long genes attenuates RTT-associated cellular deficits. In addition, we find that long genes as a population are enriched for neuronal functions and selectively expressed in the brain. These findings suggest that mutations in MeCP2 may cause neurological dysfunction by specifically disrupting long gene expression in the brain.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nature14319

Cites

53 of 53 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700
Variations of Box Plots
Mcgill, R., Tukey, J. W., & Larsen, W. A. (1978) · The American Statistician · doi:10.1080/00031305.1978.10479236 · Cited by 2,618
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
Self-citation
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
Wagner, G. P., Kin, K., & Lynch, V. J. (2012) · Theory in Biosciences · doi:10.1007/s12064-012-0162-3 · Cited by 2,085
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072

Show all 53 references

Sorted by citations

Items 301–400 of 577

Where Environment Meets Cognition: A Focus on Two Developmental Intellectual Disability Disorders
Toma, I. D., Manubens-Gil, L., Ossowski, S., & Dierssen, M. (2016) · Neural Plasticity · doi:10.1155/2016/4235898 · Cited by 21
Neural is Fundamental: Neural Stemness as the Ground State of Cell Tumorigenicity and Differentiation Potential
Cao, Y. (2021) · Stem Cell Reviews and Reports · doi:10.1007/s12015-021-10275-y · Cited by 21
Soma‐to‐germline transformation in chromatin‐linked neurodevelopmental disorders?
Bonefas, K. M., & Iwase, S. (2021) · FEBS Journal · doi:10.1111/febs.16196 · Cited by 18
Parallel gene size and isoform expansion of ancient neuronal genes
McCoy, M. J., & Fire, A. Z. (2024) · Current Biology · doi:10.1016/j.cub.2024.02.021 · Cited by 18
Trichostatin A decreases the levels of MeCP2 expression and phosphorylation and increases its chromatin binding affinity
Good, K., de Paz, A. M., Tyagi, M. V., Cheema, M. S., Thambirajah, A. A., Gretzinger, T. L., Stefanelli, G., Chow, R. L., Krupke, O. A., Hendzel, M. J., et al. (2017) · Epigenetics · doi:10.1080/15592294.2017.1380760 · Cited by 18
Length-dependent gene misexpression is associated with Alzheimer’s disease progression
Barbash, S., & Sakmar, T. P. (2017) · Scientific Reports · doi:10.1038/s41598-017-00250-4 · Cited by 19
A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline
Zhu, Q., Stöger, R. J., & Alberio, R. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00024 · Cited by 21
Role of MeCP2 in neurological disorders: current status and future perspectives
Ausió, J. (2017) · Epigenomics · doi:10.2217/epi-2017-0128 · Cited by 18
Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function
Casanova, M., Switala, A. E., Dandamudi, S., Hickman, A. R., Vandenbrink, J. P., Sharp, J. L., Feltus, F. A., & Casanova, M. F. (2019) · Autism Research · doi:10.1002/aur.2112 · Cited by 17
DNA methylation: A mechanism for sustained alteration of KIR4.1 expression following central nervous system insult
Boni, J. L., Kahanovitch, U., Nwaobi, S. E., Floyd, C. L., & Olsen, M. L. (2020) · Glia · doi:10.1002/glia.23797 · Cited by 17
Meta-Analysis Identifies BDNF and Novel Common Genes Differently Altered in Cross-Species Models of Rett Syndrome
Haase, F., Singh, R., Gloss, B., Tam, P., & Gold, W. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231911125 · Cited by 18
Enzymology of Mammalian DNA Methyltransferases
Jurkowska, R. Z., & Jeltsch, A. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_4 · Cited by 18
The Role of MicroRNAs in Cerebellar Development and Autism Spectrum Disorder During Embryogenesis
Constantin, L. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-0220-9 · Cited by 19
Intellectual and Developmental Disabilities Research Centers: A Multidisciplinary Approach to Understand the Pathogenesis of Methyl-CpG Binding Protein 2-related Disorders
Fagiolini, M., Patrizi, A., LeBlanc, J. J., Jin, L., Maezawa, I., Sinnett, S. E., Gray, S. J., Molholm, S., Foxe, J. J., Johnston, M. V., et al. (2020) · Neuroscience · doi:10.1016/j.neuroscience.2020.04.037 · Cited by 16
FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell typesPreprint
Driesche, S. J. V., Sawicka, K., Zhang, C., Hung, K. Y. S., Park, C. Y., Fak, J. J., Yang, C., Darnell, R. B., & Darnell, J. C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/762500 · Cited by 17
Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modelingPreprint
Novak, R., Lin, T., Kaushal, S., Sperry, M. M., Vigneault, F., Gardner, E., Loomba, S., Shcherbina, K., Keshari, V., Dinis, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.20.485056 · Cited by 17
MeCP2 and non-CG DNA methylation stabilize the expression of long genes that distinguish closely related neuron types
Moore, J. R., Nemera, M. T., D’Souza, R. D., Hamagami, N., Clemens, A. W., Beard, D. C., Urman, A., Razia, Y., Mendoza, V. R., Law, T. E., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01947-w · Cited by 21
Self-citation
Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain
Ross, S. E., Hesselson, D., & Bogdanović, O. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.643603 · Cited by 16
Cell type-specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder
Jin, Y., Su, K., Kong, H. E., Ma, W., Wang, Z., Li, Y., Li, R., Allen, E. G., Wu, H., & Jin, P. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac189 · Cited by 16
MeCP2 ubiquitination and sumoylation, in search of a function
Kalani, L., Kim, B.-H., Vincent, J. B., & Ausió, J. (2023) · Human Molecular Genetics · doi:10.1093/hmg/ddad150 · Cited by 14
A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder
Kuang, H., Li, Y., Wang, Y., Shi, M., Duan, R., Xiao, Q., She, H., Liu, Y., Liang, Q., Teng, Y., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113445 · Cited by 15
RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease
Kuldell, J. C., & Kaplan, C. D. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168770 · Cited by 16
Interaction of methyl-CpG-binding protein 2 (MeCP2) with distinct enhancers in the mouse cortex
Mishra, G. P., Sun, E. X., Chin, T., Eckhardt, M., Greenberg, M. E., & Stroud, H. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01808-y · Cited by 15
Self-citation
Experience‐dependent transcriptional regulation in juvenile brain development
Sakai, A., & Sugiyama, S. (2018) · Development Growth & Differentiation · doi:10.1111/dgd.12571 · Cited by 15
Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing
Chhatbar, K., Cholewa-Waclaw, J., Shah, R., Bird, A. P., & Sanguinetti, G. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009087 · Cited by 16
Modeling Rett Syndrome with Human Pluripotent Stem Cells: Mechanistic Outcomes and Future Clinical Perspectives
Gomes, A. R., Fernandes, T. G., Cabral, J. M. S., & Diogo, M. M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073751 · Cited by 15
Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system
Jaura, R., Yeh, S.-Y., Montanera, K. N., Ialongo, A., Anwar, Z., Lu, Y., Puwakdandawa, K., & Rhee, H. S. (2022) · Nature Communications · doi:10.1038/s41467-022-30192-z · Cited by 19
MeCP2, A Modulator of Neuronal Chromatin Organization Involved in Rett Syndrome
de Paz, A. M., & Ausió, J. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-53889-1_1 · Cited by 15
The role of MeCP2 in learning and memoryPreprint
Robinson, H., & Pozzo‐Miller, L. D. (2019) · Learning & Memory · doi:10.1101/lm.048876.118 · Cited by 16
Mapping recurrent mosaic copy number variation in human neurons
Sun, C., Kathuria, K., Emery, S. B., Kim, B.-J., Burbulis, I. E., Shin, J. H., Brain Somatic Mosaicism Network, Gleeson, J. G., Breuss, M. W., Yang, X., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48392-0 · Cited by 21
mRNA isoform balance in neuronal development and disease
LaForce, G. R., Philippidou, P., & Schaffer, A. E. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1762 · Cited by 15
A genomic view on epilepsy and autism candidate genes
Jabbari, K., & Nürnberg, P. (2016) · Genomics · doi:10.1016/j.ygeno.2016.01.001 · Cited by 15
Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo
Connelly, J. C., Cholewa-Waclaw, J., Webb, S., Steccanella, V., Waclaw, B., & Bird, A. P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa102 · Cited by 14
Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions
Cheema, M. S., Good, K., Kim, B., Soufari, H., O’Sullivan, C., Freeman, M. E., Stefanelli, G., Rivera-Casas, C., Zengeler, K. E., Kennedy, A. J., et al. (2020) · Cells · doi:10.3390/cells9051167 · Cited by 15
DNMT1-mediated regulation of somatostatin-positive interneuron migration impacts cortical architecture and function
Reichard, J., Wolff, P., Xie, S., Zuo, K., Fullio, C. L., Du, J., Graff, S., Linde, J., Yildiz, C. B., Pitschelatow, G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62114-0 · Cited by 17
Synergistic suppression of BDNF via epigenetic mechanism deteriorating learning and memory impairment caused by Mn and Pb co-exposure
Wei, L., He, H., Yang, S., Shi, Q., Wang, X., Huang, L., Lu, J., Shen, Y., Zhi, K., Xiang, J., et al. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.116365 · Cited by 13
MeCP2 interacts with the super elongation complex to regulate transcription
Sonn, J. Y., Kim, W., Iwanaszko, M., Aoi, Y., Li, Y., Qi, G., Parkitny, L., Brissette, J. L., Weiner, L., Botas, J., et al. (2025) · Science Advances · doi:10.1126/sciadv.adt5937 · Cited by 14
Phenotypic Subtyping and Re-Analysis of Existing Methylation Data from Autistic Probands in Simplex Families Reveal ASD Subtype-Associated Differentially Methylated Genes and Biological Functions
Lee, E. C., & Hu, V. W. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186877 · Cited by 13
MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function
Bajikar, S. S., Anderson, A. G., Zhou, J., Durham, M. A., Trostle, A. J., Wan, Y., Liu, Z., & Zoghbi, H. Y. (2023) · eLife · doi:10.7554/elife.83806 · Cited by 14
MeCP2 represses the activity of topoisomerase IIβ in long neuronal genes
Nettles, S. A., Ikeuchi, Y., Lefton, K. B., Abbasi, L., Erickson, A., Agwu, C., Papouin, T., Bonni, A., & Gabel, H. W. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113538 · Cited by 15
Self-citation
Paradoxical physiological responses to propranolol in a Rett syndrome patient: a case report
Santosh, P., Bell, L., Lievesley, K., Singh, J., & Fiori, F. (2016) · BMC Pediatrics · doi:10.1186/s12887-016-0734-3 · Cited by 13
Perinatal exposure to the SSRI paroxetine alters the methylome landscape of the developing dentate gyrus
Glover, M. E., McCoy, C. R., Shupe, E. A., Unroe, K. A., Jackson, N. L., & Clinton, S. M. (2018) · European Journal of Neuroscience · doi:10.1111/ejn.14315 · Cited by 14
Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies
Wu, N., Wang, Y., Jia, J.-Y., Pan, Y.-H., & Yuan, X. (2021) · Neuroscience Bulletin · doi:10.1007/s12264-021-00770-0 · Cited by 13
Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Vacca, M., Tripathi, K. P., Speranza, L., Cigliano, R. A., Scalabrì, F., Marracino, F., Madonna, M., Sanseverino, W., Perrone‐Capano, C., Guarracino, M. R., et al. (2016) · BMC Bioinformatics · doi:10.1186/s12859-015-0859-7 · Cited by 13
Exceptional epigenetics in the brain
Luo, C., & Ecker, J. R. (2015) · Science · doi:10.1126/science.aac5832 · Cited by 12
Epigenetics in rare neurological diseases
Roberts, C.-T., Arezoumand, K. S., Shahib, A. K., Davie, J., & Rastegar, M. (2024) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1413248 · Cited by 16
A Case of MECP2 Duplication Syndrome with Gonadotropin-Dependent Precocious Puberty
Tsuji‐Hosokawa, A., Matsuda, N., Kurosawa, K., Kashimada, K., & Morio, T. (2016) · Hormone Research in Paediatrics · doi:10.1159/000449222 · Cited by 12
Circulating microRNA associated with future relapse status in major depressive disorder
Li, Q. S., Galbraith, D., Morrison, R. L., Trivedi, M. H., & Drevets, W. C. (2022) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2022.937360 · Cited by 12
Reversibility and therapeutic development for neurodevelopmental disorders, insights from genetic animal models
Megagiannis, P., Suresh, R., Rouleau, G. A., & Zhou, Y. (2022) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2022.114562 · Cited by 12
Proteins That Read DNA Methylation
Liu, K., Shimbo, T., Song, X., Wade, P. A., & Min, J. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_11 · Cited by 13
Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein
Watts, M. E., Oksanen, M., Lejerkrans, S., Mastropasqua, F., Gorospe, M., & Tammimies, K. (2023) · BMC Biology · doi:10.1186/s12915-023-01627-w · Cited by 14
DISMISS: detection of stranded methylation in MeDIP-Seq data
Niazi, U. H. K., Geyer, K. K., Vickers, M. J., Hoffmann, K. F., & Swain, M. T. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1158-7 · Cited by 13
ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine
Schlosberg, C., Wu, D. Y., Gabel, H. W., & Edwards, J. R. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz001 · Cited by 13
Self-citation
Multifaceted behavior of PEST sequence enriched nuclear proteins in cancer biology and role in gene therapy
Sarfraz, M., Afzal, A., Khattak, S., Saddozai, U. A. K., Li, H., Zhang, Q., Madni, A., Haleem, K. S., Duan, S., Wu, D., et al. (2020) · Journal of Cellular Physiology · doi:10.1002/jcp.30011 · Cited by 14
Identification of Novel MeCP2 Cancer-Associated Target Genes and Post-Translational Modifications
Castro‐Piedras, I., Vartak, D., Sharma, M., Pandey, S., Casas, L., Molehin, D., Rasha, F. A., Fokar, M., Nichols, J., Almodóvar, S., et al. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.576362 · Cited by 12
A role for human senataxin in contending with pausing and backtracking during transcript elongation
Han, Z., Fu, S., Johansen, J. V., Martínez, D. L., Lou, J., Boissière, T., He, D., Blears, D., Olthof, A. M., Dirac-Svejstrup, A. B., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.10.019 · Cited by 11
Development of the Tailored Rett Intervention and Assessment Longitudinal (TRIAL) database and the Rett Evaluation of Symptoms and Treatments (REST) Questionnaire
Santosh, P., Lievesley, K., Fiori, F., & Singh, J. (2017) · BMJ Open · doi:10.1136/bmjopen-2016-015342 · Cited by 11
MeCP2 and CTCF: enhancing the cross-talk of silencers
Ausió, J., & Georgel, P. T. (2017) · Biochemistry and Cell Biology · doi:10.1139/bcb-2017-0147 · Cited by 11
The MECP2‐TRD domain interacts with the DNMT3A‐ADD domain at the H3 ‐tail binding site
Kunert, S., Linhard, V. L., Weirich, S., Choudalakis, M., Osswald, F., Krämer, L., Köhler, A., Bröhm, A., Wollenhaupt, J., Schwalbe, H., et al. (2022) · Protein Science · doi:10.1002/pro.4542 · Cited by 12
Breaks in the brain
Glover, T. W., & Wilson, T. E. (2016) · Nature · doi:10.1038/nature17316 · Cited by 11
MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition
Khrapunov, S. N., Tao, Y., Cheng, H., Padlan, C., Harris, R., Galanopoulou, A. S., Greally, J. M., Girvin, M. E., & Brenowitz, M. D. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00451 · Cited by 11
Genome‐wide transcriptomic and proteomic studies of Rett syndrome mouse models identify common signaling pathways and cellular functions as potential therapeutic targets
Krishnaraj, R. R., Haase, F., Coorey, B., Luca, E., Wong, I., Boyling, A., Ellaway, C., Christodoulou, J., & Gold, W. A. (2019) · Human Mutation · doi:10.1002/humu.23887 · Cited by 12
Critical regulation of a NDIME/MEF2C axis in embryonic stem cell neural differentiation and autism
Bai, M., Ye, D., Guo, X., Xi, J., Liu, N., Wu, Y., Jia, W., Wang, G., Chen, W., Li, G., et al. (2020) · EMBO Reports · doi:10.15252/embr.202050283 · Cited by 12
Simultaneous and Sensitive Detection of Multisite 5-Methylcytosine Including Non-CpG Sites at Single-5mC-Resolution
Rao, S., Chen, Y., Hong, T., He, Z., Guo, S., Lai, H., Guo, G., Du, Y., & Zhou, X. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b02625 · Cited by 11
Cell-type specialization in the brain is encoded by specific long-range chromatin topologiesPreprint
Winick‐Ng, W., Kukalev, A., Harabula, I., Redondo, L. Z., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.02.020990 · Cited by 11
Vitamin D modulates cortical transcriptome and behavioral phenotypes in an Mecp2 heterozygous Rett syndrome mouse model
Ribeiro, M. C., & MacDonald, J. L. (2022) · Neurobiology of Disease · doi:10.1016/j.nbd.2022.105636 · Cited by 10
Fate erasure logic of gene networks underlying direct neuronal conversion of somatic cells by microRNAs
Cates, K., Yuan, L., Yang, Y., & Yoo, A. S. J. (2025) · Cell Reports · doi:10.1016/j.celrep.2024.115153 · Cited by 11
A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence
Chia, J. Y., Tan, W. S., Ng, C. L., Hu, N., Foo, H. L., & Ho, K. L. (2016) · Scientific Reports · doi:10.1038/srep31210 · Cited by 10
DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons
Marion‐Poll, L., Roussarie, J.-P., Taing, L., Dard-Dascot, C., Servant, N., Jaszczyszyn, Y., Jordi, E., Mulugeta, E., Hervé, D., Bourc’his, D., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04269-w · Cited by 11
Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models
Rodrigues, D. C., Mufteev, M., Yuki, K. E., Narula, A., Wei, W., Piekna, A., Liu, J., Pasceri, P., Rissland, O. S., Wilson, M. D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37339-6 · Cited by 10
Selective repression of SINE transcription by RNA polymerase III
Varshney, D., Vavrova-Anderson, J., Oler, A. J., Cairns, B. R., & White, R. J. (2015) · Mobile Genetic Elements · doi:10.1080/2159256x.2015.1096997 · Cited by 10
Primetime for Learning Genes
Keifer, J. (2017) · Genes · doi:10.3390/genes8020069 · Cited by 10
Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampusPreprint
Heffel, M. G., Zhou, J., Zhang, Y., Lee, D.-S., Hou, K., Pastor-Alonso, O., Abuhanna, K. D., Schmitt, A. D., Li, T., Haeussler, M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.07.511350 · Cited by 10
Topoisomerases in Immune Cell Development and Function
Muralidhara, P., Kumar, A., Chaurasia, M. K., & Bansal, K. (2023) · The Journal of Immunology · doi:10.4049/jimmunol.2200650 · Cited by 9
Molecular Insights into Neurological Regression with a Focus on Rett Syndrome—A Narrative Review
Singh, J., & Santosh, P. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26115361 · Cited by 10
Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications
Nickel, G. A., & Diehl, K. L. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.1c00794 · Cited by 9
NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome
Soares, E. S., Velasco, C. D., Tarrasón, A., Soler, M., Srinivas, T., Setién, F., Oliveira-Mateos, C., Casado-Peláez, M., Martinez‐Verbo, L., Armstrong, J., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf074 · Cited by 9
Early Postnatal Treatment with Valproate Induces Gad1 Promoter Remodeling in the Brain and Reduces Apnea Episodes in Mecp2-Null Mice
Ishiyama, M., Tamura, S., Ito, H., Takei, H., Hoshi, M., Asano, M., Itoh, M., & Shirakawa, T. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20205177 · Cited by 10
Differentiating Females with Rett Syndrome and Those with Multi-Comorbid Autism Spectrum Disorder Using Physiological Biomarkers: A Novel Approach
Iakovidou, N. D., Lanzarini, E., Singh, J., Fiori, F., & Santosh, P. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9092842 · Cited by 9
A prelude to the proximity interaction mapping of CXXC5
Ayaz, G., Turan, G., Olgun, Ç. E., Kars, G., Karakaya, B., Yavuz, K., Demiralay, Ö. D., Can, T., Muyan, M., & Yaşar, P. (2021) · Scientific Reports · doi:10.1038/s41598-021-97060-6 · Cited by 9
Spatial organizations of heterochromatin underpin nuclear structural integrity of ventricular cardiomyocytes against mechanical stress
Fujiwara, K., Inoue, T., Kimoto, A., Zixian, J., Tokuhiro, K., Yasukochi, Y., Akama, T. O., Cai, C., Shiojima, I., Kimurâ, H., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115048 · Cited by 8
AI-enabled drug prediction and gene network analysis reveal therapeutic use of vorinostat for Rett Syndrome in preclinical models
Novak, R., Lin, T., Kaushal, S., Sperry, M. M., Vigneault, F., Gardner, E., Loomba, S., Shcherbina, K., Keshari, V., Dinis, A., et al. (2025) · Communications Medicine · doi:10.1038/s43856-025-00975-8 · Cited by 25
Mecp2 deletion results in profound alterations of developmental and adult functional connectivity
Rahn, R. M., Yen, A., Chen, S., Gaines, S. H., Bice, A. R., Brier, L. M., Swift, R. G., Lee, L., Maloney, S. E., Culver, J. P., et al. (2023) · Cerebral Cortex · doi:10.1093/cercor/bhad050 · Cited by 9
MBD5 regulates NMDA receptor expression and seizures by inhibiting Stat1 transcription
Tang, F.-L., Zhang, X., Ke, P., Liu, J., Zhang, Z., Hu, D., Gu, J., Zhang, H., Guo, H., Zang, Q.-W., et al. (2023) · Neurobiology of Disease · doi:10.1016/j.nbd.2023.106103 · Cited by 8
Wild‐type MECP2 expression coincides with age‐dependent sensory phenotypes in a female mouse model for Rett syndrome
Mykins, M., Layo-Carris, D. E., Dunn, L. R., Skinner, D. W., McBryar, A. H., Perez, S., Shultz, T. R., Willems, A. R., Lau, B. Y. B., Hong, T., et al. (2023) · Journal of Neuroscience Research · doi:10.1002/jnr.25190 · Cited by 9
Nuclear and Cytoplasmatic Players in Mitochondria-Related CNS Disorders: Chromatin Modifications and Subcellular Trafficking
Gasparotto, M., Lee, Y.-S., Palazzi, A., Vacca, M., & Filippini, F. (2022) · Biomolecules · doi:10.3390/biom12050625 · Cited by 8
MeCP2 loss‐of‐function dysregulates microRNAs regionally and disrupts excitatory/inhibitory synaptic transmission balance
Horvath, P. M., Piazza, M. K., Kavalali, E. T., & Monteggia, L. M. (2022) · Hippocampus · doi:10.1002/hipo.23455 · Cited by 10
Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development
Martin, S., Poppe, D., Olova, N. N., O’Leary, C. J., Ivanova, E., Pflueger, J., Dechka, J., Simmons, R. K., Cooper, H. M., Reik, W., et al. (2023) · Genes · doi:10.3390/genes14050957 · Cited by 9
A Shortcut to Activity-Dependent Transcription
Sharma, N., Gabel, H. W., & Greenberg, M. E. (2015) · Cell · doi:10.1016/j.cell.2015.06.009 · Cited by 8
Self-citation
Psychopharmacology of Neurodevelopmental Disorders in Children
Singh, J., & Santosh, P. (2016) · Springer eBooks · doi:10.1007/978-81-322-3619-1_18 · Cited by 8
Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiencyPreprint
Dugger, S. A., Dhindsa, R. S., Sampaio, G. L. D. A., Ressler, A. K., Rafikian, E. E., Petri, S., Letts, V. A., Teoh, J. J., Ye, J., Colombo, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.01.072512 · Cited by 8
The role of prenatal choline and its impact on neurodevelopmental disorders
Mujica-Coopman, M. F., Paules, E. M., & Trujillo‐Gonzalez, I. (2024) · Frontiers in Nutrition · doi:10.3389/fnut.2024.1463983 · Cited by 9
DNMT3b-mediated CpA methylation facilitates REST binding and gene silencing and exacerbates hippocampal demyelination in diabetic mice
Yao, T.-F., Wang, Z., Sun, L., Yu, S., Yu, H., Yang, Z.-Z., Li, W., Niu, L., Sun, D., Shi, Y.-H., et al. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.108137 · Cited by 10
Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders
Baker, B. H., Zhang, S.-Y., Simon, J. M., McLarnan, S. M., Chung, W., & Pearson, B. L. (2021) · bioRxiv · doi:10.3389/fnins.2023.1106573 · Cited by 3
From Environment to Gene Expression: Epigenetic Methylations and One-Carbon Metabolism in Amyotrophic Lateral Sclerosis
Hernán-Godoy, M., & Rouaux, C. (2024) · Cells · doi:10.3390/cells13110967 · Cited by 8
Catalytic Mechanism of the Bacterial Non-Heme Fe(II) and 2-Oxoglutarate Dependent Enzyme AlkB with Single-Stranded DNA Containing Complex Guanine Adducts
Melayikandy, S., Krishnan, A., Varghese, A., Rifayee, S. B. J. S., Waheed, S. O., Ramanan, R., Li, D., Christov, C. Z., & Karabencheva‐Christova, T. G. (2025) · Inorganic Chemistry · doi:10.1021/acs.inorgchem.5c02176 · Cited by 7
Mega-enhancers compartmentalize transcriptionally active long genes in the brain
Zhao, Z., Parra, O. A. P., Fujita, S.-I., Musella, F., Alvarado, N. J. S., Alber, F., Yang, Y., & Yamada, T. (2026) · Nature Cell Biology · doi:10.1038/s41556-026-02043-2 · Cited by 7
MECP2 promotes migration and invasion of gastric cancer cells via modulating the Notch1/c-Myc/mTOR signaling pathways by suppressing FBXW7 transcriptionPreprint
Zhao, L., Wang, X., Yang, J., Jiang, Q., Zhang, J., Qin, Y., Wang, L., Liu, L., Ni, L., Tong, D., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-48700/v1 · Cited by 8
Evidence Synthesis of Gene Therapy and Gene Editing from Different Disorders—Implications for Individuals with Rett Syndrome: A Systematic Review
Singh, J., Goodman-Vincent, E., & Santosh, P. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24109023 · Cited by 8
Rett Syndrome: A Tale of Altered Genetics, Synaptic Plasticity, and Neurodevelopmental Dynamics
Oluigbo, D. (2023) · Cureus · doi:10.7759/cureus.41555 · Cited by 8

Authors: Gabel, H. W., Kinde, B., Stroud, H., Gilbert, C. S., Harmin, D. A., Kastan, N. R., Hemberg, M., Ebert, D. H., & Greenberg, M. E.
Affiliations: Harvard University (US)
Boston Children's Hospital (US)
Corresponding author: Greenberg, Michael E.
ORCID: Gabel, Harrison W.
Kinde, Benyam
Stroud, Hume
Kastan, Nathaniel R.
Hemberg, Martin
Greenberg, Michael E.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2015-03-11
Volume: 522
Issue: 7554
Pages: 89-93
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature14319
PMC: PMC4480648
OpenAlex: W2035016973
Cited by: 569
References: 53
Citations by year: 2026: 29 · 2025: 42 · 2024: 41 · 2023: 39 · 2022: 50 · 2021: 49 · 2020: 51 · 2019: 52 · 2018: 55 · 2017: 61 · 2016: 67 · 2015: 31
FWCI: 48.74
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute
National Institutes of Health (5r01ns048276-15)
National Institute of General Medical Sciences (T32GM007753)
National Institute of Neurological Disorders and Stroke (R01-NS-048276, 1R01NS048276)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (P30HD018655)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: Rett syndrome, MeCP2, DNA methylation, gene length, gene expression inhibition, neuronal gene expression, autism spectrum disorder, transcriptional regulation, brain
MeSH terms: DNA Methyltransferase 3A, Animals, Base Sequence, Brain, Disease Models, Animal, DNA (Cytosine-5-)-Methyltransferases, Female, Gene Expression Regulation, Humans, Male, Molecular Sequence Data, Mutation, Neurons, Rett Syndrome, DNA Methylation, Mice, Methyl-CpG-Binding Protein 2

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks