MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation

Vijay Swahari; Ayumi Nakamura; Emilie Hollville; Hume Stroud; Jeremy M. Simon; Travis S. Ptacek; Matthew V. Beck; Cornelius Flowers; Jiami Guo; Charlotte Plestant; Jie Liang; C. Lisa Kurtz; Matt Kanke; Scott M. Hammond; You Wen He; E. S. Anton; Praveen Sethupathy; Sheryl S. Moy; Michael E. Greenberg; Mohanish Deshmukh

doi:10.1016/j.celrep.2021.108946

MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation

Vijay Swahari^* (Corresponding Author), Ayumi Nakamura, Emilie Hollville, Hume Stroud, Jeremy M. Simon, Travis S. Ptacek, Matthew V. Beck, Cornelius Flowers, Jiami Guo, Charlotte Plestant, Jie Liang, C. Lisa Kurtz, Matt Kanke, Scott M. Hammond, You Wen He, E. S. Anton, Praveen Sethupathy, Sheryl S. Moy, Michael E. Greenberg, Mohanish Deshmukh^* (Corresponding Author)

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

20 Citations (Scopus)

Abstract

Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.

Original language	English
Article number	108946
Journal	Cell Reports
Volume	35
Issue number	1
Early online date	6 Apr 2021
DOIs	https://doi.org/10.1016/j.celrep.2021.108946
Publication status	Published - 6 Apr 2021

Bibliographical note

Acknowledgments
We thank the members of the Deshmukh Lab for critical review of this manuscript. We also acknowledge Dr. Natallia Riddick, Viktoriya Nikolova, and Dr. Kara Agster at the UNC Mouse Behavioral Phenotyping Laboratory, for their technical assistance. We thank Mervi Eeva, Ying Li, and Bentley Midkiff at the UNC Translational Pathology Laboratory for expert technical assistance. We also appreciate the technical assistance provided by Janice Weaver and Carolyn Suitt at the UNC Animal Histopathology and the Center for Gastrointestinal Biology and Disease (CGIBD), respectively. The graphical abstract was created partly with BioRender.com. This work was supported by NIH, United States (GM118331 and AG055304 to M.D.). H.S. is a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation, United States (DRG-2194-14). J.M.S. and T.S.P. were supported by The Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD079124) and NINDS (P30NS045892) of United States. The UNC Mouse Behavioral Phenotyping Laboratory is supported by a grant from the National Institute of Child Health and Human Development (NICHD), United States (U54-HD079124). The UNC Translational Pathology Laboratory is supported in part by grants from the NCI (5P30CA016086-42), NIH (U54-CA156733), NIEHS (5 P30 ES010126-17), UCRF, and NCBT (2015-IDG-1007) of United States.

Author contributions
V.S., A.N., and E.H. conducted most of the experiments with help as described here. H.S. and M.E.G. performed the whole-genome bisulfite sequencing and its analyses. J.M.S. and T.S.P. analyzed all RNA-seq data. C.L.K., M.K., P.S., and S.M.H. performed small RNA-seq and miRHub analysis. C.P., J.G., and E.A. helped with imaging and analysis of immunohistochemical stains. C.F. and M.B. helped manage the mouse colony. J.L. and Y.-W.H. generated the miR-29-floxed mice. S.M. conducted and analyzed many of the neurobehavioral assessments. V.S., M.E.G., and M.D. outlined the project. M.D. supervised the project. V.S., A.N., E.H., and M.D. produced the final version of the manuscript.

Data Availability Statement

Supplemental information can be found online at https://doi.org/10.1016/j.celrep.2021.108946.

Keywords

autism
CH methylation
DNMT3A
epilepsy
MeCP2
miR-29
miRNA
neurodevelopmental disorders
non-CG methylation
seizures

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Swahari_etal_CR_MicroRNA-29_is_an_VoR
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Cite this

Swahari, V., Nakamura, A., Hollville, E., Stroud, H., Simon, J. M., Ptacek, T. S., Beck, M. V., Flowers, C., Guo, J., Plestant, C., Liang, J., Kurtz, C. L., Kanke, M., Hammond, S. M., He, Y. W., Anton, E. S., Sethupathy, P., Moy, S. S., Greenberg, M. E., & Deshmukh, M. (2021). MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Reports, 35(1), Article 108946. https://doi.org/10.1016/j.celrep.2021.108946

Swahari, V, Nakamura, A, Hollville, E, Stroud, H, Simon, JM, Ptacek, TS, Beck, MV, Flowers, C, Guo, J, Plestant, C, Liang, J, Kurtz, CL, Kanke, M, Hammond, SM, He, YW, Anton, ES, Sethupathy, P, Moy, SS, Greenberg, ME & Deshmukh, M 2021, 'MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation', Cell Reports, vol. 35, no. 1, 108946. https://doi.org/10.1016/j.celrep.2021.108946

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title = "MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation",

abstract = "Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.",

keywords = "autism, CH methylation, DNMT3A, epilepsy, MeCP2, miR-29, miRNA, neurodevelopmental disorders, non-CG methylation, seizures",

author = "Vijay Swahari and Ayumi Nakamura and Emilie Hollville and Hume Stroud and Simon, {Jeremy M.} and Ptacek, {Travis S.} and Beck, {Matthew V.} and Cornelius Flowers and Jiami Guo and Charlotte Plestant and Jie Liang and Kurtz, {C. Lisa} and Matt Kanke and Hammond, {Scott M.} and He, {You Wen} and Anton, {E. S.} and Praveen Sethupathy and Moy, {Sheryl S.} and Greenberg, {Michael E.} and Mohanish Deshmukh",

note = "Acknowledgments We thank the members of the Deshmukh Lab for critical review of this manuscript. We also acknowledge Dr. Natallia Riddick, Viktoriya Nikolova, and Dr. Kara Agster at the UNC Mouse Behavioral Phenotyping Laboratory, for their technical assistance. We thank Mervi Eeva, Ying Li, and Bentley Midkiff at the UNC Translational Pathology Laboratory for expert technical assistance. We also appreciate the technical assistance provided by Janice Weaver and Carolyn Suitt at the UNC Animal Histopathology and the Center for Gastrointestinal Biology and Disease (CGIBD), respectively. The graphical abstract was created partly with BioRender.com. This work was supported by NIH, United States (GM118331 and AG055304 to M.D.). H.S. is a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation, United States (DRG-2194-14). J.M.S. and T.S.P. were supported by The Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD079124) and NINDS (P30NS045892) of United States. The UNC Mouse Behavioral Phenotyping Laboratory is supported by a grant from the National Institute of Child Health and Human Development (NICHD), United States (U54-HD079124). The UNC Translational Pathology Laboratory is supported in part by grants from the NCI (5P30CA016086-42), NIH (U54-CA156733), NIEHS (5 P30 ES010126-17), UCRF, and NCBT (2015-IDG-1007) of United States. Author contributions V.S., A.N., and E.H. conducted most of the experiments with help as described here. H.S. and M.E.G. performed the whole-genome bisulfite sequencing and its analyses. J.M.S. and T.S.P. analyzed all RNA-seq data. C.L.K., M.K., P.S., and S.M.H. performed small RNA-seq and miRHub analysis. C.P., J.G., and E.A. helped with imaging and analysis of immunohistochemical stains. C.F. and M.B. helped manage the mouse colony. J.L. and Y.-W.H. generated the miR-29-floxed mice. S.M. conducted and analyzed many of the neurobehavioral assessments. V.S., M.E.G., and M.D. outlined the project. M.D. supervised the project. V.S., A.N., E.H., and M.D. produced the final version of the manuscript.",

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T1 - MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation

AU - Swahari, Vijay

AU - Nakamura, Ayumi

AU - Hollville, Emilie

AU - Stroud, Hume

AU - Simon, Jeremy M.

AU - Ptacek, Travis S.

AU - Beck, Matthew V.

AU - Flowers, Cornelius

AU - Guo, Jiami

AU - Plestant, Charlotte

AU - Liang, Jie

AU - Kurtz, C. Lisa

AU - Kanke, Matt

AU - Hammond, Scott M.

AU - He, You Wen

AU - Anton, E. S.

AU - Sethupathy, Praveen

AU - Moy, Sheryl S.

AU - Greenberg, Michael E.

AU - Deshmukh, Mohanish

N1 - Acknowledgments We thank the members of the Deshmukh Lab for critical review of this manuscript. We also acknowledge Dr. Natallia Riddick, Viktoriya Nikolova, and Dr. Kara Agster at the UNC Mouse Behavioral Phenotyping Laboratory, for their technical assistance. We thank Mervi Eeva, Ying Li, and Bentley Midkiff at the UNC Translational Pathology Laboratory for expert technical assistance. We also appreciate the technical assistance provided by Janice Weaver and Carolyn Suitt at the UNC Animal Histopathology and the Center for Gastrointestinal Biology and Disease (CGIBD), respectively. The graphical abstract was created partly with BioRender.com. This work was supported by NIH, United States (GM118331 and AG055304 to M.D.). H.S. is a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation, United States (DRG-2194-14). J.M.S. and T.S.P. were supported by The Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD079124) and NINDS (P30NS045892) of United States. The UNC Mouse Behavioral Phenotyping Laboratory is supported by a grant from the National Institute of Child Health and Human Development (NICHD), United States (U54-HD079124). The UNC Translational Pathology Laboratory is supported in part by grants from the NCI (5P30CA016086-42), NIH (U54-CA156733), NIEHS (5 P30 ES010126-17), UCRF, and NCBT (2015-IDG-1007) of United States. Author contributions V.S., A.N., and E.H. conducted most of the experiments with help as described here. H.S. and M.E.G. performed the whole-genome bisulfite sequencing and its analyses. J.M.S. and T.S.P. analyzed all RNA-seq data. C.L.K., M.K., P.S., and S.M.H. performed small RNA-seq and miRHub analysis. C.P., J.G., and E.A. helped with imaging and analysis of immunohistochemical stains. C.F. and M.B. helped manage the mouse colony. J.L. and Y.-W.H. generated the miR-29-floxed mice. S.M. conducted and analyzed many of the neurobehavioral assessments. V.S., M.E.G., and M.D. outlined the project. M.D. supervised the project. V.S., A.N., E.H., and M.D. produced the final version of the manuscript.

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N2 - Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.

AB - Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.

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MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation

Abstract

Bibliographical note

Data Availability Statement

Keywords

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