Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models

Maite Mendioroz, Catherine Do, Xiaoling Jiang, Chunhong Liu, Huferesh K. Darbary, Charles F. Lang, John Lin, Anna Thomas, Sayeda Abu-Amero, Philip Stanier, Alexis Temkin, Alexander Yale, Meng Min Liu, Yang Li, Martha Salas, Kristi Kerkel, George T Capone, Wayne P Silverman, Y. Eugene Yu, Gudrun MooreJerzy Wegiel, Benjamin Tycko

Research output: Contribution to journalArticle

Abstract

Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.

Original languageEnglish (US)
Article number263
JournalGenome Biology
Volume16
Issue number1
DOIs
StatePublished - Nov 25 2015

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Down syndrome
aneuploidy
methylation
Aneuploidy
DNA methylation
DNA Methylation
Down Syndrome
brain
chromosome
Chromosomes
animal models
chromosomes
DNA
gene
epigenetics
Epigenomics
Chromosome Duplication
Methylation
maturation
Brain

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. / Mendioroz, Maite; Do, Catherine; Jiang, Xiaoling; Liu, Chunhong; Darbary, Huferesh K.; Lang, Charles F.; Lin, John; Thomas, Anna; Abu-Amero, Sayeda; Stanier, Philip; Temkin, Alexis; Yale, Alexander; Liu, Meng Min; Li, Yang; Salas, Martha; Kerkel, Kristi; Capone, George T; Silverman, Wayne P; Yu, Y. Eugene; Moore, Gudrun; Wegiel, Jerzy; Tycko, Benjamin.

In: Genome Biology, Vol. 16, No. 1, 263, 25.11.2015.

Research output: Contribution to journalArticle

Mendioroz, M, Do, C, Jiang, X, Liu, C, Darbary, HK, Lang, CF, Lin, J, Thomas, A, Abu-Amero, S, Stanier, P, Temkin, A, Yale, A, Liu, MM, Li, Y, Salas, M, Kerkel, K, Capone, GT, Silverman, WP, Yu, YE, Moore, G, Wegiel, J & Tycko, B 2015, 'Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models', Genome Biology, vol. 16, no. 1, 263. https://doi.org/10.1186/s13059-015-0827-6
Mendioroz, Maite ; Do, Catherine ; Jiang, Xiaoling ; Liu, Chunhong ; Darbary, Huferesh K. ; Lang, Charles F. ; Lin, John ; Thomas, Anna ; Abu-Amero, Sayeda ; Stanier, Philip ; Temkin, Alexis ; Yale, Alexander ; Liu, Meng Min ; Li, Yang ; Salas, Martha ; Kerkel, Kristi ; Capone, George T ; Silverman, Wayne P ; Yu, Y. Eugene ; Moore, Gudrun ; Wegiel, Jerzy ; Tycko, Benjamin. / Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. In: Genome Biology. 2015 ; Vol. 16, No. 1.
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abstract = "Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.",
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AU - Liu, Chunhong

AU - Darbary, Huferesh K.

AU - Lang, Charles F.

AU - Lin, John

AU - Thomas, Anna

AU - Abu-Amero, Sayeda

AU - Stanier, Philip

AU - Temkin, Alexis

AU - Yale, Alexander

AU - Liu, Meng Min

AU - Li, Yang

AU - Salas, Martha

AU - Kerkel, Kristi

AU - Capone, George T

AU - Silverman, Wayne P

AU - Yu, Y. Eugene

AU - Moore, Gudrun

AU - Wegiel, Jerzy

AU - Tycko, Benjamin

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N2 - Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.

AB - Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.

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