Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung.

Epigenetics : Official Journal of the DNA Methylation Society
Xiao DongSimon D Spivack

Abstract

Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchi...Continue Reading

References

Sep 21, 2000·Journal of the National Cancer Institute·S B BaylinJ G Herman
Sep 16, 2003·Molecular Cancer·Jürgen Dittmer
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Avrum SpiraJerome S Brody
Mar 14, 2008·The New England Journal of Medicine·Malcolm V BrockJames G Herman
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 19, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Shuguang LengSteven A Belinsky
May 30, 2012·Nature Reviews. Genetics·Peter A Jones
Sep 19, 2012·Nature Reviews. Genetics·Christoph Bock
Feb 13, 2013·Nature Reviews. Genetics·Zachary D Smith, Alexander Meissner
Aug 9, 2013·Nature·Michael J ZillerAlexander Meissner
Sep 6, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Weiguo HanSimon D Spivack
Aug 17, 2014·The American Journal of Pathology·Juan LinSimon D Spivack
Oct 4, 2014·Frontiers in Genetics·Mark D RobinsonXiaobei Zhou
May 20, 2015·The New England Journal of Medicine·Gerard A SilvestriUNKNOWN AEGIS Study Team
Nov 7, 2015·Cell·Dominic Grün, Alexander van Oudenaarden
Dec 20, 2015·PloS One·Nandita MullapudiSimon D Spivack
Jan 28, 2016·Genome Biology·Ana ConesaAli Mortazavi
Oct 13, 2016·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Alicia HulbertJames G Herman

❮ Previous
Next ❯

Citations

Jun 25, 2020·Proteomics·Ferdinand von Eggeling, Franziska Hoffmann
Feb 10, 2021·Nature Neuroscience·Kristen R MaynardAndrew E Jaffe

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP130768

Methods Mentioned

BETA
RNA-seq
laser capture microdissection
electrophoresis
WGBS
Illumina sequencing
GTPase
GTPases
chips

Software Mentioned

Bowtie2
David
R
FastQC
cufflinks
RegNetwork
Bismark
igraph
Ensembl
R package “ preprocessCore ”

Related Concepts

Related Feeds

Cell Signaling & Cancer Epigenetics (Keystone)

Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. This feed covers the latest research on signaling and epigenetics in cell growth and cancer.