From Genes to Milk: Genomic Organization and Epigenetic Regulation of the Mammary Transcriptome

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Lemay, Danielle G ^a   Pollard, Katherine S ^b   Martin, William F ^a   Freeman Zadrowski, Courtneay ^c   Hernandez, Joseph ^c   Korf, Ian ^a   German, J Bruce ^a   Rijnkels, Monique ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; BREAST MILK; CHROMATIN; CONTROLLED STUDY; EPIGENETICS; FEMALE; GENE EXPRESSION; GENE LOCATION; GENE REPRESSION; GENETIC ORGANIZATION; HISTONE MODIFICATION; LACTATION; LIVER; MAMMARY GLAND; MOUSE; NONHUMAN; PREGNANCY; TRANSCRIPTION REGULATION;

ANIMALS; CHROMATIN; CHROMOSOMES, MAMMALIAN; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE SILENCING; GENES; GENOMICS; HISTONES; HUMANS; LACTATION; MAMMARY GLANDS, ANIMAL; MICE; MICE, INBRED ICR; MILK; ORGAN SPECIFICITY; PREGNANCY; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84884614980     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075030     Document Type: Article

References (34)

1. De S, Teichmann SA, Babu MM, (2009) The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res 19: 785-794.
2. Yanai I, Hunter CP, (2009) Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Res 19: 2214-2220.
3. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, et al. (2012) G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics 13: 253.
4. Bhaumik SR, Smith E, Shilatifard A, (2007) Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 14: 1008-1016.
5. Wang Z, Schones DE, Zhao K, (2009) Characterization of human epigenomes. Curr Opin Genet Dev 19: 127-134.
6. Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
7. Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, et al. (2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19: 221-233.
8. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
9. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
10. Rudolph MC, McManaman JL, Hunter L, Phang T, Neville MC, (2003) Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution. J Mammary Gland Biol Neoplasia 8: 287-307.
11. Dai M, Wang P, Boyd AD, Kostov G, Athey B, et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33: e175.
12. Flicek P, Ahmed I, Amode MR, Barrell D, Brent S, et al. (2013) Ensmble 2013. Nucleic Acids Res 41: D48-D55.
13. Harr B, Schlotterer C, (2006) Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res 34: e8.
14. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
15. Sinha AU, Meller J, (2007) Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 8: 82.
16. Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, et al. (2013) Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One 8: e53270.
17. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
18. Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, et al. (2007) Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics 89: 580-587.
19. Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
20. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
21. Yu P, Xiao S, Xin X, Song CX, Huang W, et al. (2013) Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Res 23: 352-364.
22. Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP, (2009) Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41: 246-250.
23. Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, et al. (2013) Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152: 642-654.
24. Kress C, Ballester M, Devinoy E, Rijnkels M, (2010) Epigenetic modifications in 3D: nuclear organization of the differentiating mammary epithelial cell. J Mammary Gland Biol Neoplasia 15: 73-83.
25. Kabotyanski EB, Rijnkels M, Freeman-Zadrowski C, Buser AC, Edwards DP, et al. (2009) Lactogenic hormonal induction of long distance interactions between beta-casein gene regulatory elements. J Biol Chem 284: 22815-22824.
26. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950): 289-293.
27. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398): 376-380.
28. Phillips-Cremins JE, Corces VG, (2013) Chromatin insulators: linking genome organization to cellular function. Mol Cell 50: 461-474.
29. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB, (2007) Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol 1: 56.
30. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169-181.
31. Roh TY, Wei G, Farrell CM, Zhao K, (2007) Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res 17: 74-81.
32. Sandberg R, Yasuda R, Pankratz DG, Carter TA, Del Rio JA, et al. (2000) Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A 97: 11038-11043.
33. Pritchard C, Coil D, Hawley S, Hsu L, Nelson PS, (2006) The contributions of normal variation and genetic background to mammalian gene expression. Genome Biol 7: R26.
34. Turk R, 't Hoen PA, Sterrenburg E, de Menezes RX, de Meijer EJ, et al. (2004) Gene expression variation between mouse inbred strains. BMC Genomics 5: 57.