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Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

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236 Chapter 4: DNA, Chromosomes, and Genomes

References

General

Armstrong L (2014) Epigenetics. New York: Garland Science.

Hartwell L, Hood L, Goldberg ML et al. (2010) Genetics: From Genes to

Genomes, 4th ed. Boston, MA: McGraw Hill.

Jobling M, Hollox E, Hurles M et al. (2014) Human Evolutionary

Genetics, 2nd ed. New York: Garland Science.

Strachan T & Read AP (2010) Human Molecular Genetics, 4th ed. New

York: Garland Science.

The Structure and Function of DNA

Avery OT, MacLeod CM & McCarty M (1944) Studies on the chemical

nature of the substance inducing transformation of pneumococcal

types. J. Exp. Med. 79, 137–158.

Meselson M & Stahl FW (1958) The replication of DNA in Escherichia

coli. Proc. Natl Acad. Sci. USA 44, 671–682.

Watson JD & Crick FHC (1953) Molecular structure of nucleic acids.

A structure for deoxyribose nucleic acid. Nature 171, 737–738.

Chromosomal DNA and Its Packaging in the Chromatin

Fiber

Andrews AJ & Luger K (2011) Nucleosome structure(s) and stability:

variations on a theme. Annu. Rev. Biophys. 40, 99–117.

Avvakumov N, Nourani A & Cõté J (2011) Histone chaperones:

modulators of chromatin marks. Mol. Cell 41, 502–514.

Deal RB, Henikoff JG & Henikoff S (2010) Genome-wide kinetics of

nucleosome turnover determined by metabolic labeling of histones.

Science 328, 1161–1164.

Grigoryev SA & Woodcock CL (2012) Chromatin organization—the

30 nm fiber. Exp. Cell Res. 318, 1448–1455.

Li G, Levitus M, Bustamante C & Widom J (2005) Rapid spontaneous

accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol. 12, 46–53.

Luger K, Mäder AW, Richmond RK et al. (1997) Crystal structure of the

nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260.

Narlikar GJ, Sundaramoorthy R & Owen-Hughes T (2013) Mechanisms

and functions of ATP-dependent chromatin-remodeling enzymes.

Cell 154, 490–503.

Song F, Chen P, Sun D et al. (2014) Cryo-EM study of the chromatin

fiber reveals a double helix twisted by tetranucleosomal units.

Science 344, 376–380.

Chromatin Structure and Function

Al-Sady B, Madhani HD & Narlikar GJ (2013) Division of labor between

the chromodomains of HP1 and Suv39 methylase enables

coordination of heterochromatin spread. Mol. Cell 51, 80–91.

Beisel C & Paro R (2011) Silencing chromatin: comparing modes and

mechanisms. Nat. Rev. Genet. 12, 123–135.

Black BE, Jansen LET, Foltz DR & Cleveland DW (2011) Centromere

identity, function, and epigenetic propagation across cell divisions.

Cold Spring Harb. Symp. Quant. Biol. 75, 403–418.

Elgin SCR & Reuter G (2013) Position-effect variegation,

heterochromatin formation, and gene silencing in Drosophila. Cold

Spring Harb. Perspect. Biol. 5, a017780.

Felsenfeld G (2014) A brief history of epigenetics. Cold Spring Harb.

Perspect. Biol. 6, a018200.

Feng S, Jacobsen SE & Reik W (2010) Epigenetic reprogramming in

plant and animal development. Science 330, 622–627.

Filion GJ, van Bemmel JG, Braunschweig U et al. (2010) Systematic

protein location mapping reveals five principal chromatin types in

Drosophila cells. Cell 143, 212–224.

Fodor BD, Shukeir N, Reuter G & Jenuwein T (2010) Mammalian

Su(var) genes in chromatin control. Annu. Rev. Cell Dev. Biol.

26, 471–501.

Giles KE, Gowher H, Ghirlando R et al. (2010) Chromatin boundaries,

insulators, and long-range interactions in the nucleus. Cold Spring

Harb. Symp. Quant. Biol. 75, 79–85.

Gohl D, Aoki T, Blanton J et al. (2011) Mechanism of chromosomal

boundary action: roadblock, sink, or loop? Genetics 187, 731–748.

Mellone B, Erhardt S & Karpen GH (2006) The ABCs of centromeres.

Nat. Cell Biol. 8, 427–429.

Morris SA, Baek S, Sung M-H et al. (2014) Overlapping chromatinremodeling

systems collaborate genome wide at dynamic

chromatin transitions. Nat. Struct. Mol. Biol. 21, 73–81.

Politz JCR, Scalzo D & Groudine M (2013) Something silent this

way forms: the functional organization of the repressive nuclear

compartment. Annu. Rev. Cell Dev. Biol. 29, 241–270.

Rothbart SB & Strahl BD (2014) Interpreting the language of histone

and DNA modifications. Biochim. Biophys. Acta 1839, 627–643.

Weber CM & Henikoff S (2014) Histone variants: dynamic punctuation

in transcription. Genes Dev. 28, 672–682.

Xu M, Long C, Chen X et al. (2010) Partitioning of histone H3-H4

tetramers during DNA replication-dependent chromatin assembly.

Science 328, 94–98.

The Global Structure of Chromosomes

Belmont AS (2014) Large-scale chromatin organization: the good, the

surprising, and the still perplexing. Curr. Opin. Cell Biol. 26, 69–78.

Bickmore W (2013) The spatial organization of the human genome.

Annu. Rev. Genomics Hum. Genet. 14, 67–84.

Callan HG (1982) Lampbrush chromosomes. Proc. R. Soc. Lond. B

Biol. Sci. 214, 417–448.

Cheutin T, Bantignies F, Leblanc B & Cavalli G (2010) Chromatin folding:

from linear chromosomes to the 4D nucleus. Cold Spring Harb.

Symp. Quant. Biol. 75, 461–473.

Cremer T & Cremer M (2010) Chromosome territories. Cold Spring

Harb. Perspect. Biol. 2, a003889.

Lieberman-Aiden E, van Berkum NL, Williams L et al. (2009)

Comprehensive mapping of long-range interactions reveals folding

principles of the human genome. Science 326, 289–293.

Maeshima K & Laemmli UK (2003) A two-step scaffolding model for

mitotic chromosome assembly. Dev. Cell 4, 467–480.

Moser SC & Swedlow JR (2011) How to be a mitotic chromosome.

Chromosome Res. 19, 307–319.

Nizami ZF, Deryusheva S & Gall JG (2010) Cajal bodies and histone

locus bodies in Drosophila and Xenopus. Cold Spring Harb. Symp.

Quant. Biol. 75, 313–320.

Zhimulev IF (1997) Polytene chromosomes, heterochromatin, and

position effect variegation. Adv. Genet. 37, 1–566.

How Genomes Evolve

Batzer MA & Deininger PL (2002) Alu repeats and human genomic

diversity. Nat. Rev. Genet. 3, 370–379.

Feuk L, Carson AR & Scherer S (2006) Structural variation in the human

genome. Nat. Rev. Genet. 7, 85–97.

Green RE, Krause J, Briggs AW et al. (2010) A draft sequence of the

Neandertal genome. Science 328, 710–722.

International Human Genome Sequencing Consortium (2001) Initial

sequencing and analysis of the human genome. Nature

409, 860–921.

International Human Genome Sequencing Consortium (2004) Finishing

the euchromatic sequence of the human genome. Nature

431, 931–945.

Kellis M, Wold B, Snyder MP et al. (2014) Defining functional DNA

elements in the human genome. Proc. Natl Acad. Sci. USA

111, 6131–6138.

Lander ES (2011) Initial impact of the sequencing of the human

genome. Nature 470, 187–197.

Lee C & Scherer SW (2010) The clinical context of copy number

variation in the human genome. Expert Rev. Mol. Med. 12, e8.

Mouse Genome Sequencing Consortium (2002) Initial sequencing and

comparative analysis of the mouse genome. Nature 420, 520–562.

Pollard KS, Salama SR, Lambert N et al. (2006) An RNA gene

expressed during cortical development evolved rapidly in humans.

Nature 443, 167–172.

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