13.09.2022 Views

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

Create successful ePaper yourself

Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.

438 Chapter 7: Control of Gene Expression

References

General

Brown TA (2007) Genomes 3. New York: Garland Science.

Epigenetics (2004) Cold Spring Harb. Symp. Quant. Biol. 69.

Gilbert SF (2013) Developmental Biology, 10th ed. Sunderland, MA:

Sinauer Associates, Inc.

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

Genomes, 4th ed. Boston: McGraw Hill.

McKnight SL & Yamamoto KR (eds) (1993) Transcriptional Regulation.

Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Mechanisms of Transcription (1998) Cold Spring Harb. Symp. Quant. Biol. 63.

Ptashne M & Gann A (2002) Genes and Signals. Cold Spring Harbor,

NY: Cold Spring Harbor Laboratory Press.

Watson J, Baker T, Bell S et al. (2013) Molecular Biology of the Gene,

7th ed. Menlo Park, CA: Benjamin Cummings.

An Overview of Gene Control

Davidson EH (2006) The Regulatory Genome: Gene Regulatory

Networks in Development and Evolution. Burlington, MA: Elsevier.

Gurdon JB (1992) The generation of diversity and pattern in animal

development. Cell 68, 185–199.

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

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

111, 6131–6138.

Control Of Transcription By Sequence-Specific

DNA-Binding Proteins

McKnight SL (1991) Molecular zippers in gene regulation. Sci. Am.

264, 54–64.

Pabo CO & Sauer rt (1992) Transcription factors: structural families

and principles of DNA recognition. Annu. Rev. Biochem. 61,

1053–1095.

Seeman NC, Rosenberg JM & Rich A (1976) Sequence-specific

recognition of double helical nucleic acids by proteins. Proc. Natl.

Acad. Sci. USA 73, 804–808.

Weirauch MT & Hughes TR (2011) A catalogue of eukaryotic

transcription factor types, their evolutionary origin, and species

distribution. In A Handbook of Transcription Factors. New York, NY:

Springer Publishing Company.

Transcription Regulators Switch Genes On and Off

Beckwith J (1987) The operon: an historical account. In Escherichia

coli and Salmonella typhimurium: Cellular and Molecular Biology

(Neidhart FC, Ingraham JL, Low KB et al. eds), vol. 2,

pp. 1439–1443. Washington, DC: ASM Press.

Gilbert W & Müller-Hill B (1967) The lac operator is DNA. Proc. Natl.

Acad. Sci. USA 58, 2415.

Jacob F & Monod J (1961) Genetic regulatory mechanisms in the

synthesis of proteins. J. Mol. Biol. 3, 318–356.

Levine M, Cattoglio C & Tjian R (2014) Looping back to leap forward:

transcription enters a new era. Cell 157, 13–25.

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

and Functions of ATP-dependent chromatin-remodeling enzymes.

Cell 154, 490–503.

Ptashne M (2004) A Genetic Switch: Phage and Lambda Revisited, 3rd

ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Ptashne M (1967) Specific binding of the lambda phage repressor to

lambda DNA. Nature 214, 232–234.

St Johnston D & Nusslein-Volhard C (1992) The origin of pattern and

polarity in the Drosophila embryo. Cell 68, 201–219.

Turner BM (2014) Nucleosome signaling: an evolving concept.

Biochim. Biophys. Acta 1839, 623–626.

Molecular Genetic Mechanisms that Create and

Maintain Specialized Cell Types

Alon U (2007) Network motifs: theory and experimental approaches.

Nature 8, 450–461.

Buganim Y, Faddah DA & Jaenisch R (2013) Mechanisms and models

of somatic cell reprogramming. Nat. Rev. Genet. 14, 427–439.

Hobert O (2011) Regulation of Terminal differentiation programs in the

nervous system. Annu. Rev. Cell Dev. Biol. 27, 681–696.

Lawrence PA (1992) The Making of a Fly: The Genetics of Animal

Design. New York: Blackwell Scientific Publications.

Mechanisms That Reinforce Cell Memory in Plants and

Animals

Bird A (2011) Putting the DNA back into DNA methylation. Nat. Genet.

43, 1050–1051.

Gehring M (2013) Genomic imprinting: insights from plants. Annu. Rev.

Genet. 47, 187–208.

Lawson HA, Cheverud JM & Wolf JB (2013) Genomic imprinting and

parent-of-origin effects on complex traits. Genetics 14, 609–617.

Lee JT & Bartolomei MS (2013) X-Inactivation, imprinting, and long

noncoding RNAs in Health and disease. Cell 152, 1308–1323.

Li E & Zhang Y (2014) DNA methylation in mammals. Cold Spring Harb.

Perspect. Biol. 6, a019133.

Post-Transcriptional Controls

DiGiammartino DC, Nishida K & Manley JL (2011) Mechanisms and

consequences of alternative polyadenylation. Mol Cell 43, 853–866.

Gottesman S & Storz G (2011) Bacterial small RNA regulators: versatile

roles and rapidly evolving variations. Cold Spring Harb. Perspect.

Biol. 3, a003798.

Hershey JWB, Sonenberg N & Mathews MB (2012) Principles of

translational control: an overview. Cold Spring Harb. Perspect. Biol.

4, a011528.

Hundley HA & Bass BL (2010) ADAR editing in double-stranded UTRs

and other noncoding RNA sequences. Trends Biochem. Sci.

35, 377–383.

Kalsotra A & Cooper TA (2011) Functional consequences of

developmentally regulated alternative splicing. Nat. Rev. Genet.

12, 715–729.

Kortmann J & Narberhaus F (2012) Bacterial RNA thermometers:

molecular zippers and switches. Nat. Rev. Microbiol. 10, 255–265.

Parker R (2012) RNA degradation in Saccharomyces cerevisae.

Genetics 191, 671–702.

Popp MW & Maquat LE (2013) Organizing principles of mammalian

nonsense-mediated mRNA decay. Annu. Rev. Genet. 47, 139–165.

Serganov A & Nudler E (2013) A decade of riboswitches. Cell 152,

17–24.

Thompson SR (2012) Tricks an IRES uses to enslave ribosomes. Trends

Microbiol. 20, 558–566.

Regulation of Gene Expression By Noncoding RNAs

Bhaya D, Davison M & Barrangou R (2011) CRISPR-Cas systems in

bacteria and archaea: Versatile small RNAs for adaptive defense

and regulation. Annu. Rev. Genet. 45, 273–297.

Cech TR & Steitz JA (2014) The noncoding RNA revolution–trashing old

rules to forge new ones. Cell 157, 77–94.

Fire A, Xu S, Montgomery MK et al (1998) Potent and specific genetic

interference by double-stranded RNA in Caenorhabditis elegans.

Nature 391, 806–811.

Guttman M & Rinn JL (2012) Modular regulatory principles of large

non-coding RNAs. Nature 482, 339–346.

Lee HC, Gu W, Shirayama M et al. (2012) C. elegans piRNAs mediate

the genome-wide surveillance of germline transcripts. Cell

150, 78–87.

Meister G (2013) Argonaute proteins: functional insights and emerging

roles. Nat. Rev. Genet. 14, 447–459.

Rinn JL & Chang HY (2012) Genome regulation by long noncoding

RNAs. Annu. Rev. Biochem. 81, 145–166.

tenOever BR (2013) RNA viruses and the host microRNA machinery.

Nat. Rev. Microbiol. 11, 169–180.

Ulitsky I & Bartel DP (2013) lincRNAs: genomics, evolution, and

mechanisms. Cell 154, 26–46.

Wiedenheft B, Sternberg SH & Doudna JA (2012) RNA-guided genetic

silencing systems in bacteria and archaea. Nature 482, 331–338.

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!