Nature Reviews Genetics

Genomic instability: Shattered details.

Publication Date: 2012 Feb 2 PMID: 22298233
Authors: Burgess, D. J.
Journal: Nat Rev Genet

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Understanding transgenerational epigenetic inheritance via the gametes in mammals.

Publication Date: 2012 Jan 31 PMID: 22290458
Authors: Daxinger, L. - Whitelaw, E.
Journal: Nat Rev Genet

It is known that information that is not contained in the DNA sequence - epigenetic information - can be inherited from the parent to the offspring. However, many questions remain unanswered regarding the extent and mechanisms of such inheritance. In this Review, we consider the evidence for transgenerational epigenetic inheritance via the gametes, including cases of environmentally induced epigenetic changes. The molecular basis of this inheritance remains unclear, but recent evidence points towards diffusible factors, in particular RNA, rather than DNA methylation or chromatin. Interestingly, many cases of epigenetic inheritance seem to involve repeat sequences.

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Gene regulation: Inner control.

Publication Date: 2012 Jan 31 PMID: 22290416
Authors: Casci, T.
Journal: Nat Rev Genet

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Development: Parental influences on plant development.

Publication Date: 2012 Jan 31 PMID: 22290415
Authors: Stower, H.
Journal: Nat Rev Genet

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Causes and consequences of aneuploidy in cancer.

Publication Date: 2012 Jan 24 PMID: 22269907
Authors: Gordon, D. J. - Resio, B. - Pellman, D.
Journal: Nat Rev Genet

Genetic instability, which includes both numerical and structural chromosomal abnormalities, is a hallmark of cancer. Whereas the structural chromosome rearrangements have received substantial attention, the role of whole-chromosome aneuploidy in cancer is much less well-understood. Here we review recent progress in understanding the roles of whole-chromosome aneuploidy in cancer, including the mechanistic causes of aneuploidy, the cellular responses to chromosome gains or losses and how cells might adapt to tolerate these usually detrimental alterations. We also explore the role of aneuploidy in cellular transformation and discuss the possibility of developing aneuploidy-specific therapies.

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Rare and common variants: twenty arguments.

Publication Date: 2011 Feb PMID: 22251874
Authors: Gibson, G.
Journal: Nat Rev Genet

Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small effect. Here I review 20 arguments for and against each of these models of the genetic basis of complex traits and conclude that both classes of effect can be readily reconciled.

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Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription.

Publication Date: 2011 Feb PMID: 22251873
Authors: Conrad, T. - Akhtar, A.
Journal: Nat Rev Genet

Dosage compensation is an epigenetic mechanism that normalizes gene expression from unequal copy numbers of sex chromosomes. Different organisms have evolved alternative molecular solutions to this task. In Drosophila melanogaster, transcription of the single male X chromosome is upregulated by twofold in a process orchestrated by the dosage compensation complex. Despite this conceptual simplicity, dosage compensation involves multiple coordinated steps to recognize and activate the entire X chromosome. We are only beginning to understand the intriguing interplay between multiple levels of local and long-range chromatin regulation required for the fine-tuned transcriptional activation of a heterogeneous gene population. This Review highlights the known facts and open questions of dosage compensation in D. melanogaster.

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Protein-RNA interactions: new genomic technologies and perspectives.

Publication Date: 2011 Feb PMID: 22251872
Authors: Konig, J. - Zarnack, K. - Luscombe, N. M. - Ule, J.
Journal: Nat Rev Genet

RNA-binding proteins are key players in the regulation of gene expression. In this Progress article, we discuss state-of-the-art technologies that can be used to study individual RNA-binding proteins or large complexes such as the ribosome. We also describe how these approaches can be used to study interactions with different types of RNAs, including nascent transcripts, mRNAs, microRNAs and ribosomal RNAs, in order to investigate transcription, RNA processing and translation. Finally, we highlight current challenges in data analysis and the future steps that are needed to obtain a quantitative and high-resolution picture of protein-RNA interactions on a genome-wide scale.

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Gene expression: A simple model for ensuring signalling specificity.

Publication Date: 2011 Feb PMID: 22249615
Authors: Casci, T.
Journal: Nat Rev Genet

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Bioinformatics: Data compression facilitates genome assembly.

Publication Date: 2011 Feb PMID: 22249614
Authors: Casci, T.
Journal: Nat Rev Genet

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Genomics: Repetitive elements underestimated?

Publication Date: 2011 Feb PMID: 22249613
Authors: Burgess, D. J.
Journal: Nat Rev Genet

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Development: Role found for DNMT3A in somatic stem cells.

Publication Date: 2011 Feb PMID: 22249612
Authors: Casci, T.
Journal: Nat Rev Genet

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Differentiation: Asymmetry caused by replication-coupled chromatin assembly.

Publication Date: 2011 Feb PMID: 22249611
Authors: Burgess, D. J.
Journal: Nat Rev Genet

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Familial risks in understanding type 1 diabetes genetics.

Publication Date: 2011 Feb PMID: 22249610
Authors: Hemminki, K.
Journal: Nat Rev Genet

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Response to 'Familial risks in understanding type 1 diabetes genetics'.

Publication Date: 2011 Feb PMID: 22249609
Authors: Polychronakos, C. - Li, Q.
Journal: Nat Rev Genet

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Synthetic biology: Simplifying design.

Publication Date: 2011 Feb PMID: 22249608
Authors: Muers, M.
Journal: Nat Rev Genet

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Mutation: Linking transcription and genome instability.

Publication Date: 2011 Feb PMID: 22249607
Authors: Muers, M.
Journal: Nat Rev Genet

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Non-coding RNA: Zebrafish provide insight into lincRNA evolution.

Publication Date: 2011 Feb PMID: 22249606
Authors: Muers, M.
Journal: Nat Rev Genet

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Evolution: Paths of antibiotic resistance.

Publication Date: 2011 Feb PMID: 22249605
Authors: Muers, M.
Journal: Nat Rev Genet

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Small RNAs: Little transgressions.

Publication Date: 2011 Feb PMID: 22230818
Authors: Casci, T.
Journal: Nat Rev Genet

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Computer simulations: tools for population and evolutionary genetics.

Publication Date: 2011 Feb PMID: 22230817
Authors: Hoban, S. - Bertorelle, G. - Gaggiotti, O. E.
Journal: Nat Rev Genet

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions.

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RNA stability: Remember your driver.

Publication Date: 2011 Feb PMID: 22230816
Authors: Burgess, D. J.
Journal: Nat Rev Genet

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