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A high-coverage genome sequence from an archaic Denisovan individual.

Meyer, Matthias Kircher, Martin Gansauge, Marie-Theres Li, Heng Racimo, Fernando Mallick, Swapan Schraiber, Joshua G Jay, Flora Prüfer, Kay de Filippo, Cesare ...

Published in Science (New York, N.Y.)

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tenta...

Gene repression. H3K27me and PRC2 transmit a memory of repression across generations and during development.

Gaydos, Laura J Wang, Wenchao Strome, Susan

Published in Science (New York, N.Y.)

For proper development, cells must retain patterns of gene expression and repression through cell division. Repression via methylation of histone H3 on Lys27 (H3K27me) by Polycomb repressive complex 2 (PRC2) is conserved, but its transmission is not well understood. Our studies suggest that PRC2 represses the X chromosomes in Caenorhabditis elegans...

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang, Guojie Li, Cai Li, Qiye Li, Bo Larkin, Denis M Lee, Chul Storz, Jay F Antunes, Agostinho Greenwold, Matthew J Meredith, Robert W ...

Published in Science (New York, N.Y.)

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Three periods of regulatory innovation during vertebrate evolution.

Lowe, Craig B Kellis, Manolis Siepel, Adam Raney, Brian J Clamp, Michele Salama, Sofie R Kingsley, David M Lindblad-Toh, Kerstin Haussler, David

Published in Science (New York, N.Y.)

The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory r...

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis, Erich D Mirarab, Siavash Aberer, Andre J Li, Bo Houde, Peter Li, Cai Ho, Simon Y W Faircloth, Brant C Nabholz, Benoit Howard, Jason T ...

Published in Science (New York, N.Y.)

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergen...

Targeted retrieval and analysis of five Neandertal mtDNA genomes.

Briggs, Adrian W Good, Jeffrey M Green, Richard E Krause, Johannes Maricic, Tomislav Stenzel, Udo Lalueza-Fox, Carles Rudan, Pavao Brajkovic, Dejana Kucan, Zeljko ...

Published in Science (New York, N.Y.)

Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this metho...

Neuroscience. Toward reprogramming gonads to brains.

Strome, Susan

Published in Science (New York, N.Y.)

Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments.

Zhang, Qiucen Lambert, Guillaume Liao, David Kim, Hyunsung Robin, Kristelle Tung, Chih-kuan Pourmand, Nader Austin, Robert H

Published in Science (New York, N.Y.)

The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence the rate of emergence of resistance are not well understood. In a microfluidic device designed to mimic naturally occurring bacterial niches, resistance of Escherichia coli to the antibiotic ciprofloxacin developed within 10 hours. Resistance eme...

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Zhou, Jie Lancaster, Laura Donohue, John Paul Noller, Harry F

Published in Science (New York, N.Y.)

Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring duri...

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana, Ekta Fu, Yao Colonna, Vincenza Mu, Xinmeng Jasmine Kang, Hyun Min Lappalainen, Tuuli Sboner, Andrea Lochovsky, Lucas Chen, Jieming Harmanci, Arif ...

Published in Science (New York, N.Y.)

Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating ...

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