Browsing by Subject "X Chromosome"

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Open Access
Expression in aneuploid Drosophila S2 cells.
(PLoS Biol, 2010-02-23) Zhang, Yu; Malone, John H; Powell, Sara K; Periwal, Vipul; Spana, Eric; Macalpine, David M; Oliver, Brian
Extensive departures from balanced gene dose in aneuploids are highly deleterious. However, we know very little about the relationship between gene copy number and expression in aneuploid cells. We determined copy number and transcript abundance (expression) genome-wide in Drosophila S2 cells by DNA-Seq and RNA-Seq. We found that S2 cells are aneuploid for >43 Mb of the genome, primarily in the range of one to five copies, and show a male genotype ( approximately two X chromosomes and four sets of autosomes, or 2X;4A). Both X chromosomes and autosomes showed expression dosage compensation. X chromosome expression was elevated in a fixed-fold manner regardless of actual gene dose. In engineering terms, the system "anticipates" the perturbation caused by X dose, rather than responding to an error caused by the perturbation. This feed-forward regulation resulted in precise dosage compensation only when X dose was half of the autosome dose. Insufficient compensation occurred at lower X chromosome dose and excessive expression occurred at higher doses. RNAi knockdown of the Male Specific Lethal complex abolished feed-forward regulation. Both autosome and X chromosome genes show Male Specific Lethal-independent compensation that fits a first order dose-response curve. Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide. For the X chromosome, compensation includes fixed and dose-dependent components.
Open Access
The genome of the green anole lizard and a comparative analysis with birds and mammals.
(Nature, 2011-08-31) Alföldi, Jessica; Di Palma, Federica; Grabherr, Manfred; Williams, Christina; Kong, Lesheng; Mauceli, Evan; Russell, Pamela; Lowe, Craig B; Glor, Richard E; Jaffe, Jacob D; Ray, David A; Boissinot, Stephane; Shedlock, Andrew M; Botka, Christopher; Castoe, Todd A; Colbourne, John K; Fujita, Matthew K; Moreno, Ricardo Godinez; ten Hallers, Boudewijn F; Haussler, David; Heger, Andreas; Heiman, David; Janes, Daniel E; Johnson, Jeremy; de Jong, Pieter J; Koriabine, Maxim Y; Lara, Marcia; Novick, Peter A; Organ, Chris L; Peach, Sally E; Poe, Steven; Pollock, David D; de Queiroz, Kevin; Sanger, Thomas; Searle, Steve; Smith, Jeremy D; Smith, Zachary; Swofford, Ross; Turner-Maier, Jason; Wade, Juli; Young, Sarah; Zadissa, Amonida; Edwards, Scott V; Glenn, Travis C; Schneider, Christopher J; Losos, Jonathan B; Lander, Eric S; Breen, Matthew; Ponting, Chris P; Lindblad-Toh, Kerstin
The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.