Recent CIG publications Archive

Genome Res. 2012 Jan 27. [Epub ahead of print]

Canella D, Bernasconi D, Gilardi F, Lemartelot G, Migliavacca E, Praz V, Cousin P, Delorenzi M, Hernandez N; The CycliX Consortium.

Source

Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland;

Abstract

The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine Rn4.5s (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.

Nat Genet. 2012 Jan 27;44(2):121-6. doi: 10.1038/ng.1054.

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.

Source

1] Oxford e-Research Centre, University of Oxford, Oxford, UK. [2].

Abstract

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared ‘Investigation-Study-Assay’ framework to support that vision.

Sleep Med. 2012 Jan 17. [Epub ahead of print]

Heinzer RC, Pellaton C, Rey V, Rossetti AO, Lecciso G, Haba-Rubio J, Tafti M, Lavigne G.

Source

Centre for Investigation and Research in Sleep (CIRS), Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland.

Abstract

BACKGROUND:

Positional therapy that prevents patients from sleeping supine has been used for many years to manage positional obstructive sleep apnea (OSA). However, patients’ usage at home and the long term efficacy of this therapy have never been objectively assessed.

METHODS:

Sixteen patients with positional OSA who refused or could not tolerate continuous positive airway pressure (CPAP) were enrolled after a test night study (T0) to test the efficacy of the positional therapy device. The patients who had a successful test night were instructed to use the device every night for threemonths. Nightly usage was monitored by an actigraphic recorder placed inside the positional device. A follow-up night study (T3) was performed after threemonths of positional therapy.

RESULTS:

Patients used the device on average 73.7±29.3% (mean±SD) of the nights for 8.0±2.0h/night. 10/16 patients used the device more than 80% of the nights. Compared to the baseline (diagnostic) night, mean apnea-hypopnea index (AHI) decreased from 26.7±17.5 to 6.0±3.4 with the positional device (p<0.0001) during T0 night. Oxygen desaturation (3%) index also fell from 18.4±11.1 to 7.1±5.7 (p=0.001). Time spent supine fell from 42.8±26.2% to 5.8±7.2% (p<0.0001). At threemonths (T3), the benefits persisted with no difference in AHI (p=0.58) or in time spent supine (p=0.98) compared to T0 night. The Epworth sleepiness scale showed a significant decrease from 9.4±4.5 to 6.6±4.7 (p=0.02) after threemonths.

CONCLUSIONS:

Selected patients with positional OSA can be effectively treated by a positional therapy with an objective compliance of 73.7% of the nights and a persistent efficacy after threemonths.

Copyright © 2011 Elsevier B.V. All rights reserved.