Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

/pdf/analysis-of-protein-coding-genetic-variation-in-60-706-43wjw7d23z.pdf

Analysis of protein-coding genetic variation in 60,706 humans

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group.

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm’s speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human β T cell receptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface at c3.biomath.mssm.edu/trf.html has been established for automated use of the program.

/pdf/tandem-repeats-finder-a-program-to-analyze-dna-sequences-1oo3g6vnch.pdf

Tandem repeats finder: a program to analyze DNA sequences

Nucleoporins (Nups) build highly organized nuclear pore complexes (NPCs) at the nuclear envelope (NE). Several Nups assemble into a sieve-like hydrogel within the central channel of the NPCs. In the cytoplasm, the soluble Nups exist, but how their assembly is restricted to the NE is currently unknown. Here, we show that fragile X-related protein 1 (FXR1) can interact with several Nups and facilitate their localization to the NE during interphase through a microtubule-dependent mechanism. Downregulation of FXR1 or closely related orthologs FXR2 and fragile X mental retardation protein (FMRP) leads to the accumulation of cytoplasmic Nup condensates. Likewise, models of fragile X syndrome (FXS), characterized by a loss of FMRP, accumulate Nup granules. The Nup granule-containing cells show defects in protein export, nuclear morphology and cell cycle progression. Our results reveal an unexpected role for the FXR protein family in the spatial regulation of nucleoporin condensation.

https://www.embopress.org/doi/pdf/10.15252/embj.2020104467

Spatial control of nucleoporin condensation by fragile X-related proteins.

The BCEI gene codes for a small secreted protein and is expressed in the human mammary tumour cell line MCF7 under oestrogen control and in some breast cancers. We have mapped the gene to chromosome 21 using a panel of somatic hybrid lines, and in situ hybridization has allowed a precise assignment to band 21q223. Two restriction fragment length polymorphisms (RFLP) are described that should be of use in linkage or population studies to test a possible involvement of the BCEI gene in genetic predisposition to breast cancer. This gene should also be a useful marker for the genetic and physical mapping of chromosome 21, and for a better definition of the region involved in the clinical phenotype of Downs syndrome.

Chromosome localization and polymorphism of an oestrogen-inducible gene specifically expressed in some breast cancers.

Means for treating and diagnosing neurodegenerative diseases related to the presence of polyglutamine chains by means of a 1C2 antibody are disclosed.

Method for treating neurodegenerative diseases using a 1c2 antibody or a fragment or derivative thereof, and corresponding pharmaceutical compositions

Exclusion of haemophilia b in male fetus by chorionic villus biopsy

Dystrophln cONA clones were isolated from a library constructed with poly A* RNA from leg muscle of 13 days old chicken (1). The sequence of 13575 base pairs contains an open reading frame beginning with ATG at nucleotide 151 and ending with TAG at nucleotide 11131, and encodes a 3660 amino acid protein (1). The 3 untranslated sequence (2442 nucleotides) does not contain the polyadenylation signal and may lack only about 50 nucleotides as shown by alignment with the human sequence (2). A previously sequenced exon (3) and two incompletely spliced cONA clones allow us to place exon limits at position 811-812, 993-994, 5310-5311, 8013-8014 (exon-1ntron junction sequence for the two last exons is given 1n the figure). Most of the sequence was determined on at least two independent clones (1). Sequence variants which might be due either to polymorphism or to cloning artefacts are presented in the table.

Jean-Louis Mandel

Papers

Spatial control of nucleoporin condensation by fragile X-related proteins.

Chromosome localization and polymorphism of an oestrogen-inducible gene specifically expressed in some breast cancers.

Method for treating neurodegenerative diseases using a 1c2 antibody or a fragment or derivative thereof, and corresponding pharmaceutical compositions

Exclusion of haemophilia b in male fetus by chorionic villus biopsy

Nucleotide sequence of chicken dystrophin cDNA.