Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing

The pig X and Y Chromosomes: structure, sequence, and evolution.

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.This work was funded by BBSRC grant BB/F021372/1. The Flow Cytometry and Cytogenetics Core Facilities at the Wellcome Trust Sanger Institute and Sanger investigators are funded by the Wellcome Trust (grant number WT098051). K.B., D.C.-S., and J.H. acknowledge support from the Wellcome Trust (WT095908), the BBSRC (BB/I025506/1), and the European Molecular Biology Laboratory. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007–2013) under grant agreement no. 222664 (“Quantomics”).This is the final version of the article. It first appeared from Cold Spring Harbor Laboratory Press via http://dx.doi.org/10.1101/gr.188839.11

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature0315

اللاجئين الفلسطينيين في ضوء القانون الدولي للاجئين (من غياب الحماية والرعاية إلى ضياع حق العودة)

قضية اللاجئين الفلسطينيين واحدة من أهم القضايا المعاصرة في نطاق القانون الدولي للاجئين. ومع ذلك شهدت هذه القضية ضعفًا وهشاشة من حيث الرعاية والحماية القانونية نتيجة التفسير الضيق لقواعد القانون الدولي للاجئين من قِبل الأطراف المسؤولة عن توفير تلك الحماية والرعاية القانونية للاجئين الفلسطنيين. ساهم في هذا الإهمال غياب هذه القضية في الجوانب القانونية والسياسية المؤثرة على الحالة الفلسطينية بشكل عام حيث تم الاهتمام بحق تقرير المصير والحكم الذاتي ووقف الاستطيان وغيره من القضايا الأخرى. في حين أن قضية اللاجئين الفلسطينيين لا تقل أهمية عن تلك القضايا المرتبطة بحقوق الشعب الفلسطيني. في عام 1948 أنشأت الأمم المتحدة منظمة (الأونروا) بموجب القرار الصادر من الجمعية العامة رقم 302 لرعاية اللاجئين الفلسطينيين داخل فلسطين والأردن ولبنان وسوريا. وفي عام 1951 تم توثيق اتفاقية جنيف لرعاية وحماية اللاجئين الدولي ونصت هذه الاتفاقية من خلال الفقرة 4 المادة الأولى على استثناء اللاجئين الذين يتلقون رعاية من أجهزة الأمم المتحدة الأخرى من البنود القانونية الواردة في هذه الاتفاقية. تم تفسير هذا النص من قِبل المفوضية السامية المنبثقة من هذه الاتفاقية على استبعاد جميع اللاجئين الفلسطنيين في العالم من هذه الاتفاقية لأنهم يتلقون رعاية من (الأونروا) في حين أن القرار رقم 302 نص على أن عمل الأونروا يقتصر فقط على أربعة دول وهي فلسطين والأردن ولبنان وسوريا.هذا التفسير الضيق أدى إلى غياب تام في توفير الحماية القانونية للاجئين الفلسطينيين الذين يعيشون خارج هذه الدول. وفي نفس السياق أصدرت الأمم المتحدة في عام 1998 المبادئ التوجيهية للمشردين داخليًا وهي نصوص توضح حقوق هولاء النازحين والتزامات المجتمع الدولي بحقهم. وهذه المبادئ تتسم بقوة قانونية لأنها ترتب حقوق واضحة للمشردين داخليًا وخاصة في إنهاء السبب الذي حدث منه التشرد والنزوح وترتيب التزامات على المجتمع الدولي لتنفيذ ذلك. بعكس عمل الأونروا والذي ينحصر في تقديم خدمات صحية وتعليمية ولا تتضمن بنود قانونية ترتب حقوق قانونية يلتزم المجتمع الدولي على منحها النازحيين الفلسطينيين. استمرت الأمم المتحدة بالتعامل مع النازحين الفلسطينيين داخل حدود فلسطين تحت وصف لاجئين وحرمتهم من امتيازات قانونية تمنحها إياهم المبادئ التوجيهية للمشردين داخليًا. تكمن أهمية قضية اللاجئين الفلسطينيين في أنها تؤثر في تمسك هولاء اللاجئين بحق عودتهم لأن هذا الإهمال يؤدي إلى تخليهم عن حقهم في استعادة أرضهم المسلوبة والبحث في الحصول على جنسيات دول جديدة والاستقرار فيها. وبالتالي لا بد من تفعيل الحقوق القانونية لهولاء اللاجئين أو العمل لإنشاء وترتيب نصوص قانونية خاصة تتعامل مع هذه القضية نظرًا لاستمرار حالة اللاجئين الفلسطينيين وأهميتها في التمسك بحقهم الأصيل بالعودة إلى وطنه

The DNA sequence of the human X chromosome

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of th

Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci

The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hematopoiesis and vasculogenesis and a pattern of expression that is highly conserved between mammals and zebrafish. Here we report the isolation and characterization of the zebrafish SCL locus together with the identification of three neighboring genes, IER5, MAP17, and MUPP1. This region spans 68 kb and comprises the longest zebrafish genomic sequence currently available for comparison with mammalian, chicken, and pufferfish sequences. Our data show conserved synteny between zebrafish and mammalian SCL and MAP17 loci, thus suggesting the likely genomic domain necessary for the conserved pattern of SCL expression. Long-range comparative sequence analysis/phylogenetic footprinting was used to identify noncoding conserved sequences representing candidate transcriptional regulatory elements. The SCL promoter/enhancer, exon 1, and the poly(A) region were highly conserved, but no homology to other known mouse SCL enhancers was detected in the zebrafish sequence. A combined homology/structure analysis of the poly(A) region predicted consistent structural features, suggesting a conserved functional role in mRNA regulation. Analysis of the SCL promoter/enhancer revealed five motifs, which were conserved from zebrafish to mammals, and each of which is essential for the appropriate pattern or level of SCL transcription. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Tanese.