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Fishing for Function in the Human Gene Pool

TRENDS IN GENETICS 2016年第7期32卷 392-394页

作者： Barozzi, Iros Visel, Axel Dickel, Diane E. Lawrence Berkeley Natl Lab Berkeley CA 94720 USA US DOE Joint Genome Inst Walnut Creek CA 94598 USA Univ Calif Sch Nat Sci Merced CA USA

Identification and characterization of causal non-coding variants in human genomes is challenging and requires substantial experimental resources. A new study by Tehranchi et al. describes a cost-effective approach for accurate mapping of molecular quantitative trait loci (QTLs) from pooled samples, a powerful way to link disease associated changes to molecular functions.

关键词： non-coding dna cis-regulation QTL GWAS

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Regulated Formation of lncRNA-dna Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation (vol 61, pg 393, 2016)

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MOLECULAR CELL 2016年第1期62卷 148-148页

作者： Cloutier, Sara C. Wang, Siwen Ma, Wai Kit Al Husini, Nadra Dhoondia, Zuzer Ansari, Athar Pascuzzi, Pete E. Tran, Elizabeth J.

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Plastid Genotyping Reveals the Uniformity of Cytoplasmic Male Sterile-T Maize Cytoplasms

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PLANT PHYSIOLOGY 2015年第3期169卷 2129-2137页

作者： Bosacchi, Massimo Gurdon, Csanad Maliga, Pal Rutgers State Univ Waksman Inst Microbiol Piscataway NJ 08854 USA

Cytoplasmic male-sterile (CMS) lines in maize (Zea mays) have been classified by their response to specific restorer genes into three categories: cms-C, cms-S, and cms-T. A mitochondrial genome representing each of the CMS cytotypes has been sequenced, and male sterility in the cms-S and cms-T cytotypes is linked to chimeric mitochondrial genes. To identify markers for plastid genotyping, we sequenced the plastid genomes of three fertile maize lines (B37, B73, and A188) and the B37 cms-C, cms-S, and cms-T cytoplasmic substitution lines. We found that the plastid genomes of B37 and B73 lines are identical. Furthermore, the fertile and CMS plastid genomes are conserved, differing only by zero to three single-nucleotide polymorphisms (SNPs) in coding regions and by eight to 22 SNPs and 10 to 21 short insertions/deletions in noncoding regions. To gain insight into the origin and transmission of the cms-T trait, we identified three SNPs unique to the cms-T plastids and tested the three diagnostic SNPs in 27 cms-T lines, representing the HA, I, Q, RS, and T male-sterile cytoplasms. We report that each of the tested 27 cms-T group accessions have the same three diagnostic plastid SNPs, indicating a single origin and maternal cotransmission of the cms-T mitochondria and plastids to the seed progeny. Our data exclude exceptional pollen transmission of organelles or multiple horizontal gene transfer events as the source of the mitochondrial urf13-T (unidentified reading frame encoding 13-kD cms-T protein) gene in the cms-T cytoplasms. Plastid genotyping enables a reassessment of the evolutionary relationships of cytoplasms in cultivated maize.

关键词： CYTOPLASM SINGLE nucleotide polymorphisms MITOCHONDRIAL enzymes GENE expression non-coding dna

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Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

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MOLECULAR PHYLOGENETICS AND EVOLUTION 2015年 92卷 140-146页

作者： Gilbert, Princess S. Chang, Jonathan Pan, Calvin Sobel, Eric M. Sinsheimer, Janet S. Faircloth, Brant C. Alfaro, Michael E. Univ Calif Los Angeles Dept Ecol & Evolutionary Biol Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biomath Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA Louisiana State Univ Dept Biol Sci Baton Rouge LA 70803 USA Louisiana State Univ Museum Nat Sci Baton Rouge LA 70803 USA

Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life. (C) 2015 Elsevier Inc. All rights reserved.

关键词： Ultraconserved elements Next-generation sequencing non-coding dna Phylogenomics Molecular evolution Phylogenetic informativeness

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A dna shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites

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BIOINFORMATICS 2015年第21期31卷 3445-3450页

作者： Yang, Jichen Ramsey, Stephen A. Oregon State Univ Dept Biomed Sci Corvallis OR 97331 USA Oregon State Univ Sch Elect Engn & Comp Sci Corvallis OR 97331 USA

Motivation: The position-weight matrix (PWM) is a useful representation of a transcription factor binding site (TFBS) sequence pattern because the PWM can be estimated from a small number of representative TFBS sequences. However, because the PWM probability model assumes independence between individual nucleotide positions, the PWMs for some TFs poorly discriminate binding sites from non-binding-sites that have similar sequence content. Since the local three-dimensional dna structure ('shape') is a determinant of TF binding specificity and since dna shape has a significant sequence-dependence, we combined dna shape-derived features into a TF-generalized regulatory score and tested whether the score could improve PWM-based discrimination of TFBS from non-binding-sites. Results: We compared a traditional PWM model to a model that combines the PWM with a dna shape feature-based regulatory potential score, for accuracy in detecting binding sites for 75 vertebrate transcription factors. The PWM + shape model was more accurate than the PWM-only model, for 45% of TFs tested, with no significant loss of accuracy for the remaining TFs.

关键词： TRANSCRIPTION factors PROBABILITY theory dna structure GENETIC regulation non-coding dna GENE expression

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In silico identification and characterisation of 17 polymorphic anonymous non-coding sequence markers (ANMs) for red grouse (Lagopus lagopus scotica)

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CONSERVATION GENETICS RESOURCES 2015年第2期7卷 319-323页

作者： Wenzel, Marius A. Piertney, Stuart B. Univ Aberdeen Inst Biol & Environm Sci Aberdeen AB24 2TZ Scotland

Anonymous non-coding sequence markers (ANMs) are powerful neutral genetic markers with great utility in phylogeography, population genetics and population genomics. Developing ANMs has previously relied on sequencing random fragments of genomic dna in the target species and then querying bioinformatics databases to identify unannotated, putatively neutral fragments. Here, we describe an alternative in silico approach that is based on identifying large unannotated genomic regions in model species to provide a priori neutral targets for candidate ANMs that are remote from exonic regions. We illustrate this approach by developing a set of 17 polymorphic ANMs for red grouse (Lagopus lagopus scotica) from c. 1 Mbp non-coding chromosome regions of chicken, turkey and zebrafinch genomes. This pipeline presents a powerful and efficient approach when appropriate model genomes are available for the target species of interest.

关键词： Anonymous nuclear markers non-coding dna Neutral evolution Red grouse Lagopus

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motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites

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BIOINFORMATICS 2015年第23期31卷 3847-3849页

作者： Coetzee, Simon G. Coetzee, Gerhard A. Hazelett, Dennis J. Cedars Sinai Med Ctr Bioinformat & Computat Biol Res Ctr Los Angeles CA 90048 USA USC Norris Comprehens Canc Ctr Dept Urol & Prevent Med Los Angeles CA USA

The Summary: Functional annotation represents a key step toward the understanding and interpretation of germline and somatic variation as revealed by genome-wide association studies (GWAS) and The Cancer Genome Atlas (TCGA), respectively. GWAS have revealed numerous genetic risk variants residing in non-coding dna associated with complex diseases. For sequences that lie within enhancers or promoters of transcription, it is not straightforward to assess the effects of variants on likely transcription factor binding sites. Consequently we introduce motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation is a good match, and how much information is gained or lost in one allele of the polymorphism or mutation relative to the other. MotifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from many public sources that users can choose from. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within bioconductor.

关键词： RESEARCH Germ cells non-coding dna Genetic polymorphisms Transcription factors Binding sites (Biochemistry)

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Rare pseudoautosomal copy-number variations involving SHOX and/or its flanking regions in individuals with and without short stature

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JOURNAL OF HUMAN GENETICS 2015年第9期60卷 553-556页

作者： Fukami, Maki Naiki, Yasuhiro Muroya, Koji Hamajima, Takashi Soneda, Shun Horikawa, Reiko Jinno, Tomoko Katsumi, Momori Nakamura, Akie Asakura, Yumi Adachi, Masanori Ogata, Tsutomu Kanzaki, Susumu Natl Res Inst Child Hlth & Dev Dept Mol Endocrinol Tokyo 1578535 Japan Natl Ctr Child Hlth & Dev Div Endocrinol & Metab Tokyo Japan Kanagawa Childrens Med Ctr Dept Endocrinol & Metab Yokohama Kanagawa Japan Aichi Childrens Hlth & Med Ctr Div Endocrinol & Metab Obu Japan St Marianna Univ Sch Med Dept Pediat Kawasaki Kanagawa Japan Hokkaido Univ Sch Med Dept Pediat Sapporo Hokkaido 060 Japan Hamamatsu Univ Sch Med Dept Pediat Hamamatsu Shizuoka 4313192 Japan Tottori Univ Fac Med Div Pediat & Perinatol Tottori 680 Japan

Pseudoautosomal region 1 (PAR1) contains SHOX, in addition to seven highly conserved non-coding dna elements (CNEs) with cis-regulatory activity. Microdeletions involving SHOX exons 1-6a and/or the CNEs result in idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). Here, we report six rare copy-number variations (CNVs) in PAR1 identified through copy-number analyzes of 245 ISS/LWD patients and 15 unaffected individuals. The six CNVs consisted of three microduplications encompassing SHOX and some of the CNEs, two microduplications in the SHOX 3'-region affecting one or four of the downstream CNEs, and a microdeletion involving SHOX exon 6b and its neighboring CNE. The amplified dna fragments of two SHOX-containing duplications were detected at chromosomal regions adjacent to the original positions. The breakpoints of a SHOX-containing duplication resided within Alu repeats. A microduplication encompassing four downstream CNEs was identified in an unaffected father-daughter pair, whereas the other five CNVs were detected in ISS patients. These results suggest that microduplications involving SHOX cause ISS by disrupting the cis-regulatory machinery of this gene and that at least some of microduplications in PAR1 arise from Alu-mediated non-allelic homologous recombination. The pathogenicity of other rare PAR1-linked CNVs, such as CNE-containing microduplications and exon 6b-flanking microdeletions, merits further investigation.

关键词： SHORT stature dna copy number variations HOMEOBOX genes CIS-regulatory elements (Genetics) non-coding dna CONSERVED sequences (Genetics) GENETIC aspects

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Running spell-check to identify regulatory variants

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NATURE GENETICS 2015年第8期47卷 853-855页

作者： Kircher, Martin Shendure, Jay Univ Washington Dept Genome Sci Seattle WA 98195 USA

A major challenge in human genetics is pinpointing which non-coding genetic variants affect gene expression and disease risk. A new study in this issue describes a broadly applicable approach for this task that explicitly models cell type-specific regulatory motifs and generates variant effect predictions that are more accurate and interpretable than those of alternative tools.

关键词： HUMAN genetics non-coding dna GENE expression DISEASE risk factors TISSUES

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Integrating regulatory and methylome data for the discovery of clear cell Renal Cell Carcinoma (ccRCC) variants

Integrating regulatory and methylome data for the discovery ...

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作者： Calvert-Joshua, Tracey University of the Western Cape

学位级别：master

Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer is considered the most lethal cancer of the genitourinary system. Despite advances in its treatment, the mortality- and incidence rates across all stages of the disease have continued to climb. Since the release of the Human Genome Project in the early 2000’s, most genetics studies have focused on the protein coding region of the human genome, which accounts for a mere 2% of the entire genome. It has been suggested that diverting our focus to the other 98% of the genome, which was previously dismissed as non-functional “junk dna”, could possibly contribute significantly to our understanding of the underlying mechanisms of complex *** this study a whole genome sequencing somatic mutation data set from the International Cancer Genome Consortium was used. The non-coding somatic mutations within the promoter, intronic, 5-prime untranslated and 3-prime untranslated regions of clear cell renal cell carcinoma-implicated genes were extracted and submitted to RegulomDB for their functional *** expected, most of the variants were located within the intronic regions and only a small subset of identified variants was predicted to be deleterious. Although the variants all belonged to a selected subset of kidney cancer-associated genes, the genes frequently mutated in the non-coding regions were not the same genes that were frequently mutated in the whole exome studies (where the focus is on the coding sequences). This indicates that with whole genome sequencing studies a new set of genes/variants previously unassociated with the clear cell renal cell carcinoma could be identified. In addition, most of the non-coding somatic variants fell within multiple transcriptions factor binding sites. Since many of these variants were also deleterious (a

关键词： non-coding dna Gene dysregulation Aberrant methylation Renal cell carcinoma Clear cell renal cell carcinoma

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