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Genome Research

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https://www.readbyqxmd.com/read/27903646/whole-transcriptome-sequencing-identified-a-distinct-subtype-of-acute-lymphoblastic-leukemia-with-predominant-genomic-abnormalities-of-ep300-and-crebbp
#1
Maoxiang Qian, Hui Zhang, Shirley Kow-Yin Kham, Shuguang Liu, Chuang Jiang, Xujie Zhao, Yi Lu, Charnise Goodings, Ting-Nien Lin, Ranran Zhang, Takaya Moriyama, Zhaohong Yin, Zhenhua Li, Thuan Chong Quah, Hany Ariffin, Ah Moy Tan, Shuhong Shen, Deepa Bhojwani, Shaoyan Hu, Suning Chen, Huyong Zheng, Ching-Hon Pui, Allen Eng-Juh Yeoh, Jun J Yang
Chromosomal translocations are a genomic hallmark of many hematologic malignancies. Often as initiating events, these structural abnormalities result in fusion proteins involving transcription factors important for hematopoietic differentiation and/or signaling molecules regulating cell proliferation and cell cycle. In contrast, epigenetic regulator genes are more frequently targeted by somatic sequence mutations, possibly as secondary events to further potentiate leukemogenesis. Through comprehensive whole transcriptome sequencing of 231 children with acute lymphoblastic leukemia (ALL), we identified 58 putative functional and predominant fusion genes in 54...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27903645/upgrading-short-read-animal-genome-assemblies-to-chromosome-level-using-comparative-genomics-and-a-universal-probe-set
#2
Joana Damas, Rebecca O'Connor, Marta Farré, Vasileios Panagiotis E Lenis, Henry J Martell, Anjali Mandawala, Katie Fowler, Sunitha Joseph, Martin T Swain, Darren K Griffin, Denis M Larkin
Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes. Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27903644/a-reference-data-set-of-5-4-million-phased-human-variants-validated-by-genetic-inheritance-from-sequencing-a-three-generation-17-member-pedigree
#3
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern, Semyon Kruglyak, Elliott H Margulies, Gil McVean, David R Bentley
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27895111/discovery-and-genotyping-of-structural-variation-from-long-read-haploid-genome-sequence-data
#4
John Huddleston, Mark Jp Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David S Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. Using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF >1%)...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27895110/nucleosome-occupancy-as-a-novel-chromatin-parameter-for-replication-origin-functions
#5
Jairo Rodriguez, Laura Lee, Bryony Lynch, Toshio Tsukiyama
Eukaryotic DNA replication initiates from multiple discrete sites in the genome termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regulated. At the population level, each origin has a distinct firing time and frequency of activation within S phase. Many studies have showed that chromatin can strongly influence initiation of DNA replication...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27895109/enhancers-and-super-enhancers-have-an-equivalent-regulatory-role-in-embryonic-stem-cells-through-regulation-of-single-or-multiple-genes
#6
Sakthi D Moorthy, Scott Davidson, Virlana M Shchuka, Gurdeep Singh, Nakisa Malek-Gilani, Lida Langroudi, Alexandre Martchenko, Vincent So, Neil N Macpherson, Jennifer A Mitchell
Transcriptional enhancers are critical for maintaining cell type-specific gene expression and driving cell fate changes during development. Highly transcribed genes are often associated with a cluster of individual enhancers such as those found in locus control regions. Recently these have been termed stretch enhancers or super-enhancers, which have been predicted to regulate critical cell identity genes. We employed a CRISPR/Cas9-mediated deletion approach to study the function of several enhancer clusters (ECs) and isolated enhancers in mouse embryonic stem (ES) cells...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27864353/identification-of-clinically-predictive-metagenes-that-encode-components-of-a-network-coupling-cell-shape-to-transcription-by-image-omics
#7
Heba Z Sailem, Chris Bakal
The associations between clinical phenotypes (tumour grade, survival), and cell phenotypes, such as shape, signalling activity, and gene expression, are the basis for cancer pathology; but the mechanisms explaining these relationships are not always clear. The generation of large datasets containing information regarding cell phenotypes, and clinical data, provides an opportunity to describe these mechanisms. Here we develop an image-omics approach to integrate quantitative cell imaging data, gene expression, and protein-protein interaction data to systematically describe a 'shape-gene network' that couples specific aspects of breast cancer cell shape to signalling and transcriptional events...
November 18, 2016: Genome Research
https://www.readbyqxmd.com/read/27864352/single-cell-transcriptomes-identify-human-islet-cell-signatures-and-reveal-cell-type-specific-expression-changes-in-type-2-diabetes
#8
Nathan Lawlor, Joshy George, Mohan Bolisetty, Romy Kursawe, Lili Sun, Sivakamasundari V, Ina Kycia, Paul Robson, Michael L Stitzel
Blood glucose levels are tightly controlled by the coordinated action of at least four cell types constituting pancreatic islets. Changes in the proportion and/or function of these cells are associated with genetic and molecular pathophysiology of monogenic, type 1, and type 2 diabetes (T2D). Cellular heterogeneity impedes precise understanding of the molecular components of each islet cell type that govern islet dysfunction, particularly the less abundant delta and gamma/pancreatic polypeptide (PP) cells. Here, we report single cell transcriptomes for 638 cells from non-diabetic (ND) and T2D human islet samples...
November 18, 2016: Genome Research
https://www.readbyqxmd.com/read/27864351/detecting-differential-growth-of-microbial-populations-with-gaussian-process-regression
#9
Peter D Tonner, Cynthia L Darnell, Barbara E Engelhardt, Amy K Schmid
Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form. Extensions to these models are required to quantify the effects of perturbations, which often exhibit non-standard growth curves. Rather than assume specific functional forms for experimental perturbations, we developed a general and robust model of microbial population growth curves using Gaussian process (GP) regression...
November 18, 2016: Genome Research
https://www.readbyqxmd.com/read/27856494/the-dynamic-landscape-of-fission-yeast-meiosis-alternative-splice-isoforms
#10
Zheng Kuang, Jef D Boeke, Stefan Canzar
Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter to characterize the transcriptome in the meiosis of fission yeast. We reveal 14353 alternative splicing events in 17669 novel isoforms at different stages of meiosis, including antisense and read-through transcripts...
November 17, 2016: Genome Research
https://www.readbyqxmd.com/read/27852650/multiparameter-functional-diversity-of-human-c2h2-zinc-finger-proteins
#11
Frank W Schmitges, Ernest Radovani, Hamed S Najafabadi, Marjan Barazandeh, Laura F Campitelli, Yimeng Yin, Arttu Jolma, Guoqing Zhong, Hongbo Guo, Tharsan Kanagalingam, Wei F Dai, Jussi Taipale, Andrew Emili, Jack F Greenblatt, Timothy R Hughes
C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions...
November 16, 2016: Genome Research
https://www.readbyqxmd.com/read/27831498/a-systematic-comparison-reveals-substantial-differences-in-chromosomal-versus-episomal-encoding-of-enhancer-activity
#12
Fumitaka Inoue, Martin Kircher, Beth Martin, Gregory M Cooper, Daniela M Witten, Michael T McManus, Nadav Ahituv, Jay Shendure
Candidate enhancers can be identified on the basis of chromatin modifications, the binding of chromatin modifiers and transcription factors and cofactors, or chromatin accessibility. However, validating such candidates as bona fide enhancers requires functional characterization, typically achieved through reporter assays that test whether a sequence can increase expression of a transcriptional reporter via a minimal promoter. A longstanding concern is that reporter assays are mainly implemented on episomes, which are thought to lack physiological chromatin...
November 9, 2016: Genome Research
https://www.readbyqxmd.com/read/27821409/the-evolution-of-inflorescence-diversity-in-the-nightshades-and-heterochrony-during-meristem-maturation
#13
Zachary H Lemmon, Soon Ju Park, Ke Jiang, Joyce Van Eck, Michael C Schatz, Zachary B Lippman
One of the most remarkable manifestations of plant evolution is the diversity for floral branching systems. These "inflorescences" arise from stem cell populations in shoot meristems that mature gradually to reproductive states in response to environmental and endogenous signals. The morphology of the shoot meristem maturation process is conserved across distantly related plants, raising the question of how diverse inflorescence architectures arise from seemingly common maturation programs. In tomato and related nightshades (Solanaceae), inflorescences range from solitary flowers to highly branched structures bearing hundreds of flowers...
November 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27821408/a-novel-translational-control-mechanism-involving-rna-structures-within-coding-sequences
#14
Jennifer Jungfleisch, Danny D Nedialkova, Ivan Dotu, Katherine E Sloan, Neus Martinez-Bosch, Lukas Brüning, Emanuele Raineri, Pilar Navarro, Markus T Bohnsack, Sebastian A Leidel, Juana Diez
The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features...
November 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27789526/an-integrated-3-dimensional-genome-modeling-engine-for-data-driven-simulation-of-spatial-genome-organization
#15
Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Michal J Pietal, Oscar J Luo, Michał Sadowski, Xingwang Li, Kamen Radew, Yijun Ruan, Dariusz Plewczynski
ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding...
October 27, 2016: Genome Research
https://www.readbyqxmd.com/read/27789525/a-privacy-preserving-solution-for-compressed-storage-and-selective-retrieval-of-genomic-data
#16
Zhicong Huang, Erman Ayday, Huang Lin, Raeka S Aiyar, Adam Molyneaux, Zhenyu Xu, Jacques Fellay, Lars M Steinmetz, Jean-Pierre Hubaux
In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30GB to 200GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern; yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval...
October 27, 2016: Genome Research
https://www.readbyqxmd.com/read/27852649/centrifuge-rapid-and-sensitive-classification-of-metagenomic-sequences
#17
Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg
Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes...
October 17, 2016: Genome Research
https://www.readbyqxmd.com/read/27737935/whole-genome-analysis-of-the-methylome-and-hydroxymethylome-in-normal-and-malignant-lung-and-liver
#18
Xin Li, Yun Liu, Tal Salz, Kasper D Hansen, Andrew Feinberg
DNA methylation at the 5-position of cytosine (5mC) is an epigenetic modification that regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family oxidizes 5mC to 5-hydroxymethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and it may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in human normal liver and lung as well as paired tumor tissues...
October 13, 2016: Genome Research
https://www.readbyqxmd.com/read/27733415/genome-wide-dynamics-of-alternative-polyadenylation-in-rice
#19
Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xinfu Ye, Xiaohui Wu, Qingshun Q Li
Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3'-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression...
October 12, 2016: Genome Research
https://www.readbyqxmd.com/read/27831497/improved-assembly-of-noisy-long-reads-by-k-mer-validation
#20
Antonio Bernardo Carvalho, Eduardo G Dupim, Gabriel Goldstein
Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads...
October 7, 2016: Genome Research
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