Top 8 Biorxiv Papers Today in Genomics


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#1. Genome-wide discovery of lupus genetic risk variant allelic regulatory activity
Xiaoming Lu, Xiaoting Chen, Carmy Forney, Omer Donmez, Daniel Miller, Sreeja Parameswaran, Ted Hong, Yongbo Huang, Mario Pujato, Tareian Cazares, Emily R Miraldi, John P Ray, Carl G de Boer, John B Harley, Matthew T Weirauch, Leah C Kottyan
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into EBV-infected B cells revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around these 51 variants identified one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second, larger class of TFs that also bind allelically but do not have their motifs directly altered by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional...
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CarldeBoerPhD: RT @biorxiv_genomic: Genome-wide discovery of lupus genetic risk variant allelic regulatory activity https://t.co/yJjNvKKDVu #biorxiv_geno…
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Sample Sizes : None.
Authors: 16
Total Words: 12452
Unqiue Words: 3322

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#2. The RNA-binding protein, Rasputin/G3BP, enhances the stability and translation of its target mRNAs
John D Laver, Jimmy Ly, Allison K Winn, Angelo Karaiskakis, Sichun Lin, Kun Nie, Giulia Benic, Nima Jaberi-Lashkari, Wen Xi Cao, Alireza Khademi, J Timothy Westwood, Sachdev S Sidhu, Quaid Morris, Stephane Angers, Craig A Smibert, Howard D Lipshitz
G3BP RNA-binding proteins are important components of stress granules (SGs). Here we analyze the role of Drosophila G3BP, Rasputin (RIN), in unstressed cells, where RIN is not SG associated. Immunoprecipitation followed by microarray analysis identified over 550 mRNAs that copurify with RIN. The mRNAs found in SGs are long and translationally silent. In contrast, we find that RIN-bound mRNAs, which encode core components of the transcription, splicing and translation machinery, are short, stable and highly translated. We show that RIN is associated with polysomes and provide evidence for a direct role for RIN and its human homologs in stabilizing and upregulating the translation of their target mRNAs. We propose that when cells are stressed the resulting incorporation of RIN/G3BPs into SGs sequesters them away from their short target mRNAs. This would downregulate the expression of these transcripts, even though they are not incorporated into stress granules.
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Sample Sizes : [3]
Authors: 16
Total Words: 23559
Unqiue Words: 6380

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#3. Smchd1 is a maternal effect gene required for autosomal imprinting
Iromi Wanigasuriya, Quentin Gouil, Sarah A. Kinkel, Andrés Tapia del Fierro, Tamara Beck, Ellise E.A. Roper, Kelsey Breslin, Jessica Stringer, Karla Hutt, Heather J. Lee, Andrew Keniry, Matthew E. Ritchie, Marnie E. Blewitt
Genomic imprinting establishes allele-biased expression of a suite of mammalian genes based on their parent of origin. Imprinted expression is achieved via parent-of-origin specific epigenetic marks under the control of maternal effect proteins supplied in the oocyte. Here we report Structural maintenance of chromosomes hinge domain containing 1 (Smchd1) as a novel maternal effect gene that regulates the imprinting of 16 genes. The majority of these genes only show loss of imprinting post-implantation, indicating maternal Smchd1 imparts a long-lived epigenetic effect. Smchd1-sensitive genes include both those controlled by germline polycomb marks and by germline DNA methylation imprints. In contrast to other known maternal effect genes affecting the latter set of genes, maternal Smchd1 does not affect germline DNA methylation imprints. Smchd1-sensitive genes are united by their reliance on polycomb-mediated histone methylation as germline or secondary imprints, suggesting Smchd1 acts downstream of polycomb imprints to mediate its...
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Authors: 13
Total Words: 0
Unqiue Words: 0

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#4. Translation is required for miRNA-dependent decay of endogenous transcripts.
Adriano Biasini, Stefano de Pretis, Jennifer Yihong Tan, Baroj Abdulkarim, Harry Wischnewski, Rene Dreos, Mattia Pelizzola, Constance Ciaudo, Ana Claudia Marques
Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cytosolic long noncoding RNAs (lncRNAs). We show, that despite interacting with miRNA loaded RNA-induced silencing complex (miRISC), the steady state abundance and degradation rates of these endogenously expressed non-translated transcripts are minimally impacted by miRNA loss. To validate the requirement of translation for miRNA-dependent decay, we fused a miRISC bound lncRNA, whose levels are unaffected by miRNAs, to the 3 prime end of a protein-coding gene reporter and show that this results in its miRNA-dependent...
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Authors: 9
Total Words: 0
Unqiue Words: 0

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#5. Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients
Zheng Zhao, Kenan Zhang, Qiangwei Wang, Guanzhang Li, Fan Zeng, Ying Zhang, Fan Wu, Ruichao Chai, Zheng Wang, Chuanbao Zhang, Wei Zhang, Zhaoshi Bao, Tao Jiang
Gliomas are the most common and malignant intracranial tumours in adults. Recent studies have shown that functional genomics greatly aids in the understanding of the pathophysiology and therapy of glioma. However, comprehensive genomic data and analysis platforms are relatively limited. In this study, we developed the Chinese Glioma Genome Atlas (CGGA, http://www.cgga.org.cn), a user-friendly data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes nearly 2,000 primary and recurrent glioma samples from Chinese cohorts. CGGA currently provides access to whole-exome sequencing (286 samples), messenger RNA sequencing (1,018 samples) and microarray (301 samples), DNA methylation microarray (159 samples), and microRNA microarray (198 samples) data, as well as detailed clinical data (e.g., WHO grade, histological type, critical molecular genetic information, age, sex, chemoradiotherapy status and survival data). In addition, we developed an analysis tool to allow users to browse...
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Sample Sizes : None.
Authors: 13
Total Words: 7094
Unqiue Words: 2264

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#6. Super-resolution visualization of distinct stalled and broken replication fork structures
Donna R Whelan, Wei Ting Chelsea Lee, Frances Marks, Yu Tina Kong, Yandong Yin, Eli Rothenberg
Endogenous genotoxic stress occurs in healthy cells due to competition between DNA replication machinery, and transcription and topographic relaxation processes. This causes replication fork (RF) stalling and regression, which can further collapse to form single-ended double strand breaks (seDSBs). To avoid mutagenesis, these breaks require repair via Homologous Recombination (HR). Here we apply multicolor single molecule super resolution microscopy to visualize individual RFs under mild stress from the trapping of Topoisomerase I cleavage complexes, a damage induction which closely mimics endogenous replicative stress. We identify RAD51 and RAD52, alongside RECQ1, as the first responder proteins to stalled but unbroken forks, whereas Ku and MRE11 are initially recruited to seDSBs. Ku loads directly onto the DSB end whereas MRE11 associates with nascent DNA away from the break, and both proteins colocalize contemporaneously with a single seDSB. We are thus able to discern closely related RF stress motifs and their repair pathways...
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science_SRH: RT @biorxivpreprint: Super-resolution visualization of distinct stalled and broken replication fork structures https://t.co/nmsotEIKZ0 #bi…
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Sample Sizes : None.
Authors: 6
Total Words: 14745
Unqiue Words: 3922

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#7. Three genomes of Osteoglossidae shed light on ancient teleost evolution
Shijie Hao, Kai Han, Lingfeng Meng, Xiaoyun Huang, Chengcheng Shi, Mengqi Zhang, Yilin Wang, Qun Liu, Yaolei Zhang, Inge Seim, Xun Xu, Xin Liu, Guangyi Fan
Osteoglossiformes is a basal clade of teleost, originated from late Jurassic and had seen the process of continental drift. The genomic differences amongst Osteoglossiformes species should reflect the unique evolve history of that time. Here, we presented the chromosome-level genome of Heterotis niloticus which is the only omnivore species of Osteoglossidae spreading in Africa. Together with other two Osteoglossidae species genomes of Arapaima gigas and Scleropages formosus which spread in South America and Australia respectively, we found great evolutionary differences in gene families and transposable elements. Phylogenetic analysis showed that the ancestor of H. niloticus and A. gigas diverged with S. formosus at ~106.1Mya, consistent with the time of Afro-South American drift and A. gigas speciated from the ancestor of H. niloticus and A. gigas at ~59.2 Mya, consistent with the separation of Eurasia and North American continents. And we proposed the evolutionary traces of Osteoglossidae species based on comparative genomics...
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Sample Sizes : None.
Authors: 13
Total Words: 6162
Unqiue Words: 2241

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#8. Strategies for cellular deconvolution in human brain RNA sequencing data
Olukayode A Sosina, Matthew N Tran, Kristen Maynard, Ran Tao, Margaret A Taub, Keri Martinowich, Stephen A Semick, Daniel Weinberger, Bryan C Quach, Thomas M Hyde, Dana B Hancock, Joel E Kleinman, Jeffrey T Leek, Andrew E Jaffe
Statistical deconvolution strategies have emerged over the past decade to estimate the proportion of various cell populations in homogenate tissue sources like brain using gene expression data. Here we show that several existing deconvolution algorithms which estimate the RNA composition of homogenate tissue, relates to the amount of RNA attributable to each cell type, and not the cellular composition relating to the underlying fraction of cells. Incorporating "cell size" parameters into RNA-based deconvolution algorithms can successfully recover cellular fractions in homogenate brain RNA-seq data. We lastly show that using both cell sizes and cell type-specific gene expression profiles from brain regions other than the target/user-provided bulk tissue RNA-seq dataset consistently results in biased cell fractions. We report several independently constructed cell size estimates as a community resource and extend the MuSiC framework to accommodate these cell size estimates (https://github.com/xuranw/MuSiC/).
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Authors: 14
Total Words: 0
Unqiue Words: 0

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