Top 7 Biorxiv Papers Today in Genomics


2.001 Mikeys
#1. Integrative single-cell and bulk RNA-seq analysis in human retina identified cell type-specific composition and gene expression changes for age-related macular degeneration
Yafei Lyu, Randy Zauhar, Nico Dana, Christianne Strang, Kui Wang, Shanrun Liu, Zhen Miao, Naifei Pan, Paul Gamlin, James Kimble, Jeffrey Messinger, Christine Curcio, Dwight Stambolian, Mingyao Li
Age-related macular degeneration (AMD) preferentially affects distinct cell types and topographic regions in retina. To characterize the impact of AMD on gene expression changes across retinal cell types and regions, we generated both single-cell RNA-seq (scRNA-seq) and bulk RNA-seq data from macular and peripheral retina in postmortem human donors with and without AMD. The scRNA-seq data revealed 11 major cell types with many previously reported AMD risk genes showing substantial cell type and region specificity. Cell type proportional changes with advancing AMD stage were significant for Muller glia, rods, astrocytes, microglia and endothelium.
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MingyaoLi1: Our new paper “Integrative single-cell and bulk RNA-seq analysis in human retina identified cell type-specific composition and gene expression changes for age-related macular degeneration” led by @lyuyafeigmailc1 https://t.co/SdiHPALKka
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Sample Sizes : [39, 30]
Authors: 14
Total Words: 7038
Unqiue Words: 2316

1.998 Mikeys
#2. Remodeling of the H3 nucleosomal landscape during mouse aging
Yilin Chen, Juan I Bravo, Berenice Anath Benayoun
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the 'epigenome') can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, though alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mice tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic...
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_JayyGeeCee: RT @biorxiv_genomic: Remodeling of the H3 nucleosomal landscape during mouse aging https://t.co/P38syLSftP #biorxiv_genomic
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1.997 Mikeys
#3. Rich polymorphic variants of alpha satellite 34mer higher order repeats in hg38 assembly of human chromosome Y
Matko Gluncic, Ines Vlahović, Vladimir Paar
A challenging problem in human population genetics is related to the unique role of human Y chromosome, with properties that distinguish humans from other species. Centromeres in primate genomes are constituted of tandem repeats of ~171 bp alpha satellite monomers, commonly organized into higher order repats (HORs). Because of gaps in DNA sequencing, HOR regions as genomic "black holes" have been understudied in spite of crucial importance. Only recently the sequencing of more complete satellite DNAs becomes accessible. In human Y chromosome the largest alpha satellite higher order repeat unit 34/36mer was found, but its polymorphic variants were not investigated. Here, we study the human Y chromosome centromeric genomic sequence from hg38 assembly using our novel ALPHAsub algorithm for simple identification of alpha satellite arrays and robust GRM algorithm for HOR identification in repeat sequences. We determine the monomer alignment scheme for alpha satellite HOR array based on canonical 34mer HOR, discovering a wealth of novel...
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1.997 Mikeys
#4. PREVALENCE OF UGT1A1 GENETIC VARIANTS IN ARGENTINEAN POPULATION, POTENTIAL IMPLICATIONS FOR PHARMACOGENOMIC TESTING
Cintia Valeria Cruz, Paula Scibona, Waldo Belloso, Romina Cajal
The four groups of uridine diphosphate glucuronosyltransferase (UGT) enzymes form a superfamily responsible for the glucuronidation of target substrates. These include hormones, flavonoids, environmental mutagens and pharmaceutical drugs. Thus, UGT enzymes are relevant for pharmacogenetic research.Most of the members of the UGT family are expressed in the liver, but are also present in intestinal, stomach or breast tissue.The incidences and types of polymorphisms for different enzymes vary with geographical regions and ethnic groups. This is the first study that examined the frequency of polymorphisms for UGT1 isozymes for a population of 100 healthy argentinians.The distribution of UGT1A1 in our population was: 70.5% (70.5) for the *1 allele, 21.5% for the *28 allele and 1% for the *36 allele. 48% (48) presented the \*1/\*1 genotype, while 43 % (43) had \*1/\*28, 2% (2) had \*1/\*36 and 7% (7) showed \*28/\*28. There was no preferential sex distribution.Since most Argentinians are of Caucasian descent, a European genotype...
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biorxivpreprint: PREVALENCE OF UGT1A1 GENETIC VARIANTS IN ARGENTINEAN POPULATION, POTENTIAL IMPLICATIONS FOR PHARMACOGENOMIC TESTING https://t.co/DRvtvXM9hT #bioRxiv
biorxiv_genomic: PREVALENCE OF UGT1A1 GENETIC VARIANTS IN ARGENTINEAN POPULATION, POTENTIAL IMPLICATIONS FOR PHARMACOGENOMIC TESTING https://t.co/1vR8sD601P #biorxiv_genomic
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1.997 Mikeys
#5. ASlive: a database for alternative splicing atlas in livestock animals
Jinding Liu, Suxu Tan, Shuiqing Huang, Wen Huang
We present in this study the development and implementation of a database for alternative splicing atlas in livestock animals (ASlive.org). Alternative splicing is an important biological process whose precision must be tightly regulated during growth and development. Using publicly available RNASeq data sets across many tissues, cell types, and biological conditions totaling 28.6 tera bases, we built a database of alternative splicing events in five major livestock animal species (cattle, sheep, pigs, horses, and chickens). The database contains many types of information on alternative splicing events, including basic information such as genomic locations, genes, and event types, quantitative measurements of alternative splicing in the form of percent spliced in (PSI), overlap with known DNA variants, as well as orthologous events across different lineage groups. This database, the first of its kind in livestock animals, will provide a useful exploratory tool to assist functional annotation of animal genomes.
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biorxivpreprint: ASlive: a database for alternative splicing atlas in livestock animals https://t.co/5SoeUYR4av #bioRxiv
biorxiv_genomic: ASlive: a database for alternative splicing atlas in livestock animals https://t.co/gZYAiojFZs #biorxiv_genomic
nickschurch: RT @biorxivpreprint: ASlive: a database for alternative splicing atlas in livestock animals https://t.co/5SoeUYR4av #bioRxiv
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Total Words: 4024
Unqiue Words: 1605

1.997 Mikeys
#6. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps
Prashant S Hosmani, Mirella Flores-Gonzalez, Henri van de Geest, Florian Maumus, Linda V Bakker, Elio Schijlen, Jan van Haarst, Jan Cordewener, Gabino Sanchez-Perez, Sander Peters, Zhangjun Fei, James J Giovannoni, Lukas A Mueller, Surya Saha
The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe from a variety of input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here the latest tomato reference genome (SL4.0) assembled de novo from PacBio long reads and scaffolded using Hi-C contact maps. The assembly was validated using Bionano optical maps and 10X linked-read sequences. This assembly is highly contiguous with fewer gaps compared to previous genome builds and almost all scaffolds have been anchored and oriented to the 12 tomato chromosomes. We have found more repeats compared to the previous versions and one of the largest repeat classes identified are the LTR retrotransposons. We also describe updates to the reference genome and annotation since the last publication. The corresponding ITAG4.0 annotation has 4,794 novel genes along with 29,281 genes preserved from ITAG2.4. Most of the updated genes have extensions in the 5' and...
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biorxivpreprint: An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps https://t.co/r4XJyyp6Am #bioRxiv
biorxiv_genomic: An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation ... https://t.co/V9JHASdtBm #biorxiv_genomic
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Authors: 14
Total Words: 8888
Unqiue Words: 2776

1.997 Mikeys
#7. Decoding the transcriptional response to ischemic stroke in young and aged mouse brain
Peter Androvic, Denisa Belov Kirdajova, Jana Tureckova, Daniel Zucha, Eva Rohlova, Pavel Abaffy, Jan Kriska, Miroslava Anderova, Mikael Kubista, Lukas Valihrach
Ischemic stroke is one of the leading causes of mortality and major healthcare and economic burden. It is a well recognized disease of aging, yet it is unclear how the age-dependent vulnerability occurs and what are the underlying mechanisms. To address these issues, we performed a comprehensive RNA-Seq analysis of aging, ischemic stroke and their interaction using a model of permanent middle cerebral artery occlusion (MCAO) in 3 and 18 month old female mice. We assessed differential gene expression across injury status and age, estimated cell type proportion changes, assayed the results against a range of transcriptional signatures from the literature and performed unsupervised co-expression analysis, identifying modules of genes with varying response to injury. We uncovered selective vulnerability of neuronal populations and increased activation of type-I interferon (IFN-I) signaling and several other inflammatory path-ways in aged mice. We extended these findings via targeted expression analysis in tissue as well as acutely...
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Authors: 10
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