journal
MENU ▼
Read by QxMD icon Read
search

Genome Research

journal
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#1
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087841/single-cell-transcriptome-analysis-of-fish-immune-cells-provides-insight-into-the-evolution-of-vertebrate-immune-cell-types
#2
Santiago J Carmona, Sarah A Teichmann, Lauren Ferreira, Iain C Macaulay, Michael J T Stubbington, Ana Cvejic, David Gfeller
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analysed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared to other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA-Sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a non-mammalian species...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28073919/trub1-is-the-predominant-pseudouridine-synthase-acting-on-mammalian-mrna-via-a-predictable-and-conserved-code
#3
Modi Safra, Ronit Nir, Daneyal Farouq, Schraga Schwartz
Following synthesis, RNA can be modified with over 100 chemically distinct modifications, which can potentially regulate RNA expression post-transcriptionally. Pseudouridine (Ψ) was recently established to be widespread and dynamically regulated on yeast mRNA, but less is known about Ψ presence, regulation and biogenesis in mammalian mRNA. Here, we sought to characterize the Ψ landscape on mammalian mRNA, to identify the main Ψ-synthases (PUSs) catalyzing Ψ formation, and to understand the factors governing their specificity towards selected targets...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28073918/identical-bacterial-populations-colonize-premature-infant-gut-skin-and-oral-microbiomes-and-exhibit-different-in-situ-growth-rates
#4
Matthew R Olm, Christopher T Brown, Brandon Brooks, Brian Firek, Robyn Baker, David Burstein, Karina Soenjoyo, Brian C Thomas, Michael Morowitz, Jillian Banfield
The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28057745/reciprocal-insulation-analysis-of-hi-c-data-shows-that-tads-represent-a-functionally-but-not-structurally-privileged-scale-in-the-hierarchical-folding-of-chromosomes
#5
Yinxiu Zhan, Luca Mariani, Iros Barozzi, Edda G Schulz, Nils Bluthgen, Michael Stadler, Guido Tiana, Luca Giorgetti
Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions...
January 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28052920/evolution-of-transcript-modification-by-n6-methyladenosine-in-primates
#6
Lijia Ma, Boxuan Zhao, Kai Chen, Amber Thomas, Jigyasa H Tuteja, Xin He, Chuan He, Kevin White
Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression (King and Wilson 1975; Romero et al. 2012; Villar et al. 2014). However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and little is understood about the influence of post-transcriptional processes on transcript evolution. Post-transcriptional modification of RNA by N6-methyladenosine (m6A) has been shown to be widespread throughout the transcriptome (Desrosiers et al...
January 4, 2017: Genome Research
https://www.readbyqxmd.com/read/28049628/initiation-of-mtdna-transcription-is-followed-by-pausing-and-diverge-across-human-cell-types-and-during-evolution
#7
Amit Blumberg, Edward J Rice, Anshul Kundaje, Charles G Danko, Dan Mishmar
Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS...
January 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28031250/a-to-i-rna-editing-promotes-developmental-stage-specific-gene-and-lncrna-expression
#8
Boaz Goldstein, Lily Agranat-Tamir, Dean Light, Orna Ben-Naim Zgayer, Alla Fishman, Ayelet T Lamm
A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions. Although human RNAs contain millions of A-to-I editing sites, most of these occur in noncoding regions and their function is unknown. Mutations in ADAR enzymes in C. elegans cause defects in normal development but are not lethal as in human and mouse. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, with the observation that worms that lack both mechanisms do not exhibit defects when only RNA editing is absent...
December 28, 2016: Genome Research
https://www.readbyqxmd.com/read/28031249/transcription-factor-assisted-loading-and-enhancer-dynamics-dictate-the-hepatic-fasting-response
#9
Ido Goldstein, Songjoon Baek, Diego M Presman, Ville Pakkinaho, Erin E Swinstead, Gordon L Hager
Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understands how this complex network regulates the metabolic response to fasting we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancers features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA) and CCAAT/enhancer binding protein beta (CEBPB)...
December 28, 2016: Genome Research
https://www.readbyqxmd.com/read/28028072/model-based-analysis-of-dna-replication-profiles-predicting-replication-fork-velocity-and-initiation-rate-by-profiling-free-cycling-cells
#10
Ariel Gispan, Miri Carmi, Naama Barkai
Eukaryotic cells initiate DNA synthesis by sequential firing of hundreds of origins. This ordered replication is described by replication profiles, which measure the DNA content within a cell population. Here, we show that replication dynamics can be deduced from replication profiles of free-cycling cells. While such profiles lack explicit temporal information, they are sensitive to fork velocity and initiation capacity through the passive replication pattern, namely the replication of origins by forks emanating elsewhere...
December 27, 2016: Genome Research
https://www.readbyqxmd.com/read/27986821/using-reference-free-compressed-data-structures-to-analyse-sequencing-reads-from-thousands-of-human-genomes
#11
Dirk-Dominic Dolle, Zhicheng Liu, Matthew L Cotten, Jared T Simpson, Zamin Iqbal, Richard Durbin, Shane A McCarthy, Thomas M Keane
We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full text searchable index for read alignment and de novo assembly...
December 16, 2016: Genome Research
https://www.readbyqxmd.com/read/27965292/engineered-line-1-retrotransposition-in-non-dividing-human-neurons
#12
Angela Macia, Thomas J Widmann, Sara R Heras, Veronica Ayllon, Laura Sanchez, Meriem Benkaddour-Boumzaouad, Martin Munoz-Lopez, Alejandro Rubio, Suyapa Amador-Cubero, Eva Blanco-Jimenez, Javier Garcia-Castro, Pablo Menendez, Philip Ng, Alysson R Muotri, John L Goodier, Jose L Garcia-Perez
Half of the human genome is made of Transposable Elements (TEs) whose ongoing activity continues to impact our genome. LINE-1 (or L1) is an autonomous non-LTR retrotransposon in the human genome, comprising 17% of its genomic mass and containing an average of 80-100 active L1s per average genome that provide a source of inter-individual variation. New LINE-1 insertions are thought to accumulate mostly during human embyogenesis. Surprisingly, the activity of L1s can further impact the somatic human brain genome...
December 13, 2016: Genome Research
https://www.readbyqxmd.com/read/27965291/comparative-analyses-of-super-enhancers-reveal-conserved-elements-in-vertebrate-genomes
#13
Yuvia A Pérez-Rico, Valentina Boeva, Allison C Mallory, Angelo Bitetti, Sara Majello, Emmanuel Barillot, Alena Shkumatava
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs...
December 13, 2016: Genome Research
https://www.readbyqxmd.com/read/27965289/large-scale-reduction-of-the-bacillus-subtilis-genome-consequences-for-the-transcriptional-network-resource-allocation-and-metabolism
#14
Daniel R Reuß, Josef Altenbuchner, Ulrike Mäder, Hermann Rath, Till Ischebeck, Praveen Kumar Sappa, Andrea Thürmer, Cyprien Guerin, Pierre Nicolas, Leif Steil, Bingyao Zhu, Ivo Feussner, Stefan Klumpp, Rolf Daniel, Fabian M Commichau, Uwe Völker, Jörg Stülke
Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium Bacillus subtilis whose genomes have been reduced by about 36%. These strains are fully viable and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism...
December 13, 2016: Genome Research
https://www.readbyqxmd.com/read/27940952/hapcut2-robust-and-accurate-haplotype-assembly-for-diverse-sequencing-technologies
#15
Peter Edge, Vineet Bafna, Vikas Bansal
Many tools have been developed for haplotype assembly - the reconstruction of individual haplotypes using reads mapped to a reference genome sequence. Due to increasing interest in obtaining haplotype-resolved human genomes, a range of new sequencing protocols and technologies have been developed to enable the reconstruction of whole-genome haplotypes. However, existing computational methods designed to handle specific technologies do not scale well on data from different protocols. We describe a new algorithm, HapCUT2, that extends our previous method (HapCUT) to handle multiple sequencing technologies...
December 9, 2016: Genome Research
https://www.readbyqxmd.com/read/27940951/apobec3a-b-induced-mutagenesis-is-responsible-for-20-of-heritable-mutations-in-the-tpcpw-context
#16
Vladimir B Seplyarskiy, Maria A Andrianova, Georgii A Bazykin
APOBEC3A/B cytidine deaminase is responsible for the majority of cancerous mutations in a large fraction of cancer samples. However, its role in heritable mutagenesis remains very poorly understood. Recent studies have demonstrated that both in yeast and in human cancerous cells, most of APOBEC3A/B-induced mutations occur on the lagging strand during replication and, on the non-template strand of transcribed regions. Here, we use data on rare human polymorphisms, interspecies divergence, and de novo mutations to study germline mutagenesis, and analyze mutations at nucleotide contexts prone to attack by APOBEC3A/B...
December 9, 2016: Genome Research
https://www.readbyqxmd.com/read/27940950/a-gc-rich-sequence-feature-in-the-3-utr-directs-upf1-dependent-mrna-decay-in-mammalian-cells
#17
Naoto Imamachi, Kazi Abdus Salam, Yutaka Suzuki, Nobuyoshi Akimitsu
Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify characteristic sequence features of UPF1 targets. We identified 246 UPF1 targets by measuring RNA stabilization upon UPF1 depletion and by identifying mRNAs that associate with UPF1...
December 9, 2016: Genome Research
https://www.readbyqxmd.com/read/27927715/chromatin-environment-transcriptional-regulation-and-splicing-distinguish-lincrnas-and-mrnas
#18
Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L Rinn
While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters...
December 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27923845/numerical-and-spatial-patterning-of-yeast-meiotic-dna-breaks-by-tel1
#19
Neeman Mohibullah, Scott Keeney
The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Mechanisms of this regulation remain poorly understood. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to reveal aspects of the contribution of the Saccharomyces cerevisiae DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM). A tel1Δ mutant has globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing...
December 6, 2016: Genome Research
https://www.readbyqxmd.com/read/27923844/characterization-of-hundreds-of-regulatory-landscapes-in-developing-limbs-reveals-two-regimes-of-chromatin-folding
#20
Guillaume Andrey, Robert Schöpflin, Ivana Jerković, Verena Heinrich, Daniel Murad Ibrahim, Christina Paliou, Myriam Hochradel, Bernd Timmermann, Stefan Haas, Martin Vingron, Stefan Mundlos
Complex regulatory landscapes control the pleiotropic transcriptional activities of developmental genes. For most genes, the number, location and dynamic of their associated regulatory elements are unknown. In this work we characterized the three-dimensional chromatin micro-architecture and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq and RNA-seq in forelimb, hindlimb at three developmental stages and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains...
December 6, 2016: Genome Research
journal
journal
32413
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"