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Widespread ectopic expression of olfactory receptor genes

Ester Feldmesser, Tsviya Olender, Miriam Khen, Itai Yanai, Ron Ophir, Doron Lancet
2006 BMC Genomics  
Olfactory receptors (ORs) are the largest gene family in the human genome. Although they are expected to be expressed specifically in olfactory tissues, some ectopic expression has been reported, with special emphasis on sperm and testis. The present study systematically explores the expression patterns of OR genes in a large number of tissues and assesses the potential functional implication of such ectopic expression. We analyzed the expression of hundreds of human and mouse OR transcripts,
more » ... a EST and microarray data, in several dozens of human and mouse tissues. Different tissues had specific, relatively small OR gene subsets which had particularly high expression levels. In testis, average expression was not particularly high, and very few highly expressed genes were found, none corresponding to ORs previously implicated in sperm chemotaxis. Higher expression levels were more common for genes with a non-OR genomic neighbor. Importantly, no correlation in expression levels was detected for human-mouse orthologous pairs. Also, no significant difference in expression levels was seen between intact and pseudogenized ORs, except for the pseudogenes of subfamily 7E which has undergone a human-specific expansion. The OR superfamily as a whole, show widespread, locus-dependent and heterogeneous expression, in agreement with a neutral or near neutral evolutionary model for transcription control. These results cannot reject the possibility that small OR subsets might play functional roles in different tissues, however considerable care should be exerted when offering a functional interpretation for ectopic OR expression based only on transcription information.
doi:10.1186/1471-2164-7-121 pmid:16716209 pmcid:PMC1508154 fatcat:sldzusmtzvbn5bidywkj3ioram

Major differences in microRNA quantification are platform and sequence dependent

Ester Feldmesser, Dena Leshkowitz, Yisrael Parmet, Shirley Horn-Saban
2012 BMC Proceedings  
doi:10.1186/1753-6561-6-s6-p7 fatcat:tcku4meavzhjtfl3rvrg2m45ki

UTAP: User-friendly Transcriptome Analysis Pipeline

Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
2019 BMC Bioinformatics  
RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower price per base. However, processing this data requires bioinformatics expertise to tailor and execute specific solutions for each type of library preparation. Results: In order to enable fast and
more » ... er-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of differentially expressed genes. Output files are placed in structured folders, and results summaries are provided in rich and comprehensive reports, containing dozens of plots, tables and links. Conclusion: Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.
doi:10.1186/s12859-019-2728-2 fatcat:6ytquwm2nbgmzntbiknqaluaei

The ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms [article]

Daniella Schatz, Guy Schleyer, Marius Rydningen Saltvedt, Ruth-Anne Sandaa, Ester Feldmesser, Assaf Vardi
2021 bioRxiv   pre-print
Extracellular vesicles are produced by organisms from all kingdoms and serve a myriad of functions, many of which involve cell-cell signaling, especially during stress conditions and host-pathogen interactions. In the marine environment, communication between microorganisms can shape trophic level interactions and population succession, yet we know very little about the involvement of vesicles in these processes. In a previous study, we showed that vesicles produced during viral infection by
more » ... ecologically important model alga Emiliania huxleyi, could act as a pro-viral signal, by expediting infection and enhancing the half-life of the virus in the extracellular milieu. Here, we expand our laboratory findings and show the effect of vesicles on natural populations of E. huxleyi in a mesocosm setting. We profile the small-RNA (sRNA) cargo of vesicles that were produced by E. huxleyi during bloom succession, and show that vesicles applied to natural assemblages expedite viral infection and prolong the half-life of this major mortality agent of E. huxleyi. We subsequently assessed the effect of E. huxleyi-derived vesicles on other microbial populations, and show that there is a downstream effect on the growth of the cyanobacterium Synechococcus, thus emphasizing the importance of extracellular vesicles to microbial interactions in the marine environment.
doi:10.1101/2021.02.10.430559 fatcat:e7hv4lb3brf6johmzxb27g3dkm

Overexpression of AtSHN1/WIN1 Provokes Unique Defense Responses

Dikla Sela, Kobi Buxdorf, Jian Xin Shi, Ester Feldmesser, Lukas Schreiber, Asaph Aharoni, Maggie Levy, Murad Ghanim
2013 PLoS ONE  
Fatty acids of most free cutin monomers are probably activated in some form (eventually as CoA esters), are already linked to glycerol, or do not really occur in large amounts in planta at all.  ... 
doi:10.1371/journal.pone.0070146 pmid:23922943 pmcid:PMC3726498 fatcat:b74tzjqfunfapaojifsv5aspyi

Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration

Kfir Baruch Umansky, Ester Feldmesser, Yoram Groner
2015 Genomics Data  
doi:10.1016/j.gdata.2015.08.030 pmid:26697350 pmcid:PMC4664707 fatcat:72uimedwjvb5tfmpd345a6esc4

The olfactory receptor universe--from whole genome analysis to structure and evolution

Tsviya Olender, Ester Feldmesser, Tal Atarot, Miriam Eisenstein, Doron Lancet
2004 Genetics and Molecular Research  
This will be described in full elsewhere (Feldmesser, E., unpublished results).  ... 
pmid:15688320 fatcat:pf42e4rgojaz7igiqsbp4k7tpi

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi

Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben-Dor
2014 BMC Genomics  
The in-depth description of the experiment and its biological significance was submitted elsewhere (Rosenwasser S, Mausz MA, Schatz D, Sheyn U, Weinstock E, Tzfadia O, Ben-Dor S, Feldmesser E, Pohnert  ... 
doi:10.1186/1471-2164-15-148 pmid:24559402 pmcid:PMC4028052 fatcat:n7vdoeceavg5xmwanq5lggvx5u

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration

Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner, Gregory A. Cox
2015 PLoS Genetics  
Following myonecrosis, muscle satellite cells proliferate, differentiate and fuse, creating new myofibers. The Runx1 transcription factor is not expressed in naïve developing muscle or in adult muscle tissue. However, it is highly expressed in muscles exposed to myopathic damage yet, the role of Runx1 in muscle regeneration is completely unknown. Our study of Runx1 function in the muscle's response to myonecrosis reveals that this transcription factor is activated and cooperates with the MyoD
more » ... d AP-1/c-Jun transcription factors to drive the transcription program of muscle regeneration. Mice lacking dystrophin and muscle Runx1 (mdx -/Runx1 f/f ), exhibit impaired muscle regeneration leading to age-dependent muscle waste, gradual decrease in motor capabilities and a shortened lifespan. Runx1-deficient primary myoblasts are arrested at cell cycle G 1 and consequently differentiate. Such premature differentiation disrupts the myoblasts' normal proliferation/differentiation balance, reduces the number and size of regenerating myofibers and impairs muscle regeneration. Our combined Runx1-dependent gene expression, ChIP-seq, ATAC-seq and histone H3K4me1/H3K27ac modification analyses revealed a subset of Runx1-regulated genes that are co-occupied by MyoD and c-Jun in mdx -/Runx1 f/f muscle. The data provide unique insights into the transcriptional program driving muscle regeneration and implicate Runx1 as an important participant in the pathology of muscle wasting diseases.
doi:10.1371/journal.pgen.1005457 pmid:26275053 pmcid:PMC4537234 fatcat:vdbqy2ccafbj3gvyomemqpyjsm

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools

Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn-Saban, Noam Shomron
2016 PLoS ONE  
One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was
more » ... o assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differentiating mouse embryonic bodies, and their expression patterns were measured. This novel approach was used to assess the accuracy of the tools, as established by comparing the observed results versus the results expected of the mouse controlled spiked-in transcripts. We found that detection of differential expression at the gene level is adequate, yet on the transcript-isoform level, all tools tested lacked accuracy and precision.
doi:10.1371/journal.pone.0153782 pmid:27100792 pmcid:PMC4839710 fatcat:phejxww77jhrdm6yfdgdjelg6e

Improving automated de-novo transcriptome definition in non-model organisms by integrating manually defined gene information

Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben-Dor
2013 EMBnet journal  
doi:10.14806/ej.19.a.614 fatcat:aki5h2e23zbotobbur3y7tvcpm

Ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms

Daniella Schatz, Guy Schleyer, Marius R. Saltvedt, Ruth-Anne Sandaa, Ester Feldmesser, Assaf Vardi
2021 The ISME Journal  
AbstractExtracellular vesicles are produced by organisms from all kingdoms and serve a myriad of functions, many of which involve cell-cell signaling, especially during stress conditions and host-pathogen interactions. In the marine environment, communication between microorganisms can shape trophic level interactions and population succession, yet we know very little about the involvement of vesicles in these processes. In a previous study, we showed that vesicles produced during viral
more » ... n by the ecologically important model alga Emiliania huxleyi, could act as a pro-viral signal, by expediting infection and enhancing the half-life of the virus in the extracellular milieu. Here, we expand our laboratory findings and show the effect of vesicles on natural populations of E. huxleyi in a mesocosm setting. We profile the small-RNA (sRNA) cargo of vesicles that were produced by E. huxleyi during bloom succession, and show that vesicles applied to natural assemblages expedite viral infection and prolong the half-life of this major mortality agent of E. huxleyi. We subsequently reveal that exposure of the natural assemblage to E. huxleyi-derived vesicles modulates not only host-virus dynamics, but also other components of the microbial food webs, thus emphasizing the importance of extracellular vesicles to microbial interactions in the marine environment.
doi:10.1038/s41396-021-01018-5 pmid:34083751 pmcid:PMC8630046 fatcat:e7yalx5jcrea5fst3jjrcgovjm

Cap-independent translation by DAP5 controls cell fate decisions in human embryonic stem cells

Yael Yoffe, Maya David, Rinat Kalaora, Lital Povodovski, Gilgi Friedlander, Ester Feldmesser, Elena Ainbinder, Ann Saada, Shani Bialik, Adi Kimchi
2016 Genes & Development  
Multiple transcriptional and epigenetic changes drive differentiation of embryonic stem cells (ESCs). This study unveils an additional level of gene expression regulation involving noncanonical, cap-independent translation of a select group of mRNAs. This is driven by death-associated protein 5 (DAP5/eIF4G2/NAT1), a translation initiation factor mediating IRES-dependent translation. We found that the DAP5 knockdown from human ESCs (hESCs) resulted in persistence of pluripotent gene expression,
more » ... elayed induction of differentiation-associated genes in different cell lineages, and defective embryoid body formation. The latter involved improper cellular organization, lack of cavitation, and enhanced mislocalized apoptosis. RNA sequencing of polysome-associated mRNAs identified candidates with reduced translation efficiency in DAP5-depleted hESCs. These were enriched in mitochondrial proteins involved in oxidative respiration, a pathway essential for differentiation, the significance of which was confirmed by the aberrant mitochondrial morphology and decreased oxidative respiratory activity in DAP5 knockdown cells. Further analysis identified the chromatin modifier HMGN3 as a cap-independent DAP5 translation target whose knockdown resulted in defective differentiation. Thus, DAP5-mediated translation of a specific set of proteins is critical for the transition from pluripotency to differentiation, highlighting the importance of capindependent translation in stem cell fate decisions.
doi:10.1101/gad.285239.116 pmid:27664238 pmcid:PMC5066241 fatcat:ntog76tqarbwzlrpyrh3d3yhv4

Activation and detoxification of cassava cyanogenic glucosides by the whitefly Bemisia tabaci

Michael L. A. E. Easson, Osnat Malka, Christian Paetz, Anna Hojná, Michael Reichelt, Beate Stein, Sharon van Brunschot, Ester Feldmesser, Lahcen Campbell, John Colvin, Stephan Winter, Shai Morin (+2 others)
2021 Scientific Reports  
AbstractTwo-component plant defenses such as cyanogenic glucosides are produced by many plant species, but phloem-feeding herbivores have long been thought not to activate these defenses due to their mode of feeding, which causes only minimal tissue damage. Here, however, we report that cyanogenic glycoside defenses from cassava (Manihot esculenta), a major staple crop in Africa, are activated during feeding by a pest insect, the whitefly Bemisia tabaci, and the resulting hydrogen cyanide is
more » ... oxified by conversion to beta-cyanoalanine. Additionally, B. tabaci was found to utilize two metabolic mechanisms to detoxify cyanogenic glucosides by conversion to non-activatable derivatives. First, the cyanogenic glycoside linamarin was glucosylated 1–4 times in succession in a reaction catalyzed by two B. tabaci glycoside hydrolase family 13 enzymes in vitro utilizing sucrose as a co-substrate. Second, both linamarin and the glucosylated linamarin derivatives were phosphorylated. Both phosphorylation and glucosidation of linamarin render this plant pro-toxin inert to the activating plant enzyme linamarase, and thus these metabolic transformations can be considered pre-emptive detoxification strategies to avoid cyanogenesis.
doi:10.1038/s41598-021-92553-w pmid:34168179 fatcat:hi5543pymfd5jcvjlkw6yryjbm

RNF20 and USP44 Regulate Stem Cell Differentiation by Modulating H2B Monoubiquitylation

Gilad Fuchs, Efrat Shema, Rita Vesterman, Eran Kotler, Zohar Wolchinsky, Sylvia Wilder, Lior Golomb, Ariel Pribluda, Feng Zhang, Mahmood Haj-Yahya, Ester Feldmesser, Ashraf Brik (+5 others)
2012 Molecular Cell  
Embryonic stem cells (ESC) maintain high genomic plasticity, essential for their capacity to enter diverse differentiation pathways. Post-transcriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2Bub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly
more » ... important for the transcriptional induction of relatively long genes during ESC differentiation. Furthermore, we identify the deubiquitinase USP44 as a negative regulator of H2B ubiquitylation, whose downregulation during ESC differentiation contributes to the increase in H2Bub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.
doi:10.1016/j.molcel.2012.05.023 pmid:22681888 pmcid:PMC3374598 fatcat:sbl6vqlbwreblef4oapjerytli
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