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Article ; Online: Gene regulatory patterning codes in early cell fate specification of the

Cole, Alison G / Hashimshony, Tamar / Du, Zhuo / Yanai, Itai

2024 Volume 12

Abstract: Pattern formation originates during embryogenesis by a series of symmetry-breaking steps throughout an expanding cell lineage. ... ...

Abstract	Pattern formation originates during embryogenesis by a series of symmetry-breaking steps throughout an expanding cell lineage. In
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Gene Expression Regulation, Developmental ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Drosophila/genetics ; Body Patterning/genetics ; Embryo, Nonmammalian/metabolism
Chemical Substances	Caenorhabditis elegans Proteins
Language	English
Publishing date	2024-01-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.87099
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cnidarians layer up.

Hashimshony, Tamar

Nature ecology & evolution

2017 Volume 1, Issue 10, Page(s) 1429–1430

MeSH term(s)	Animals ; Cnidaria ; Signal Transduction
Language	English
Publishing date	2017-11-29
Publishing country	England
Document type	Journal Article ; Comment
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-017-0323-3
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Article ; Online: CEL-Seq2-Single-Cell RNA Sequencing by Multiplexed Linear Amplification.

Yanai, Itai / Hashimshony, Tamar

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1979, Page(s) 45–56

Abstract: Single-cell RNA sequencing has revolutionized the way we look at cell populations. Of the methods available, CEL-Seq was the first to use linear RNA amplification. With early barcoding and 3' sequencing, it is sensitive, cost-effective and easy to ... ...

Abstract	Single-cell RNA sequencing has revolutionized the way we look at cell populations. Of the methods available, CEL-Seq was the first to use linear RNA amplification. With early barcoding and 3' sequencing, it is sensitive, cost-effective and easy to perform. Here we describe a protocol for performing CEL-Seq2 on sorted cells, which can be performed without any special equipment.
MeSH term(s)	Animals ; Base Sequence ; DNA, Complementary/genetics ; Flow Cytometry ; Gene Expression Profiling/economics ; Gene Expression Profiling/methods ; Gene Library ; Humans ; Nucleic Acid Amplification Techniques/economics ; Nucleic Acid Amplification Techniques/methods ; RNA/genetics ; Sequence Analysis, RNA/economics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/economics ; Single-Cell Analysis/methods
Chemical Substances	DNA, Complementary ; RNA (63231-63-0)
Language	English
Publishing date	2019-04-26
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9240-9_4
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Article ; Online: A transcriptomic examination of encased rotifer embryos reveals the developmental trajectory leading to long-term dormancy; are they "animal seeds"?

Hashimshony, Tamar / Levin, Liron / Fröbius, Andreas C / Dahan, Nitsan / Chalifa-Caspi, Vered / Hamo, Reini / Gabai-Almog, Oshri / Blais, Idit / Assaraf, Yehuda G / Lubzens, Esther

BMC genomics

2024 Volume 25, Issue 1, Page(s) 119

Abstract: Background: Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied organisms exhibit seasonal or annual ...

Abstract	Background: Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied organisms exhibit seasonal or annual episodes of dormancy, but numerous less studied organisms enter long-term dormancy, lasting decades or even centuries. Intriguingly, many planktonic animals produce encased embryos known as resting eggs or cysts that, like plant seeds, may remain dormant for decades. Herein, we studied a rotifer Brachionus plicatilis as a model planktonic species that forms encased dormant embryos via sexual reproduction and non-dormant embryos via asexual reproduction and raised the following questions: Which genes are expressed at which time points during embryogenesis? How do temporal transcript abundance profiles differ between the two types of embryos? When does the cell cycle arrest? How do dormant embryos manage energy? Results: As the molecular developmental kinetics of encased embryos remain unknown, we employed single embryo RNA sequencing (CEL-seq) of samples collected during dormant and non-dormant embryogenesis. We identified comprehensive and temporal transcript abundance patterns of genes and their associated enriched functional pathways. Striking differences were uncovered between dormant and non-dormant embryos. In early development, the cell cycle-associated pathways were enriched in both embryo types but terminated with fewer nuclei in dormant embryos. As development progressed, the gene transcript abundance profiles became increasingly divergent between dormant and non-dormant embryos. Organogenesis was suspended in dormant embryos, concomitant with low transcript abundance of homeobox genes, and was replaced with an ATP-poor preparatory phase characterized by very high transcript abundance of genes encoding for hallmark dormancy proteins (e.g., LEA proteins, sHSP, and anti-ROS proteins, also found in plant seeds) and proteins involved in dormancy exit. Surprisingly, this period appeared analogous to the late maturation phase of plant seeds. Conclusions: The study highlights novel divergent temporal transcript abundance patterns between dormant and non-dormant embryos. Remarkably, several convergent functional solutions appear during the development of resting eggs and plant seeds, suggesting a similar preparatory phase for long-term dormancy. This study accentuated the broad novel molecular features of long-term dormancy in encased animal embryos that behave like "animal seeds".
MeSH term(s)	Animals ; Rotifera/genetics ; Gene Expression Profiling ; Transcriptome ; Proteins/metabolism ; Seeds ; Plant Dormancy ; Germination/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2024-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-024-09961-1
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Article ; Online: Decidual-tissue-resident memory T cells protect against nonprimary human cytomegalovirus infection at the maternal-fetal interface.

Cell reports

2024 Volume 43, Issue 2, Page(s) 113698

Abstract: Congenital cytomegalovirus (cCMV) is the most common intrauterine infection, leading to infant neurodevelopmental disabilities. An improved knowledge of correlates of protection against cCMV is needed to guide prevention strategies. Here, we employ an ex ...

Abstract	Congenital cytomegalovirus (cCMV) is the most common intrauterine infection, leading to infant neurodevelopmental disabilities. An improved knowledge of correlates of protection against cCMV is needed to guide prevention strategies. Here, we employ an ex vivo model of human CMV (HCMV) infection in decidual tissues of women with and without preconception immunity against CMV, recapitulating nonprimary vs. primary infection at the authentic maternofetal transmission site. We show that decidual tissues of women with preconception immunity against CMV exhibit intrinsic resistance to HCMV, mounting a rapid activation of tissue-resident memory CD8
MeSH term(s)	Infant ; Humans ; Female ; Cytomegalovirus ; CD8-Positive T-Lymphocytes ; Memory T Cells ; Cytomegalovirus Infections ; Fetus
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.113698
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Article ; Online: Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms.

Levin, Michal / Zalts, Harel / Mostov, Natalia / Hashimshony, Tamar / Yanai, Itai

Nucleic acids research

2020 Volume 48, Issue 11, Page(s) 5926–5938

Abstract: Alternative polyadenylation (APA) produces isoforms with distinct 3'-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect the expression levels of APA isoforms from 3'-end RNA-Seq data by ... ...

Abstract	Alternative polyadenylation (APA) produces isoforms with distinct 3'-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect the expression levels of APA isoforms from 3'-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification. We detected the expression levels of APA isoforms in individual Caenorhabditis elegans embryos at different stages throughout embryogenesis. Examining the correlation between the temporal profiles of isoforms led us to distinguish two classes of genes: those with highly correlated isoforms (HCI) and those with lowly correlated isoforms (LCI) across time. We hypothesized that variants with similar expression profiles may be the product of biological noise, while the LCI variants may be under tighter selection and consequently their distinct 3' UTR isoforms are more likely to have functional consequences. Supporting this notion, we found that LCI genes have significantly more miRNA binding sites, more correlated expression profiles with those of their targeting miRNAs and a relative lack of correspondence between their transcription and protein abundances. Collectively, our results suggest that a lack of coherence among the regulation of 3' UTR isoforms is a proxy for selective pressures acting upon APA usage and consequently for their functional relevance.
MeSH term(s)	3' Untranslated Regions/genetics ; Animals ; Caenorhabditis elegans/embryology ; Caenorhabditis elegans/genetics ; Drosophila melanogaster ; Embryonic Development/genetics ; Gene Expression Regulation, Developmental ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Nucleic Acid Conformation ; Poly A/analysis ; Polyadenylation ; Xenopus laevis
Chemical Substances	3' Untranslated Regions ; MicroRNAs ; Poly A (24937-83-5)
Language	English
Publishing date	2020-05-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa359
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Article ; Online: Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells.

Dvir, Shlomi / Argoetti, Amir / Lesnik, Chen / Roytblat, Mark / Shriki, Kohava / Amit, Michal / Hashimshony, Tamar / Mandel-Gutfreund, Yael

Cell reports

2021 Volume 35, Issue 9, Page(s) 109198

Abstract: Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) ... ...

Abstract	Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
MeSH term(s)	Cell Differentiation/genetics ; Cell Line ; DNA/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Human Embryonic Stem Cells/metabolism ; Humans ; Protein Binding ; Proteome/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; STAT3 Transcription Factor/metabolism
Chemical Substances	Proteome ; RNA, Messenger ; RNA-Binding Proteins ; STAT3 Transcription Factor ; STAT3 protein, human ; DNA (9007-49-2)
Language	English
Publishing date	2021-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109198
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Article ; Online: Spatiotemporal Gene Expression Analysis of the

Tzur, Yonatan B / Winter, Eitan / Gao, Jinmin / Hashimshony, Tamar / Yanai, Itai / Colaiácovo, Monica P

Genetics

2018 Volume 210, Issue 2, Page(s) 587–605

Abstract: Developmental programs are executed by tightly controlled gene regulatory pathways. Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear ... ...

Abstract	Developmental programs are executed by tightly controlled gene regulatory pathways. Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear amplification and sequencing) to generate a spatiotemporal gene expression map of the
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/growth & development ; Gametogenesis ; Gene Expression Regulation, Developmental ; Germ Cells/cytology ; Germ Cells/metabolism ; Meiosis ; X Chromosome/genetics ; X Chromosome Inactivation
Language	English
Publishing date	2018-08-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.118.301315
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Article ; Online: Seeing is believing: new methods for in situ single-cell transcriptomics.

Avital, Gal / Hashimshony, Tamar / Yanai, Itai

Genome biology

2014 Volume 15, Issue 3, Page(s) 110

Abstract: New methods employ RNA-seq to study single cells within complex tissues by in situ sequencing or mRNA capture from single photoactivated cells. ...

Abstract	New methods employ RNA-seq to study single cells within complex tissues by in situ sequencing or mRNA capture from single photoactivated cells.
MeSH term(s)	Animals ; Brain/metabolism ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Hippocampus/metabolism ; Humans ; Neurons/metabolism ; Sequence Analysis, RNA/methods ; Transcriptome
Language	English
Publishing date	2014-03-31
Publishing country	England
Document type	Journal Article ; Review ; Comment
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb4169
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Article ; Online: Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools.

Yelin, Idan / Aharony, Noga / Tamar, Einat Shaer / Argoetti, Amir / Messer, Esther / Berenbaum, Dina / Shafran, Einat / Kuzli, Areen / Gandali, Nagham / Shkedi, Omer / Hashimshony, Tamar / Mandel-Gutfreund, Yael / Halberthal, Michael / Geffen, Yuval / Szwarcwort-Cohen, Moran / Kishony, Roy

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2020 Volume 71, Issue 16, Page(s) 2073–2078

Abstract: Background: The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic of unprecedented scale. Although diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare ... ...

Abstract	Background: The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic of unprecedented scale. Although diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately applicable protocol. Methods: RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction, alone or in pools of different sizes (2-, 4-, 8-, 16-, 32-, and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. Results: A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, although this may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. Conclusions: As it uses the standard protocols, reagents, and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for coronavirus disease 2019 would allow expanding current screening capacities, thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/virology ; Humans ; Real-Time Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity
Keywords	covid19
Language	English
Publishing date	2020-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciaa531
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