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Article ; Online: pepgrep: A tool for peptide MS/MS pattern matching.

Chernukhin, Igor

2013 Volume 11, Issue 2, Page(s) 127–132

Abstract: Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular ... ...

Abstract	Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a compact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 fingerprint for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to-MS2 scoring algorithm. pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface (API) or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity purification techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http://bsproteomics.essex.ac.uk:8080/data/download/pepgrep-1.4.tgz.
MeSH term(s)	Algorithms ; Databases, Protein ; Pattern Recognition, Automated ; Peptides/chemistry ; Software ; Tandem Mass Spectrometry/methods
Chemical Substances	Peptides
Language	English
Publishing date	2013-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2013.02.001
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Article ; Online: ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs.

Minshall, Nicola / Chernukhin, Igor / Carroll, Jason S / Git, Anna

BioTechniques

2021 Volume 72, Issue 1, Page(s) 21–28

Abstract: Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq ... ...

Abstract	Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq protocol (ncRNAseq), allowing the capture and sequencing of mid-sized non-coding RNAs without detriment to the coverage of coding mRNAs. This protocol is coupled with a two-step alignment: a pre-alignment to a curated non-coding genome, passing only the non-mapping reads to a standard genomic alignment. ncRNAseq correctly assigns the highest read-numbers to established abundant non-coding RNAs and correctly identifies cytosolic and nuclear enrichment of known non-coding RNAs in two cell lines.
MeSH term(s)	Gene Library ; High-Throughput Nucleotide Sequencing/methods ; RNA, Untranslated ; RNA-Seq ; Sequence Analysis, RNA/methods
Chemical Substances	RNA, Untranslated
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	48453-2
ISSN	1940-9818 ; 0736-6205
ISSN (online)	1940-9818
ISSN	0736-6205
DOI	10.2144/btn-2021-0035
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Article: pepgrep: A Tool for Peptide MS/MS Pattern Matching

Chernukhin, Igor

Genomics, proteomics & bioinformatics. 2013 Apr., v. 11, no. 2

2013

Abstract	Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a compact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 fingerprint for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to-MS2 scoring algorithm. pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface (API) or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity purification techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http://bsproteomics.essex.ac.uk:8080/data/download/pepgrep-1.4.tgz.
Keywords	algorithms ; amino acid sequences ; computer software ; data collection ; databases ; dissociation ; ions ; peptides ; purification methods ; screening
Language	English
Dates of publication	2013-04
Size	p. 127-132.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2013.02.001
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Article: Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis

Chaplin, Amanda K / Chernukhin, Igor / Bechtold, Ulrike

Journal of experimental botany. 2019 Jan. 07, v. 70, no. 2

2019

Abstract: Non-enzymatic post-translational modifications of proteins can occur when the nucleophilic amino acid side chains of lysine and arginine encounter a reactive metabolite to form advanced glycation end products (AGEs). Glycation arises predominantly from ... ...

Abstract	Non-enzymatic post-translational modifications of proteins can occur when the nucleophilic amino acid side chains of lysine and arginine encounter a reactive metabolite to form advanced glycation end products (AGEs). Glycation arises predominantly from the degradation of reducing sugars, and glycation has been observed during metabolic stress from glucose metabolism in both animals and plants. The implications of glycating proteins on plant proteins and biology has received little attention, and here we describe a robust assessment of global glycation profiles. We identified 112 glycated proteins that were common under a range of growth conditions and abiotic stress treatments, but also showed rosette age, diurnal, and drought stress-specific targets. Among 18 drought stress-specific glycation targets included several thioredoxin and thioredoxin-like proteins. In vitro glycation of two carbohydrate metabolism enzymes led either to a reduction or to a complete inhibition of activity, demonstrating the impact of glycation on protein function. Taken together, our results suggest that stress-specific glycation patterns of a small number of regulatory proteins may have a much broader impact on downstream target proteins that are, for example, associated with primary metabolism.
Keywords	Arabidopsis ; Lewis bases ; abiotic stress ; advanced glycation end products ; arginine ; carbohydrate metabolism ; drought ; glucose ; glycation ; lysine ; metabolites ; plant proteins ; post-translational modification ; reducing sugars ; regulatory proteins ; thioredoxins
Language	English
Dates of publication	2019-0107
Size	p. 653-670.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/ery389
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Article ; Online: Comprehensive Genomic Analysis Reveals that the Pioneering Function of FOXA1 Is Independent of Hormonal Signaling.

Glont, Silvia-E / Chernukhin, Igor / Carroll, Jason S

Cell reports

2019 Volume 26, Issue 10, Page(s) 2558–2565.e3

Abstract: Considerable work has linked hormone receptors, such as estrogen receptor-alpha (ER), with the pioneer factor FOXA1. Altered FOXA1 levels contribute to endocrine-resistant breast cancer, where it maintains ER-chromatin interactions, even in contexts in ... ...

Abstract	Considerable work has linked hormone receptors, such as estrogen receptor-alpha (ER), with the pioneer factor FOXA1. Altered FOXA1 levels contribute to endocrine-resistant breast cancer, where it maintains ER-chromatin interactions, even in contexts in which cells are refractory to ER-targeted drugs. A recent study controversially suggests that FOXA1 binding can be induced by hormonal pathways, including the estrogen-ER complex. We now show that the vast majority (>99%) of FOXA1 binding events are unaffected by steroid activation. A small number (<1%) of FOXA1 binding sites appear to be induced by estrogen, but these are created from chromatin interactions between ER binding sites and adjacent FOXA1 binding sites and do not represent genuine new FOXA1-pioneering elements. FOXA1 is therefore not regulated by estrogen and remains a bone fide pioneer factor that is entirely upstream of the ER complex.
MeSH term(s)	Animals ; Cell Line ; Genomics/methods ; Hepatocyte Nuclear Factor 3-alpha/genetics ; Humans ; MCF-7 Cells ; Rabbits ; Signal Transduction
Chemical Substances	FOXA1 protein, human ; Hepatocyte Nuclear Factor 3-alpha
Language	English
Publishing date	2019-03-06
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.2019.02.036
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Article ; Online: Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis.

Chaplin, Amanda K / Chernukhin, Igor / Bechtold, Ulrike

Journal of experimental botany

2018 Volume 70, Issue 2, Page(s) 653–670

Abstract	Non-enzymatic post-translational modifications of proteins can occur when the nucleophilic amino acid side chains of lysine and arginine encounter a reactive metabolite to form advanced glycation end products (AGEs). Glycation arises predominantly from the degradation of reducing sugars, and glycation has been observed during metabolic stress from glucose metabolism in both animals and plants. The implications of glycating proteins on plant proteins and biology has received little attention, and here we describe a robust assessment of global glycation profiles. We identified 112 glycated proteins that were common under a range of growth conditions and abiotic stress treatments, but also showed rosette age, diurnal, and drought stress-specific targets. Among 18 drought stress-specific glycation targets included several thioredoxin and thioredoxin-like proteins. In vitro glycation of two carbohydrate metabolism enzymes led either to a reduction or to a complete inhibition of activity, demonstrating the impact of glycation on protein function. Taken together, our results suggest that stress-specific glycation patterns of a small number of regulatory proteins may have a much broader impact on downstream target proteins that are, for example, associated with primary metabolism.
MeSH term(s)	Arabidopsis/metabolism ; Arabidopsis Proteins/metabolism ; Glycation End Products, Advanced/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/metabolism ; Stress, Physiological ; Thioredoxins/metabolism ; Triose-Phosphate Isomerase/metabolism
Chemical Substances	Arabidopsis Proteins ; Glycation End Products, Advanced ; Thioredoxins (52500-60-4) ; GAPC1 protein, Arabidopsis (EC 1.2.1.12) ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) (EC 1.2.1.12) ; Triose-Phosphate Isomerase (EC 5.3.1.1)
Language	English
Publishing date	2018-11-05
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/ery389
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Article ; Online: Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation.

Redmond, Aisling M / Omarjee, Soleilmane / Chernukhin, Igor / Le Romancer, Muriel / Carroll, Jason S

PloS one

2019 Volume 14, Issue 11, Page(s) e0225180

Abstract: HER2 is a transmembrane receptor tyrosine kinase, which plays a key role in breast cancer due to a common genomic amplification. It is used as a marker to stratify patients in the clinic and is targeted by a number of drugs including Trastuzumab and ... ...

Abstract	HER2 is a transmembrane receptor tyrosine kinase, which plays a key role in breast cancer due to a common genomic amplification. It is used as a marker to stratify patients in the clinic and is targeted by a number of drugs including Trastuzumab and Lapatinib. HER2 has previously been shown to translocate to the nucleus. In this study, we have explored the properties of nuclear HER2 by analysing the binding of this protein to the chromatin in two breast cancer cell lines. We find genome-wide re-programming of HER2 binding after treatment with the growth factor EGF and have identified a de novo motif at HER2 binding sites. Over 2,000 HER2 binding sites are found in both breast cancer cell lines after EGF treatment, and according to pathway analysis, these binding sites were enriched near genes involved in protein kinase activity and signal transduction. HER2 was shown to co-localise at a small subset of regions demarcated by H3K4me1, a hallmark of functional enhancer elements and HER2/H3K4me1 co-bound regions were enriched near EGF regulated genes providing evidence for their functional role as regulatory elements. A chromatin bound role for HER2 was verified by independent methods, including Proximity Ligation Assay (PLA), which confirmed a close association between HER2 and H3K4me1. Mass spectrometry analysis of the chromatin bound HER2 complex identified EGFR and STAT3 as interacting partners in the nucleus. These findings reveal a global role for HER2 as a chromatin-associated factor that binds to enhancer elements to elicit direct gene expression events in breast cancer cells.
MeSH term(s)	Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Cell Line, Tumor ; Chromatin ; Enhancer Elements, Genetic ; Female ; Gene Expression Regulation, Neoplastic ; Histones/metabolism ; Humans ; Nucleotide Motifs ; Protein Binding ; Receptor, ErbB-2/metabolism ; Transcriptional Activation
Chemical Substances	Chromatin ; Histones ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2019-11-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0225180
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Article ; Online: Elevated ASCL1 activity creates de novo regulatory elements associated with neuronal differentiation.

Woods, Laura M / Ali, Fahad R / Gomez, Roshna / Chernukhin, Igor / Marcos, Daniel / Parkinson, Lydia M / Tayoun, Ahmad N Abou / Carroll, Jason S / Philpott, Anna

BMC genomics

2022 Volume 23, Issue 1, Page(s) 255

Abstract: Background: The pro-neural transcription factor ASCL1 is a master regulator of neurogenesis and a key factor necessary for the reprogramming of permissive cell types to neurons. Endogenously, ASCL1 expression is often associated with neuroblast stem- ... ...

Abstract	Background: The pro-neural transcription factor ASCL1 is a master regulator of neurogenesis and a key factor necessary for the reprogramming of permissive cell types to neurons. Endogenously, ASCL1 expression is often associated with neuroblast stem-ness. Moreover, ASCL1-mediated reprogramming of fibroblasts to differentiated neurons is commonly achieved using artificially high levels of ASCL1 protein, where ASCL1 acts as an "on-target" pioneer factor. However, the genome-wide effects of enhancing ASCL1 activity in a permissive neurogenic environment has not been thoroughly investigated. Here, we overexpressed ASCL1 in the neuronally-permissive context of neuroblastoma (NB) cells where modest endogenous ASCL1 supports the neuroblast programme. Results: Increasing ASCL1 in neuroblastoma cells both enhances binding at existing ASCL1 sites and also leads to creation of numerous additional, lower affinity binding sites. These extensive genome-wide changes in ASCL1 binding result in significant reprogramming of the NB transcriptome, redirecting it from a proliferative neuroblastic state towards one favouring neuronal differentiation. Mechanistically, ASCL1-mediated cell cycle exit and differentiation can be increased further by preventing its multi-site phosphorylation, which is associated with additional changes in genome-wide binding and gene activation profiles. Conclusions: Our findings show that enhancing ASCL1 activity in a neurogenic environment both increases binding at endogenous ASCL1 sites and also results in additional binding to new low affinity sites that favours neuronal differentiation over the proliferating neuroblast programme supported by the endogenous protein. These findings have important implications for controlling processes of neurogenesis in cancer and cellular reprogramming.
MeSH term(s)	Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Cellular Reprogramming/genetics ; Neural Stem Cells/metabolism ; Neurogenesis/genetics ; Neurons/metabolism
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors
Language	English
Publishing date	2022-04-03
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/s12864-022-08495-8
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Article ; Online: The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen.

Wang, Shixiong / Somisetty, Venkata S / Bai, Baoyan / Chernukhin, Igor / Niskanen, Henri / Kaikkonen, Minna U / Bellet, Meritxell / Carroll, Jason S / Hurtado, Antoni

Oncogene

2020 Volume 39, Issue 40, Page(s) 6300–6312

Abstract: Tamoxifen is the most prescribed selective estrogen receptor (ER) modulator in patients with ER-positive breast cancers. Tamoxifen requires the transcription factor paired box 2 protein (PAX2) to repress the transcription of ERBB2/HER2. Now, we ... ...

Abstract	Tamoxifen is the most prescribed selective estrogen receptor (ER) modulator in patients with ER-positive breast cancers. Tamoxifen requires the transcription factor paired box 2 protein (PAX2) to repress the transcription of ERBB2/HER2. Now, we identified that PAX2 inhibits cell growth of ER+/HER2- tumor cells in a dose-dependent manner. Moreover, we have identified that cell growth inhibition can be achieved by expressing moderate levels of PAX2 in combination with tamoxifen treatment. Global run-on sequencing of cells overexpressing PAX2, when coupled with PAX2 ChIP-seq, identified common targets regulated by both PAX2 and tamoxifen. The data revealed that PAX2 can inhibit estrogen-induced gene transcription and this effect is enhanced by tamoxifen, suggesting that they converge on repression of the same targets. Moreover, PAX2 and tamoxifen have an additive effect and both induce coding genes and enhancer RNAs (eRNAs). PAX2-tamoxifen upregulated genes are also enriched with PAX2 eRNAs. The enrichment of eRNAs is associated with the highest expression of genes that positivity regulate apoptotic processes. In luminal tumors, the expression of a subset of these proapoptotic genes predicts good outcome and their expression are significantly reduced in tumors of patients with relapse to tamoxifen treatment. Mechanistically, PAX2 and tamoxifen coexert an antitumoral effect by maintaining high levels of transcription of tumor suppressors that promote cell death. The apoptotic effect is mediated in large part by the gene interferon regulatory factor 1. Altogether, we conclude that PAX2 contributes to better clinical outcome in tamoxifen treated ER-positive breast cancer patients by repressing estrogen signaling and inducing cell death related pathways.
MeSH term(s)	Antineoplastic Agents, Hormonal/pharmacology ; Antineoplastic Agents, Hormonal/therapeutic use ; Apoptosis/drug effects ; Apoptosis/genetics ; Breast/pathology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Proliferation/genetics ; Chromatin Immunoprecipitation Sequencing ; Drug Resistance, Neoplasm/genetics ; Estrogens/metabolism ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Interferon Regulatory Factor-1/genetics ; Interferon Regulatory Factor-1/metabolism ; Neoplasm Recurrence, Local/genetics ; PAX2 Transcription Factor/metabolism ; Prognosis ; Promoter Regions, Genetic/genetics ; Receptor, ErbB-2/metabolism ; Receptors, Estrogen/antagonists & inhibitors ; Receptors, Estrogen/metabolism ; Signal Transduction/drug effects ; Tamoxifen/pharmacology ; Tamoxifen/therapeutic use ; Transcriptional Activation/drug effects ; Up-Regulation
Chemical Substances	Antineoplastic Agents, Hormonal ; Estrogens ; IRF1 protein, human ; Interferon Regulatory Factor-1 ; PAX2 Transcription Factor ; PAX2 protein, human ; Receptors, Estrogen ; Tamoxifen (094ZI81Y45) ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2020-08-25
Publishing country	England
Document type	Journal Article
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-020-01435-4
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Article: Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions

Albihlal, Waleed S / Obomighie, Irabonosi / Blein, Thomas / Persad, Ramona / Chernukhin, Igor / Crespi, Martin / Bechtold, Ulrike / Mullineaux, Philip M

Journal of experimental botany. 2018 May 19, v. 69, no. 11

2018

Abstract: In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide ... ...

Abstract	In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide targets (ChIP-seq) and its impact on the transcriptome (RNA-seq) under non-stress (NS), heat stress (HS) in the wild type, and in HSFA1b-overexpressing plants under NS. A total of 952 differentially expressed HSFA1b-targeted genes were identified, of which at least 85 are development associated and were bound predominantly under NS. A further 1780 genes were differentially expressed but not bound by HSFA1b, of which 281 were classified as having development-associated functions. These genes are indirectly regulated through a hierarchical network of 27 transcription factors (TFs). Furthermore, we identified 480 natural antisense non-coding RNA (cisNAT) genes bound by HSFA1b, defining a further mode of indirect regulation. Finally, HSFA1b-targeted genomic features not only harboured heat shock elements, but also MADS box, LEAFY, and G-Box promoter motifs. This revealed that HSFA1b is one of eight TFs that target a common group of stress defence and developmental genes. We propose that HSFA1b transduces environmental cues to many stress tolerance and developmental genes to allow plants to adjust their growth and development continually in a varying environment.
Keywords	Arabidopsis thaliana ; chromatin immunoprecipitation ; gene expression regulation ; genes ; genomics ; growth and development ; heat stress ; non-coding RNA ; reproductive fitness ; seed yield ; sequence analysis ; stress tolerance ; transcription (genetics) ; transcription factors ; transcriptome
Language	English
Dates of publication	2018-0519
Size	p. 2847-2862.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/ery142
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