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Article ; Online: Epigenetic control of transposons during plant reproduction: From meiosis to hybrid seeds.

Pachamuthu, Kannan / Borges, Filipe

2023 Volume 75, Page(s) 102419

Abstract: The regulation of transposable elements (TEs) requires overlapping epigenetic modifications that must be reinforced every cell division and generation. In plants, this is achieved by multiple pathways including small RNAs, DNA methylation, and repressive ...

Abstract	The regulation of transposable elements (TEs) requires overlapping epigenetic modifications that must be reinforced every cell division and generation. In plants, this is achieved by multiple pathways including small RNAs, DNA methylation, and repressive histone marks that act together to control TE expression and activity throughout the entire life cycle. However, transient TE activation is observed during reproductive transitions as a result of epigenome reprogramming, thus providing windows of opportunity for TE proliferation and epigenetic novelty. Ultimately, these events may originate complex TE-driven transcriptional networks or cell-to-cell communication strategies via mobile small RNAs. In this review, we discuss recent findings and current understanding of TE regulation during sexual plant reproduction, and its implications for fertility, early seed development, and epigenetic inheritance.
MeSH term(s)	Meiosis/genetics ; Seeds/genetics ; Reproduction/genetics ; Cell Communication ; Epigenesis, Genetic
Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1418472-2
ISSN	1879-0356 ; 1369-5266
ISSN (online)	1879-0356
ISSN	1369-5266
DOI	10.1016/j.pbi.2023.102419
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Article ; Online: Epigenetic control of transposons during plant reproduction: From meiosis to hybrid seeds

Pachamuthu, Kannan / Borges, Filipe

Current Opinion in Plant Biology. 2023, p.102419-

2023 , Page(s) 102419–

Abstract	The regulation of transposable elements (TEs) requires overlapping epigenetic modifications that must be reinforced every cell division and generation. In plants, this is achieved by multiple pathways including small RNAs, DNA methylation, and repressive histone marks that act together to control TE expression and activity throughout the entire life cycle. However, transient TE activation is observed during reproductive transitions as a result of epigenome reprogramming, thus providing windows of opportunity for TE proliferation and epigenetic novelty. Ultimately, these events may originate complex TE-driven transcriptional networks or cell-to-cell communication strategies via mobile small RNAs. In this review, we discuss recent findings and current understanding of TE regulation during sexual plant reproduction, and its implications for fertility, early seed development, and epigenetic inheritance.
Keywords	DNA methylation ; cell communication ; epigenetics ; epigenome ; histones ; hybrids ; meiosis ; plant reproduction ; seed development ; transcription (genetics) ; transposons
Language	English
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	1418472-2
ISSN	1879-0356 ; 1369-5266
ISSN (online)	1879-0356
ISSN	1369-5266
DOI	10.1016/j.pbi.2023.102419
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Article: Specificities and Dynamics of Transposable Elements in Land Plants.

Mhiri, Corinne / Borges, Filipe / Grandbastien, Marie-Angèle

Biology

2022 Volume 11, Issue 4

Abstract: Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This ... ...

Abstract	Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.
Language	English
Publishing date	2022-03-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11040488
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Article ; Online: Far-offset detection of normal modes and diving waves

Borges, Filipe / Landrø, Martin

A case study from the Valhall Field, southern North Sea

2022

Abstract: The use of permanent arrays for continuous reservoir monitoring has become a reality in the past decades, with Ekofisk and Valhall being its flagships. One of the possibilities when such a solution is available is to passively record data while ... ...

Abstract	The use of permanent arrays for continuous reservoir monitoring has become a reality in the past decades, with Ekofisk and Valhall being its flagships. One of the possibilities when such a solution is available is to passively record data while acquisitions with an active source are ongoing in nearby areas. These recordings might contain ultrafar-offset data (more than 30 km), which are hardly used in standard reservoir exploration and monitoring because they are mostly a combination of normal modes, deep reflections, and diving waves. We present data from the Valhall life-of-field seismic array, recorded while an active seismic survey was acquired at Ekofisk, in April 2014. Despite the lack of control on source firing time and position, analysis of the data indicates that the normal modes are remarkably clear, overcoming the ambient noise in the field. The normal modes can be well explained by a two-layer acoustic model, whereas a combination of diving waves and refracted waves can be fairly well reproduced with a regional 1D velocity model. We suggest a method to use far-offset recordings to monitor changes in shallow sediments between source and receivers, with and without a coherent seismic source in the area.
Language	English
Publishing date	2022-03-01
Publisher	SEG (Society of Exploration Geophysicists)
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of quality and quantity of randomized controlled trials in hepatobiliary surgery: A scoping/mapping review.

Majlesara, Ali / Aminizadeh, Ehsan / Ramouz, Ali / Khajeh, Elias / Shahrbaf, Mohammadamin / Borges, Filipe / Goncalves, Gil / Carvalho, Carlos / Golriz, Mohammad / Mehrabi, Arianeb

European journal of clinical investigation

2024 , Page(s) e14210

Abstract: Aim: To evaluate the quantity and quality of randomized controlled trials (RCTs) in hepatobiliary surgery and for identifying gaps in current evidences.: Methods: A systematic search was conducted in MEDLINE (via PubMed), Web of Science, and Cochrane ...

Abstract	Aim: To evaluate the quantity and quality of randomized controlled trials (RCTs) in hepatobiliary surgery and for identifying gaps in current evidences. Methods: A systematic search was conducted in MEDLINE (via PubMed), Web of Science, and Cochrane Controlled Register of Trials (CENTRAL) for RCTs of hepatobiliary surgery published from inception until the end of 2023. The quality of each study was assessed using the Cochrane risk-of-bias (RoB) tool. The associations between risk of bias and the region and publication date were also assessed. Evidence mapping was performed to identify research gaps in the field. Results: The study included 1187 records. The number and proportion of published randomized controlled trials (RCTs) in hepatobiliary surgery increased over time, from 13 RCTs (.0005% of publications) in 1970-1979 to 201 RCTs (.003% of publications) in 2020-2023. There was a significant increase in the number of studies with a low risk of bias in RoB domains (p < .01). The proportion of RCTs with low risk of bias improved significantly after the introduction of CONSORT guidelines (p < .001). The evidence mapping revealed a significant research focus on major and minor hepatectomy and cholecystectomy. However, gaps were identified in liver cyst surgery and hepatobiliary vascular surgery. Additionally, there are gaps in the field of perioperative management and nutrition intervention. Conclusion: The quantity and quality of RCTs in hepatobiliary surgery have increased over time, but there is still room for improvement. We have identified gaps in current research that can be addressed in future studies.
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	186196-7
ISSN	1365-2362 ; 0014-2972 ; 0960-135X
ISSN (online)	1365-2362
ISSN	0014-2972 ; 0960-135X
DOI	10.1111/eci.14210
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Article ; Online: Evidence mapping of randomized clinical trials in hepatobiliary surgery.

Majlesara, Ali / Aminizadeh, Ehsan / Ramouz, Ali / Khajeh, Elias / Borges, Filipe / Goncalves, Gil / Carvalho, Carlos / Golriz, Mohammad / Mehrabi, Arianeb

The British journal of surgery

2023 Volume 110, Issue 10, Page(s) 1276–1278

MeSH term(s)	Humans ; Randomized Controlled Trials as Topic ; Digestive System Diseases/surgery
Language	English
Publishing date	2023-05-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2985-3
ISSN	1365-2168 ; 0263-1202 ; 0007-1323 ; 1355-7688
ISSN (online)	1365-2168
ISSN	0263-1202 ; 0007-1323 ; 1355-7688
DOI	10.1093/bjs/znad125
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Article ; Online: Small RNA Function in Plants: From Chromatin to the Next Generation.

Parent, Jean-Sébastien / Borges, Filipe / Shimada, Atsushi / Martienssen, Robert A

Cold Spring Harbor symposia on quantitative biology

2020 Volume 84, Page(s) 133–140

Abstract: Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets ... ...

Abstract	Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets in
Language	English
Publishing date	2020-06-09
Publishing country	United States
Document type	Journal Article
ISSN	1943-4456 ; 0091-7451
ISSN (online)	1943-4456
ISSN	0091-7451
DOI	10.1101/sqb.2019.84.040394
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Article ; Online: Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis.

Huc, Jonathan / Dziasek, Katarzyna / Pachamuthu, Kannan / Woh, Tristan / Köhler, Claudia / Borges, Filipe

The Plant cell

2021 Volume 34, Issue 3, Page(s) 989–1001

Abstract: The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been ... ...

Abstract	The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
MeSH term(s)	Arabidopsis/genetics ; Diploidy ; Endosperm/genetics ; Seeds/genetics ; Triploidy
Language	English
Publishing date	2021-11-18
Publishing country	England
Document type	Journal Article
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koab284
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Article ; Online: The expanding world of small RNAs in plants.

Borges, Filipe / Martienssen, Robert A

Nature reviews. Molecular cell biology

2015 Volume 16, Issue 12, Page(s) 727–741

Abstract: Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between ... ...

Abstract	Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Argonaute Proteins/metabolism ; Gene Expression Regulation, Plant ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA Interference ; RNA Replicase/metabolism ; RNA Splicing/genetics ; RNA, Plant/genetics ; RNA, Plant/metabolism ; RNA, Small Cytoplasmic/genetics ; RNA, Small Cytoplasmic/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Ribonuclease III/metabolism
Chemical Substances	Argonaute Proteins ; MicroRNAs ; RNA, Plant ; RNA, Small Cytoplasmic ; RNA, Small Interfering ; RNA Replicase (EC 2.7.7.48) ; Ribonuclease III (EC 3.1.26.3)
Language	English
Publishing date	2015-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/nrm4085
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Article: Selection and validation of reference genes for qPCR analysis of miRNAs and their targets during somatic embryogenesis in tamarillo (Solanum betaceum Cav.)

Cordeiro, Daniela / Rito, Miguel / Borges, Filipe / Canhoto, Jorge / Correia, Sandra

Plant cell, tissue, and organ culture. 2020 Oct., v. 143, no. 1

2020

Abstract: Quantitative reverse transcriptase PCR is a powerful tool for precise gene expression quantification. Using suitable reference genes is crucial for a proper normalization and interpretation of results, particularly in dynamic transcriptional networks ... ...

Abstract	Quantitative reverse transcriptase PCR is a powerful tool for precise gene expression quantification. Using suitable reference genes is crucial for a proper normalization and interpretation of results, particularly in dynamic transcriptional networks with the involvement of several miRNAs and their targets, such as somatic embryogenesis (SE). Here, we aimed to identify genes to be used as internal controls for quantitative detection of miRNAs and mRNAs during the SE process in Solanum betaceum. The expression of EF1α, GAPDH, ACT, UBQ10, Fe-SOD, U6, snoR14, miR159a, miR162 and miR166a was tested in nine time-points of the SE process, particularly during induction, embryo development and conversion. Analyses of transcriptional stability were performed using RefFinder tool that integrates geNorm, NormFinder, BestKeeper and Delta-Ct algorithms. Among these candidates, Fe-SOD, ACT and U6 emerged consistently as the most suitable to normalize gene expression, whereas miR166a was the most appropriate for normalization in calli samples. In order to validate these results, expression of miR396 and GRF1 was quantified and normalized with the most and the least stable genes and also with the most stable miRNA. Fe-SOD + ACT revealed to be the optimal combination for precise quantification of miRNA-mediated regulation of gene expression during SE in tamarillo.
Keywords	Solanum betaceum ; algorithms ; callus ; gene expression ; gene expression regulation ; gene regulatory networks ; genes ; messenger RNA ; microRNA ; quantitative polymerase chain reaction ; reverse transcriptase polymerase chain reaction ; somatic embryogenesis ; transcription (genetics)
Language	English
Dates of publication	2020-10
Size	p. 109-120.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	406394-6
ISSN	1573-5044 ; 0167-6857
ISSN (online)	1573-5044
ISSN	0167-6857
DOI	10.1007/s11240-020-01901-7
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