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Article ; Online: The role of heterochromatin in 3D genome organization during preimplantation development.

Rang, Franka J / Kind, Jop / Guerreiro, Isabel

2023 Volume 42, Issue 4, Page(s) 112248

Abstract: During the early stages of mammalian development, the epigenetic state of the parental genome is completely reprogrammed to give rise to the totipotent embryo. An important aspect of this remodeling concerns the heterochromatin and the spatial ... ...

Abstract	During the early stages of mammalian development, the epigenetic state of the parental genome is completely reprogrammed to give rise to the totipotent embryo. An important aspect of this remodeling concerns the heterochromatin and the spatial organization of the genome. While heterochromatin and genome organization are intricately linked in pluripotent and somatic systems, little is known about their relationship in the totipotent embryo. In this review, we summarize the current knowledge on the reprogramming of both regulatory layers. In addition, we discuss available evidence on their relationship and put this in the context of findings in other systems.
MeSH term(s)	Animals ; Heterochromatin/genetics ; Embryonic Development/genetics ; Embryo, Mammalian ; Mammals/genetics ; Genome ; Epigenesis, Genetic
Chemical Substances	Heterochromatin
Language	English
Publishing date	2023-04-13
Publishing country	United States
Document type	Journal Article ; Review ; 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.2023.112248
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.

Rang, Franka J / Kloosterman, Wigard P / de Ridder, Jeroen

Genome biology

2018 Volume 19, Issue 1, Page(s) 90

Abstract: Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of ... ...

Abstract	Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.
MeSH term(s)	Artifacts ; Base Pairing ; DNA/chemistry ; DNA/genetics ; Escherichia coli/genetics ; Genome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Klebsiella pneumoniae/genetics ; Markov Chains ; Nanopores ; Neural Networks, Computer ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/statistics & numerical data
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-07-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-018-1462-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS?

Rang, Franka J / Boonstra, Johannes

Biology

2014 Volume 3, Issue 2, Page(s) 403–425

Abstract: Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of ... ...

Abstract	Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally have a higher risk of age-related diseases. However, very little is known about the mechanisms that could cause the occurrence of these changes. Moreover, there does not appear to be a clear link between popular theories of aging and alterations in the methylome. Some of the most fruitful of these theories attribute an important role to reactive oxygen species, which seem to be responsible for an increase in oxidative damage to macromolecules, such as DNA, during the lifetime of an organism. In this review, the connection between changes in DNA methylation and these reactive oxygen species is discussed, as well as the effect of these changes on health. Deeper insights into the nature, causes and consequences of the aging methylome might provide a deeper understanding of the molecular mechanisms of aging and eventually contribute to the development of new diagnostic and therapeutic tools.
Language	English
Publishing date	2014-06-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology3020403
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Article ; Online: Causes and Consequences of Age-Related Changes in DNA Methylation

Franka J. Rang / Johannes Boonstra

Biology, Vol 3, Iss 2, Pp 403-

A Role for ROS?

2014 Volume 425

Abstract	Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally have a higher risk of age-related diseases. However, very little is known about the mechanisms that could cause the occurrence of these changes. Moreover, there does not appear to be a clear link between popular theories of aging and alterations in the methylome. Some of the most fruitful of these theories attribute an important role to reactive oxygen species, which seem to be responsible for an increase in oxidative damage to macromolecules, such as DNA, during the lifetime of an organism. In this review, the connection between changes in DNA methylation and these reactive oxygen species is discussed, as well as the effect of these changes on health. Deeper insights into the nature, causes and consequences of the aging methylome might provide a deeper understanding of the molecular mechanisms of aging and eventually contribute to the development of new diagnostic and therapeutic tools.
Keywords	DNA methylation ; methylcytosine ; aging ; reactive oxygen species ; mechanisms ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2014-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: From squiggle to basepair

Franka J. Rang / Wigard P. Kloosterman / Jeroen de Ridder

Genome Biology, Vol 19, Iss 1, Pp 1-

computational approaches for improving nanopore sequencing read accuracy

2018 Volume 11

Abstract: Abstract Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a ... ...

Abstract	Abstract Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.
Keywords	Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Single-cell profiling of transcriptome and histone modifications with EpiDamID.

Rang, Franka J / de Luca, Kim L / de Vries, Sandra S / Valdes-Quezada, Christian / Boele, Ellen / Nguyen, Phong D / Guerreiro, Isabel / Sato, Yuko / Kimura, Hiroshi / Bakkers, Jeroen / Kind, Jop

Molecular cell

2022 Volume 82, Issue 10, Page(s) 1956–1970.e14

Abstract: Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained ... ...

Abstract	Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
MeSH term(s)	Animals ; Chromatin/genetics ; Histone Code ; Histones/genetics ; Histones/metabolism ; Mice ; Protein Processing, Post-Translational ; Transcriptome ; Zebrafish/genetics ; Zebrafish/metabolism
Chemical Substances	Chromatin ; Histones
Language	English
Publishing date	2022-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.03.009
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Article: Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS?

Rang, Franka J / Boonstra, Johannes

Biology. 2014 June 18, v. 3, no. 2

2014

Abstract: Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‐specific incidences of hypermethylation. This notion has received a lot of ... ...

Abstract	Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‐specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally have a higher risk of age-related diseases. However, very little is known about the mechanisms that could cause the occurrence of these changes. Moreover, there does not appear to be a clear link between popular theories of aging and alterations in the methylome. Some of the most fruitful of these theories attribute an important role to reactive oxygen species, which seem to be responsible for an increase in oxidative damage to macromolecules, such as DNA, during the lifetime of an organism. In this review, the connection between changes in DNA methylation and these reactive oxygen species is discussed, as well as the effect of these changes on health. Deeper insights into the nature, causes and consequences of the aging methylome might provide a deeper understanding of the molecular mechanisms of aging and eventually contribute to the development of new diagnostic and therapeutic tools.
Keywords	DNA ; DNA methylation ; genome-wide association study ; health effects assessments ; reactive oxygen species ; therapeutics
Language	English
Dates of publication	2014-0618
Size	p. 403-425.
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology3020403
Database	NAL-Catalogue (AGRICOLA)

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Article: From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

Rang, Franka J / Kloosterman, Wigard P / de Ridder, Jeroen

Genome biology. 2018 Dec., v. 19, no. 1

2018

Abstract	Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.
Keywords	chemistry ; nanopores ; portable equipment ; translation (genetics)
Language	English
Dates of publication	2018-12
Size	p. 90.
Publishing place	BioMed Central
Document type	Article
Note	Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-018-1462-9
Database	NAL-Catalogue (AGRICOLA)

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Article: Single-cell profiling of transcriptome and histone modifications with EpiDamID

Rang, Franka J. / de Luca, Kim L. / de Vries, Sandra S. / Valdes-Quezada, Christian / Boele, Ellen / Nguyen, Phong D. / Guerreiro, Isabel / Sato, Yuko / Kimura, Hiroshi / Bakkers, Jeroen / Kind, Jop

Molecular cell. 2022 May 19, v. 82, no. 10

2022

Abstract	Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
Keywords	Danio rerio ; embryogenesis ; genes ; heterochromatin ; histones ; mice ; transcriptome
Language	English
Dates of publication	2022-0519
Size	p. 1956-1970.e14.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.03.009
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq.

Markodimitraki, Corina M / Rang, Franka J / Rooijers, Koos / de Vries, Sandra S / Chialastri, Alex / de Luca, Kim L / Lochs, Silke J A / Mooijman, Dylan / Dey, Siddharth S / Kind, Jop

Nature protocols

2020 Volume 15, Issue 6, Page(s) 1922–1953

Abstract: Protein-DNA interactions are essential for establishing cell type-specific chromatin architecture and gene expression. We recently developed scDam&T-seq, a multi-omics method that can simultaneously quantify protein-DNA interactions and the transcriptome ...

Abstract	Protein-DNA interactions are essential for establishing cell type-specific chromatin architecture and gene expression. We recently developed scDam&T-seq, a multi-omics method that can simultaneously quantify protein-DNA interactions and the transcriptome in single cells. The method effectively combines two existing methods: DNA adenine methyltransferase identification (DamID) and CEL-Seq2. DamID works through the tethering of a protein of interest (POI) to the Escherichia coli DNA adenine methyltransferase (Dam). Upon expression of this fusion protein, DNA in proximity to the POI is methylated by Dam and can be selectively digested and amplified. CEL-Seq2, in contrast, makes use of poly-dT primers to reverse transcribe mRNA, followed by linear amplification through in vitro transcription. scDam&T-seq is the first technique capable of providing a combined readout of protein-DNA contact and transcription from single-cell samples. Once suitable cell lines have been established, the protocol can be completed in 5 d, with a throughput of hundreds to thousands of cells. The processing of raw sequencing data takes an additional 1-2 d. Our method can be used to understand the transcriptional changes a cell undergoes upon the DNA binding of a POI. It can be performed in any laboratory with access to FACS, robotic and high-throughput-sequencing facilities.
MeSH term(s)	Animals ; Cell Line ; Cell Line, Tumor ; DNA/genetics ; DNA/metabolism ; DNA Methylation ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Profiling/methods ; Genomics/methods ; Humans ; Mice ; Protein Binding ; Proteins/genetics ; Proteins/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Sequence Analysis, DNA/methods ; Single-Cell Analysis/methods ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/metabolism ; Transcriptome
Chemical Substances	Escherichia coli Proteins ; Proteins ; Recombinant Fusion Proteins ; DNA (9007-49-2) ; Site-Specific DNA-Methyltransferase (Adenine-Specific) (EC 2.1.1.72) ; dam protein, E coli (EC 2.1.1.72)
Language	English
Publishing date	2020-04-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-020-0314-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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