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Article ; Online: Integrator facilitates RNAPII removal to prevent transcription-replication collisions and genome instability.

Bhowmick, Rahul / Mehta, Kavi P M / Lerdrup, Mads / Cortez, David

2023 Volume 83, Issue 13, Page(s) 2357–2366.e8

Abstract: DNA replication preferentially initiates close to active transcription start sites (TSSs) in the human genome. Transcription proceeds discontinuously with an accumulation of RNA polymerase II (RNAPII) in a paused state near the TSS. Consequently, ... ...

Abstract	DNA replication preferentially initiates close to active transcription start sites (TSSs) in the human genome. Transcription proceeds discontinuously with an accumulation of RNA polymerase II (RNAPII) in a paused state near the TSS. Consequently, replication forks inevitably encounter paused RNAPII soon after replication initiates. Hence, dedicated machinery may be needed to remove RNAPII and facilitate unperturbed fork progression. In this study, we discovered that Integrator, a transcription termination machinery involved in the processing of RNAPII transcripts, interacts with the replicative helicase at active forks and promotes the removal of RNAPII from the path of the replication fork. Integrator-deficient cells have impaired replication fork progression and accumulate hallmarks of genome instability including chromosome breaks and micronuclei. The Integrator complex resolves co-directional transcription-replication conflicts to facilitate faithful DNA replication.
MeSH term(s)	Humans ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; DNA Replication ; Transcription, Genetic ; DNA Helicases/genetics ; DNA Helicases/metabolism ; Genomic Instability
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.05.015
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Article ; Online: User-Friendly and Interactive Analysis of ChIP-Seq Data Using EaSeq.

Lerdrup, Mads / Hansen, Klaus

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

2020 Volume 2117, Page(s) 35–63

Abstract: ChIP-seq is a central method to gain understanding of the regulatory networks in the genome of stem cells and during differentiation. Exploration and analysis of such genome-wide data often leads to unexpected discoveries and new hypotheses. It therefore ...

Abstract	ChIP-seq is a central method to gain understanding of the regulatory networks in the genome of stem cells and during differentiation. Exploration and analysis of such genome-wide data often leads to unexpected discoveries and new hypotheses. It therefore accelerates and improves the discovery phase, when scientists with biological understanding are enabled to analyze and visualize data. EaSeq ( http://easeq.net ) offers integrated exploration of genome-wide data in a visual, versatile, user-friendly, and interactive manner that connects abstract interpretations to the signal distribution at the underlying loci. Here we introduce the interface, data types, and acquisition, and guide the reader through two example workflows. These workflows will enable the reader to perform genome-wide analysis and visualization of transcription factor binding sites and histone marks. This includes making basic plots; finding, annotating, sorting, and filtering of peaks; using EaSeq as a genome browser; measuring ChIP-seq signal and calculating ratios; as well as data import and export.
MeSH term(s)	Animals ; Binding Sites ; Chromatin Immunoprecipitation Sequencing/methods ; Computational Biology/methods ; DNA/chemistry ; DNA/metabolism ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; Histones/metabolism ; Humans ; Mice ; Sequence Analysis, DNA ; Software ; Transcription Factors/metabolism ; User-Computer Interface ; Workflow
Chemical Substances	Histones ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2020-01-20
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0301-7_2
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Article: Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2.

Garribba, Lorenza / Vogel, Ivan / Lerdrup, Mads / Gonçalves Dinis, Marisa M / Ren, Liqun / Liu, Ying

Frontiers in genetics

2021 Volume 12, Page(s) 695124

Abstract: Folate deficiency is associated with a broad range of human disorders, including anemia, fetal neural tube defects, age-associated dementia and several types of cancer. It is well established that a subgroup of rare fragile sites (RFSs) containing ... ...

Abstract	Folate deficiency is associated with a broad range of human disorders, including anemia, fetal neural tube defects, age-associated dementia and several types of cancer. It is well established that a subgroup of rare fragile sites (RFSs) containing expanded CGG trinucleotide repeat (TNR) sequences display instability when cells are deprived of folate. However, given that folate sensitive RFSs exist in a very small percentage of the population, they are unlikely to be the cause of the widespread health problems associated with folate deficiency. We hypothesized that folate deficiency could specifically affect DNA replication at regions containing CG-rich repeat sequences. For this, we identified a region on human chromosome 2 (Chr2) comprising more than 300 CG-rich TNRs (termed "FOLD1") by examining the human genome database. Via the analysis of chromosome shape and segregation in mitosis, we demonstrate that, when human cells are cultured under folate stress conditions, Chr2 is prone to display a "kink" or "bending" at FOLD1 in metaphase and nondisjunction in anaphase. Furthermore, long-term folate deprivation causes Chr2 aneuploidy. Our results provide new evidence on the abnormalities folate deficiency could cause in human cells. This could facilitate future studies on the deleterious health conditions associated with folate deficiency.
Language	English
Publishing date	2021-07-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.695124
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Article ; Online: RAD51 protects human cells from transcription-replication conflicts.

Bhowmick, Rahul / Lerdrup, Mads / Gadi, Sampath Amitash / Rossetti, Giacomo G / Singh, Manika I / Liu, Ying / Halazonetis, Thanos D / Hickson, Ian D

Molecular cell

2022 Volume 82, Issue 18, Page(s) 3366–3381.e9

Abstract: Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA ... ...

Abstract	Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA replication and transcription machineries operating simultaneously at the same loci. One role of the RAD51 recombinase in human cells is to protect replication forks undergoing RS. Here, we have identified a key role for RAD51 in preventing transcription-replication conflicts (TRCs) from triggering replication fork breakage. The genomic regions most affected by RAD51 deficiency are characterized by being replicated and transcribed in early S-phase and show significant overlap with loci prone to cancer-associated amplification. Consistent with a role for RAD51 in protecting against transcription-replication conflicts, many of the adverse effects of RAD51 depletion are ameliorated by inhibiting early S-phase transcription. We propose a model whereby RAD51 suppresses fork breakage and subsequent inadvertent amplification of genomic loci prone to experiencing TRCs.
MeSH term(s)	Chromosomes/metabolism ; DNA Replication ; Humans ; Rad51 Recombinase/genetics ; Rad51 Recombinase/metabolism ; S Phase/genetics ; Transcription, Genetic
Chemical Substances	RAD51 protein, human (EC 2.7.7.-) ; Rad51 Recombinase (EC 2.7.7.-)
Language	English
Publishing date	2022-08-23
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.2022.07.010
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Article ; Online: Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals.

Sankar, Aditya / Mohammad, Faizaan / Sundaramurthy, Arun Kumar / Wang, Hua / Lerdrup, Mads / Tatar, Tulin / Helin, Kristian

Nature genetics

2022 Volume 54, Issue 6, Page(s) 754–760

Abstract: Posttranslational modifications of histones (PTMs) are associated with specific chromatin and gene expression ... ...

Abstract	Posttranslational modifications of histones (PTMs) are associated with specific chromatin and gene expression states
MeSH term(s)	Acetylation ; Animals ; Chromatin/genetics ; Chromatin/metabolism ; Drosophila melanogaster/genetics ; Histones/genetics ; Histones/metabolism ; Mammals/genetics ; Methylation ; Mice ; Polycomb Repressive Complex 2/genetics ; Protein Processing, Post-Translational/genetics
Chemical Substances	Chromatin ; Histones ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2022-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-022-01091-2
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Article: The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition

Zonderland, Gijs / Vanzo, Riccardo / Amitash, Sampath / Martín-Doncel, Elena / Coscia, Fabian / Mund, Andreas / Lerdrup, Mads / Benada, Jan / Boos, Dominik / Toledo, Luis

Molecular cell. 2022 Sept. 15, v. 82, no. 18

2022

Abstract: It has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ... ...

Abstract	It has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases. TRESLIN-MTBP acts transiently at pre-replication complexes (preRCs) to initiate origin firing and is released after the subsequent recruitment of CDC45. This dynamic behavior of TRESLIN-MTBP implements a monitoring system that checks the activation of replication forks and senses the rate of origin firing to prevent the entry into G2. This system detects the decline in the number of origins of replication that naturally occurs in very late S, which is the signature that cells use to determine the completion of DNA replication and permit the S/G2 transition. Our work introduces TRESLIN-MTBP as a key player in cell-cycle control independent of canonical checkpoints.
Keywords	DNA replication ; cell cycle ; models ; phosphotransferases (kinases)
Language	English
Dates of publication	2022-0915
Size	p. 3350-3365.e7.
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.2022.08.006
Database	NAL-Catalogue (AGRICOLA)

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Article: RAD51 protects human cells from transcription-replication conflicts

Bhowmick, Rahul / Lerdrup, Mads / Gadi, Sampath Amitash / Rossetti, Giacomo G. / Singh, Manika I. / Liu, Ying / Halazonetis, Thanos D. / Hickson, Ian D.

Molecular cell. 2022 Sept. 15, v. 82, no. 18

2022

Abstract	Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA replication and transcription machineries operating simultaneously at the same loci. One role of the RAD51 recombinase in human cells is to protect replication forks undergoing RS. Here, we have identified a key role for RAD51 in preventing transcription-replication conflicts (TRCs) from triggering replication fork breakage. The genomic regions most affected by RAD51 deficiency are characterized by being replicated and transcribed in early S-phase and show significant overlap with loci prone to cancer-associated amplification. Consistent with a role for RAD51 in protecting against transcription-replication conflicts, many of the adverse effects of RAD51 depletion are ameliorated by inhibiting early S-phase transcription. We propose a model whereby RAD51 suppresses fork breakage and subsequent inadvertent amplification of genomic loci prone to experiencing TRCs.
Keywords	DNA replication ; carcinogenesis ; genomics ; humans ; models ; oncogenes ; recombinases
Language	English
Dates of publication	2022-0915
Size	p. 3366-3381.e9.
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.2022.07.010
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate.

Hansen, Stine L / Larsen, Hjalte L / Pikkupeura, Laura M / Maciag, Grzegorz / Guiu, Jordi / Müller, Iris / Clement, Ditte L / Mueller, Christina / Johansen, Jens Vilstrup / Helin, Kristian / Lerdrup, Mads / Jensen, Kim B

Science advances

2023 Volume 9, Issue 28, Page(s) eadg4055

Abstract: Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the ... ...

Abstract	Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids have an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR-Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish
MeSH term(s)	Animals ; Mice ; CRISPR-Cas Systems ; Cell Differentiation/genetics ; Fetus ; Adult Stem Cells ; Organoids
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adg4055
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Article ; Online: Going low to reach high: Small-scale ChIP-seq maps new terrain.

Fosslie, Madeleine / Manaf, Adeel / Lerdrup, Mads / Hansen, Klaus / Gilfillan, Gregor D / Dahl, John Arne

Wiley interdisciplinary reviews. Systems biology and medicine

2019 Volume 12, Issue 1, Page(s) e1465

Abstract: Chromatin immunoprecipitation (ChIP) enables mapping of specific histone modifications or chromatin-associated factors in the genome and represents a powerful tool in the study of chromatin and genome regulation. Importantly, recent technological ... ...

Abstract	Chromatin immunoprecipitation (ChIP) enables mapping of specific histone modifications or chromatin-associated factors in the genome and represents a powerful tool in the study of chromatin and genome regulation. Importantly, recent technological advances that couple ChIP with whole-genome high-throughput sequencing (ChIP-seq) now allow the mapping of chromatin factors throughout the genome. However, the requirement for large amounts of ChIP-seq input material has long made it challenging to assess chromatin profiles of cell types only available in limited numbers. For many cell types, it is not feasible to reach high numbers when collecting them as homogeneous cell populations in vivo. Nonetheless, it is an advantage to work with pure cell populations to reach robust biological conclusions. Here, we review (a) how ChIP protocols have been scaled down for use with as little as a few hundred cells; (b) which considerations to be aware of when preparing small-scale ChIP-seq and analyzing data; and (c) the potential of small-scale ChIP-seq datasets for elucidating chromatin dynamics in various biological systems, including some examples such as oocyte maturation and preimplantation embryo development. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Developmental Biology > Developmental Processes in Health and Disease Biological Mechanisms > Cell Fates.
Language	English
Publishing date	2019-09-03
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2503323-2
ISSN	1939-005X ; 1939-5094
ISSN (online)	1939-005X
ISSN	1939-5094
DOI	10.1002/wsbm.1465
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Article ; Online: Lamin A/C impairments cause mitochondrial dysfunction by attenuating PGC1α and the NAMPT-NAD+ pathway.

Maynard, Scott / Hall, Arnaldur / Galanos, Panagiotis / Rizza, Salvatore / Yamamoto, Tatsuro / Gram, Helena Hagner / Munk, Sebastian H N / Shoaib, Muhammad / Sørensen, Claus Storgaard / Bohr, Vilhelm A / Lerdrup, Mads / Maya-Mendoza, Apolinar / Bartek, Jiri

Nucleic acids research

2022 Volume 50, Issue 17, Page(s) 9948–9965

Abstract: Mutations in the lamin A/C gene (LMNA) cause laminopathies such as the premature aging Hutchinson Gilford progeria syndrome (HGPS) and altered lamin A/C levels are found in diverse malignancies. The underlying lamin-associated mechanisms remain poorly ... ...

Abstract	Mutations in the lamin A/C gene (LMNA) cause laminopathies such as the premature aging Hutchinson Gilford progeria syndrome (HGPS) and altered lamin A/C levels are found in diverse malignancies. The underlying lamin-associated mechanisms remain poorly understood. Here we report that lamin A/C-null mouse embryo fibroblasts (Lmna-/- MEFs) and human progerin-expressing HGPS fibroblasts both display reduced NAD+ levels, unstable mitochondrial DNA and attenuated bioenergetics. This mitochondrial dysfunction is associated with reduced chromatin recruitment (Lmna-/- MEFs) or low levels (HGPS) of PGC1α, the key transcription factor for mitochondrial homeostasis. Lmna-/- MEFs showed reduced expression of the NAD+-biosynthesis enzyme NAMPT and attenuated activity of the NAD+-dependent deacetylase SIRT1. We find high PARylation in lamin A/C-aberrant cells, further decreasing the NAD+ pool and consistent with impaired DNA base excision repair in both cell models, a condition that fuels DNA damage-induced PARylation under oxidative stress. Further, ATAC-sequencing revealed a substantially altered chromatin landscape in Lmna-/- MEFs, including aberrantly reduced accessibility at the Nampt gene promoter. Thus, we identified a new role of lamin A/C as a key modulator of mitochondrial function through impairments of PGC1α and the NAMPT-NAD+ pathway, with broader implications for the aging process.
MeSH term(s)	Animals ; Chromatin/metabolism ; DNA, Mitochondrial/metabolism ; Fibroblasts/metabolism ; Humans ; Lamin Type A/genetics ; Lamin Type A/metabolism ; Mice ; Mitochondria/metabolism ; NAD/metabolism ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism ; Progeria/metabolism ; Sirtuin 1/genetics
Chemical Substances	Chromatin ; DNA, Mitochondrial ; LMNA protein, human ; Lamin Type A ; PPARGC1A protein, human ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; NAD (0U46U6E8UK) ; Sirtuin 1 (EC 3.5.1.-)
Language	English
Publishing date	2022-09-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
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/gkac741
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