Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria

Ikegami, Kohta; Secchia, Stefano; Almakki, Omar; Lieb, Jason D.; Moskowitz, Ivan P.

doi:10.1016/j.devcel.2020.02.011

Cited by 87 publications

(96 citation statements)

References 92 publications

(132 reference statements)

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“…1G), although for Lamin A/C we observed a somewhat smaller dynamic range. This may be due to some interactions of Lamin A/C with inter-LAD regions [31,32]. Together, these results show that pA-DamID can be used to map NL associations effectively.…”

Section: Genome-wide Pa-damid Maps Are Reproducible and Specificmentioning

confidence: 72%

Cell cycle dynamics of lamina associated DNA

Schaik

Vos

Peric-Hupkes

et al. 2019

Preprint

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words)In mammalian interphase nuclei more than one thousand large genomic regions are positioned at the nuclear lamina (NL). These lamina associated domains (LADs) are involved in gene regulation and may provide a backbone for the overall folding of interphase chromosomes. While LADs have been characterized in great detail, little is known about their dynamics during interphase, in particular at the onset of G1 phase and during DNA replication. To study these dynamics, we developed an antibody-based variant of the DamID technology (named pA-DamID) that allows us to map and visualize genome -NL interactions with high temporal resolution. Application of pA-DamID combined with synchronization and cell sorting experiments reveals that LAD -NL contacts are generally rapidly established early in G1 phase. However, LADs on the distal ~25 Mb of most chromosomes tend to contact the NL first and then gradually detach, while centromere-proximal LADs accumulate gradually at the NL. Furthermore, our data indicate that S-phase chromatin shows transiently increased lamin interactions. These findings highlight a dynamic choreography of LAD -NL contacts during interphase progression, and illustrate the usefulness of pA-DamID to study the dynamics of genome compartmentalization.genome-wide mapping of NL interactions, DamID has been the major method [1,22]. DamID is based on expression of a fusion protein of Dam and a NL protein (e.g. Lamin B1), which results in gradual accumulation of adenine methylation ( m6 A) on DNA that contacts the NL [23]. This m6 A labeled DNA is then amplified and sequenced. An added advantage of DamID is that the m6 A tags can be detected by a GFP-labeled m6 A-Tracer protein [8]. This enables visualization of LAD -NL contacts in situ, which greatly assists in the interpretation of genome-wide DamID mapping data.However, a major limitation of DamID is its poor temporal resolution. The activation of Dam and deposition of m6 A requires at least several hours [8,24], precluding detailed analysis of the NL interaction dynamics. To overcome these limitations, we developed pA-DamID -a hybrid of DamID and the CUT&RUN method [25]. This allows for both mapping and visualization of NL contacts with high temporal resolution. Using pA-DamID, we show that after mitosis NL contacts do not initiate at defined loci, but rather are widespread with an enrichment at LADs on distal regions of chromosomes. Furthermore, small LADs appear to be gradually displaced from the NL by larger LADs. Additionally, we found that replicating DNA shows transiently increasing lamin contacts. Results Principle of pA-DamID to map and visualize NL associated DNAThe pA-DamID method is a hybrid of the CUT&RUN and DamID technologies (Fig. 1A). In CUT&RUN, cells are permeabilized and incubated with an antibody against a nuclear protein of interest, followed by protein A (pA) fused to micrococcal nuclease (MNase). Subsequent activation of the tethered MNase by Ca ++ ions results in excision of DNA sequences that are in molecular proximity to the pro...

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Section: Genome-wide Pa-damid Maps Are Reproducible and Specificmentioning

confidence: 72%

Cell cycle dynamics of lamina associated DNA

Schaik

Vos

Peric-Hupkes

et al. 2019

Preprint

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“…G. Lund, Duband-Goulet, Oldenburg, Buendia, & Collas, 2015) and affect their epigenetic landscape (Bianchi et al, 2020; Briand et al, 2018; Cesarini et al, 2015; Oldenburg et al, 2017). Furthermore, lamin A/C has also been shown to directly interact with promoters and enhancers and seems to be involved in both positive and negative gene regulation (Ikegami et al, 2020; E. Lund & Collas, 2013; E.…”

Section: Discussionmentioning

confidence: 99%

“…It is conceivable that gene regulatory pathways have to be highly flexible and dynamic to respond efficiently to internal and external cues and thus require a dynamic lamin complex that can dynamically associate with and regulate chromatin. Indeed, loss of LAP2α (Gesson et al, 2016) or disease-linked mutations in lamins (Bianchi et al, 2020; Briand et al, 2018; Ikegami et al, 2020; Oldenburg et al, 2017) affect epigenetic regulation and/or gene expression.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, intranuclear A-type lamins are required for the proper assembly of repressive polycomb protein foci (Bianchi et al, 2020; Cesarini et al, 2015) and are involved in the regulation of telomere function (Chojnowski et al, 2015; Gonzalez-Suarez et al, 2009; Wood et al, 2014). Nucleoplasmic lamins were also found to affect gene expression directly by binding to gene regulatory sequences, such as promoters and enhancers (Briand et al, 2018; Ikegami, Secchia, Almakki, Lieb, & Moskowitz, 2020; Oldenburg et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior

Naetar

Georgiou

Knapp

et al. 2020

Preprint

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Lamins form stable filaments at the nuclear periphery in metazoans. Unlike B-type lamins, lamins A and C localize also in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). We show that lamin A in the nuclear interior is formed from newly expressed pre-lamin A during processing and from soluble mitotic mature lamins in a LAP2α-independent manner. Binding of LAP2α to lamins A/C in the nuclear interior during interphase inhibits formation of higher order structures of lamin A/C in vitro and in vivo, keeping lamin A/C in a mobile low assembly state independent of lamin A/C S22 phosphorylation. Loss of LAP2α causes formation of larger, less mobile and biochemically stable lamin A/C structures in the nuclear interior, which reduce the mobility of chromatin. We propose that LAP2α is essential to maintain a mobile lamin A/C pool in the nuclear interior, which is required for proper nuclear functions.

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“…The fact that lamins are notoriously insoluble, form filaments and lack any catalytic activity led to the initial notion that lamins function primarily to maintain nuclear shape and integrity. However, research in the past 20 years demonstrated that lamins play a crucial role in various cellular processes including mechanotransduction, modulation of nuclear stiffness and elasticity, chromatin organization, DNA replication and repair, and transcriptional regulation [4,17,18].…”

Section: The Nuclear Laminamentioning

confidence: 99%

Towards delineating the chain of events that cause premature senescence in the accelerated aging syndrome Hutchinson–Gilford progeria (HGPS)

Dreesen¹

2020

Biochemical Society Transactions

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The metazoan nucleus is equipped with a meshwork of intermediate filament proteins called the A- and B-type lamins. Lamins lie beneath the inner nuclear membrane and serve as a nexus to maintain the architectural integrity of the nucleus, chromatin organization, DNA repair and replication and to regulate nucleocytoplasmic transport. Perturbations or mutations in various components of the nuclear lamina result in a large spectrum of human diseases collectively called laminopathies. One of the most well-characterized laminopathies is Hutchinson–Gilford progeria (HGPS), a rare segmental premature aging syndrome that resembles many features of normal human aging. HGPS patients exhibit alopecia, skin abnormalities, osteoporosis and succumb to cardiovascular complications in their teens. HGPS is caused by a mutation in LMNA, resulting in a mutated form of lamin A, termed progerin. Progerin expression results in a myriad of cellular phenotypes including abnormal nuclear morphology, loss of peripheral heterochromatin, transcriptional changes, DNA replication defects, DNA damage and premature cellular senescence. A key challenge is to elucidate how these different phenotypes are causally and mechanistically linked. In this mini-review, we highlight some key findings and present a model on how progerin-induced phenotypes may be temporally and mechanistically linked.

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Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria

Cited by 87 publications

References 92 publications

Cell cycle dynamics of lamina associated DNA

Cell cycle dynamics of lamina associated DNA

LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior

Towards delineating the chain of events that cause premature senescence in the accelerated aging syndrome Hutchinson–Gilford progeria (HGPS)

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