H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

Poleshko, Andrey; Smith, C. Lavett; Nguyen, Son C.; Sivaramakrishnan, Priya; Wong, Karen; Murray, John I.; Lakadamyali, Melike; Joyce, Eric F.; Jain, Rajan; Epstein, Jonathan A.

doi:10.7554/elife.49278

Cited by 93 publications

(104 citation statements)

References 63 publications

(117 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to the H3K9me3 pattern, the immunofluorescence signal for both marks was detected in smaller and blurrier clusters, referred to as puncta. In agreement with previous studies using the same commercial H3K9me2 antibody [45,46], we found that these puncta did not co-localize with chromocenters in control or C9BAC astrocytes ( Fig. 2a, b).…”

Section: Reduced Levels Of Nuclear H3k9me3 In Primary Spinal Cord Astsupporting

confidence: 93%

Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice

et al. 2020

View full text Add to dashboard Cite

Background: Hexanucleotide repeat expansions of the G 4 C 2 motif in a non-coding region of the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Tissues from C9ALS/FTD patients and from mouse models of ALS show RNA foci, dipeptide-repeat proteins, and notably, widespread alterations in the transcriptome. Epigenetic processes regulate gene expression without changing DNA sequences and therefore could account for the altered transcriptome profiles in C9ALS/FTD; here, we explore whether the critical repressive marks H3K9me2 and H3K9me3 are altered in a recently developed C9ALS/FTD BAC mouse model (C9BAC). Results: Chromocenters that constitute pericentric constitutive heterochromatin were visualized as DAPI-or Nucblue-dense foci in nuclei. Cultured C9BAC astrocytes exhibited a reduced staining signal for H3K9me3 (but not for H3K9me2) at chromocenters that was accompanied by a marked decline in the global nuclear level of this mark. Similar depletion of H3K9me3 at chromocenters was detected in astrocytes and neurons of the spinal cord, motor cortex, and hippocampus of C9BAC mice. The alterations of H3K9me3 in the hippocampus of C9BAC mice led us to identify previously undetected neuronal loss in CA1, CA3, and dentate gyrus, as well as hippocampal-dependent cognitive deficits. Conclusions: Our data indicate that a loss of the repressive mark H3K9me3 in astrocytes and neurons in the central nervous system of C9BAC mice represents a signature during neurodegeneration and memory deficit of C9ALS/FTD.

show abstract

Section: Reduced Levels Of Nuclear H3k9me3 In Primary Spinal Cord Astsupporting

confidence: 93%

Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice

et al. 2020

View full text Add to dashboard Cite

show abstract

“…However, it is also possible that distal chromosome regions are more probable sites for early NL interactions because they are more likely to be at the surface of the telophase chromatin mass, as a consequence of the pulling motion on centromeres earlier in mitosis (Dechat et al , 2004). Because most LADs begin to interact with the NL soon after mitosis, it is possible that LADs are generally “bookmarked” for such interactions, for example by heterochromatin marks such as H3K9me2 (Poleshko et al , 2019).…”

Section: Discussionmentioning

confidence: 99%

Cell cycle dynamics of lamina‐associated DNA

et al. 2020

View full text Add to dashboard Cite

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 folding of interphase chromosomes. Little is known about the dynamics of LADs during interphase, in particular at the onset of G1 phase and during DNA replication. 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.

show abstract

“…However, it is also possible that distal chromosome regions are more probable sites for early NL interactions because they are more likely to be at the surface of the telophase chromatin mass, as a consequence of the pulling motion on centromeres earlier in mitosis [12]. Because most LADs begin to interact with the NL soon after mitosis, it is possible that LADs are generally "bookmarked" for such interactions, for example by heterochromatin marks such as H3K9me2 [40].…”

Section: Cell Cycle Dynamics Of Genome -Nl Interactionsmentioning

confidence: 99%

Cell cycle dynamics of lamina associated DNA

Schaik

Vos

Peric-Hupkes

et al. 2019

Preprint

View full text Add to dashboard Cite

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...

show abstract

H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

Cited by 93 publications

References 63 publications

Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice

Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice

Cell cycle dynamics of lamina‐associated DNA

Cell cycle dynamics of lamina associated DNA

Contact Info

Product

Resources

About