scholarly journals Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria

2019 ◽  
Author(s):  
Kohta Ikegami ◽  
Stefano Secchia ◽  
Omar Almakki ◽  
Jason D. Lieb ◽  
Ivan P. Moskowitz
Keyword(s):  
Binding Sites ◽  
Human Fibroblasts ◽  
Nuclear Periphery ◽  
Transcriptional Activator ◽  
Premature Aging ◽  
Lamin A ◽  
List Type ◽  
Enhancer Activity ◽  
Nuclear Interior ◽  
Specific Subset

ABSTRACTLMNA encodes nuclear lamin A/C that tethers lamina-associated heterochromatin domains (LADs) to the nuclear periphery. Point mutations in LMNA cause degenerative disorders including the premature aging disorder Hutchinson-Gilford progeria, but the mechanisms are unknown. We report that Ser22-phosphorylated Lamin A/C (pS22-Lamin A/C) was localized to the interior of the nucleus in human fibroblasts throughout the cell cycle. pS22-Lamin A/C interacted with a specific subset of putative active enhancers, not LADs, primarily at locations co-bound by the transcriptional activator c-Jun. In progeria-patient fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost whereas new pS22-Lamin A/C-binding sites emerged in normally quiescent loci. These new pS22-Lamin A/C-binding sites displayed increased histone acetylation and c-Jun binding, implying increased enhancer activity. The genes near these new binding sites, implicated in clinical components of progeria including carotid artery diseases, hypertension, and cardiomegaly, were upregulated in progeria. These results suggest that Lamin A/C regulates gene expression by direct enhancer binding in the nuclear interior. Disruption of the gene regulatory rather than LAD function of Lamin A/C presents a novel mechanism for disorders caused by LMNA mutations including progeria.HIGHLIGHTSpS22-Lamin A/C is present in the nuclear interior throughout interphase.pS22-Lamin A/C associates with active enhancers, not lamina-associated domains.pS22-Lamin A/C-genomic binding sites are co-bound by the transcriptional activator c-Jun.New pS22-Lamin A/C binding in progeria accompanies upregulation of disease-related genes.

Abstract 508: Nuclear Lamins At Enhancers: A New Hypothesis for Laminopathies

2020 ◽  
Vol 127 (Suppl_1) ◽  
Author(s):  
Kohta Ikegami ◽  
Stefano Secchia ◽  
Omar Almakki ◽  
Alexis V Stutzman ◽  
Sachie Ikegami ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Acetylation ◽  
Binding Sites ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Lamin A ◽  
New Paradigm ◽  
Control Of Gene Expression ◽  
Nuclear Lamins ◽  
Nuclear Interior

The segregation of heterochromatin domains (LADs) at the nuclear periphery by the nuclear lamina, composed by polymerized nuclear Lamin A/C, provides a longstanding paradigm for the control of gene expression and for the mechanisms underlying Lamin-A/C-associated disorders, including progeria and cardiomyopathy. Here, we provide evidence supporting a novel paradigm that Lamin A/C functions as a transcription factor in the nuclear interior. We discovered that Ser22-phosphorylated Lamin A/C (pS22-Lamin A/C), required for lamin depolymerization during mitosis, populated the nuclear interior throughout the cell cycle. pS22-Lamin A/C ChIP-deq demonstrated localization at a large subset of putative active enhancers, not LADs. pS22-Lamin A/C-binding sites were co-occupied by the transcriptional activator c-Jun. In progeria patient-derived fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost whereas new pS22-Lamin A/C-binding sites emerged. New pS22-Lamin A/C binding was accompanied by increased histone acetylation and increased c-Jun binding, whereas loss of pS22-Lamin A/C-binding was accompanied by loss of histone acetylation and c-Jun binding. New pS22-Lamin A/C enhancer binding in progeria was associated with upregulated expression of genes implicated in progeria pathophysiology, including cardiovascular disease. In contrast, alteration of LADs in progeria-patient cells could not explain the observed gene expression changes. These results suggest that Lamin A/C regulates gene expression by enhancer binding in the nuclear interior, independent of its function at the nuclear lamina, providing a new paradigm for the pathogenesis of lamin-associated disorders. pS22-Lamin A/C was also present in the nuclear interior of adult mouse cardiomyocytes. Cardiomyocyte-specific deletion of Lmna encoding Lamin A/C in adult mice caused extensive transcriptional changes in the heart and dilated cardiomyopathy, without apparent reduction of nuclear peripheral Lamin A/C. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C may underlie the pathogenesis of disorders caused by LMNA mutations, including cardiomyopathy.

scholarly journals Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

2015 ◽  
Vol 208 (1) ◽  
pp. 33-52 ◽  
Author(s):  
Jennifer C. Harr ◽  
Teresa Romeo Luperchio ◽  
Xianrong Wong ◽  
Erez Cohen ◽  
Sarah J. Wheelan ◽  
...  
Keyword(s):  
Binding Sites ◽  
Nuclear Organization ◽  
Insertion Site ◽  
Nuclear Periphery ◽  
Histone H3 ◽  
Nuclear Lamina ◽  
Lamin A ◽  
Developmentally Regulated ◽  
Specific Variable ◽  
Endogenous Loci

Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina. We use our tagged chromosomal insertion site system to identify small sequences from borders of fibroblast-specific variable LADs that are sufficient to target these ectopic sites to the nuclear periphery. We identify YY1 (Ying-Yang1) binding sites as enriched in relocating sequences. Knockdown of YY1 or lamin A/C, but not lamin A, led to a loss of lamina association. In addition, targeted recruitment of YY1 proteins facilitated ectopic LAD formation dependent on histone H3 lysine 27 trimethylation and histone H3 lysine di- and trimethylation. Our results also reveal that endogenous loci appear to be dependent on lamin A/C, YY1, H3K27me3, and H3K9me2/3 for maintenance of lamina-proximal positioning.

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

2020 ◽  
Author(s):  
Nana Naetar ◽  
Konstantina Georgiou ◽  
Christian Knapp ◽  
Irena Bronshtein ◽  
Elisabeth Zier ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Higher Order ◽  
Lamin A ◽  
Independent Manner ◽  
Nuclear Interior ◽  
Order Structures

AbstractLamins 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.

scholarly journals Chromosome positioning is largely unaffected in lymphoblastoid cell lines containing emerin or A-type lamin mutations

2005 ◽  
Vol 33 (6) ◽  
pp. 1438-1440 ◽  
Author(s):  
K.J. Meaburn ◽  
N. Levy ◽  
D. Toniolo ◽  
J.M. Bridger
Keyword(s):  
Muscular Dystrophy ◽  
Cell Lines ◽  
Nuclear Periphery ◽  
Premature Aging ◽  
Lamin A ◽  
Lymphoblastoid Cell Lines ◽  
Human Chromosomes ◽  
Chromosome Location ◽  
Proliferating Cells ◽  
Tissue Degeneration

Gene-poor human chromosomes are reproducibly found at the nuclear periphery in proliferating cells. There are a number of inner nuclear envelope proteins that may have roles in chromosome location and anchorage, e.g. emerin and A-type lamins. In the last decade, a number of diseases associated with tissue degeneration and premature aging have been linked with mutations in lamin A or emerin. These are termed laminopathies, with mutations in emerin causing Emery–Dreifuss muscular dystrophy. Despite highly aberrant nuclear distributions of A-type lamins and emerin in lymphoblastoid cell lines derived from patients with emerin or lamin A mutations, little or no change in chromosome location was detected.

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

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Nana Naetar ◽  
Konstantina Georgiou ◽  
Christian Knapp ◽  
Irena Bronshtein ◽  
Elisabeth Zier ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Higher Order ◽  
Lamin A ◽  
Independent Manner ◽  
Mobile State ◽  
Nuclear Interior ◽  
Mouse Cells ◽  
Antibody Labeling ◽  
Order Structures

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). Using antibody labeling, we previously observed a depletion of nucleoplasmic A-type lamins in mouse cells lacking LAP2α. Here, we show that loss of LAP2α actually causes formation of larger, biochemically stable lamin A/C structures in the nuclear interior that are inaccessible to lamin A/C antibodies. While nucleoplasmic lamin A forms from newly expressed pre-lamin A during processing and from soluble mitotic lamins in a LAP2α-independent manner, binding of LAP2α to lamin A/C during interphase inhibits formation of higher order structures, keeping nucleoplasmic lamin A/C in a mobile state independent of lamin A/C S22 phosphorylation. 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.

scholarly journals Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

2021 ◽  
Vol 49 (7) ◽  
pp. 3856-3875
Author(s):  
Marina Kulik ◽  
Melissa Bothe ◽  
Gözde Kibar ◽  
Alisa Fuchs ◽  
Stefanie Schöne ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Dna Binding ◽  
Receptor Binding ◽  
Binding Sites ◽  
Specific Gene ◽  
Functional Diversification ◽  
Enhancer Activity ◽  
Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

scholarly journals Human WRN is an intrinsic inhibitor of progerin, abnormal splicing product of lamin A

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
So-mi Kang ◽  
Min-Ho Yoon ◽  
Su-Jin Lee ◽  
Jinsook Ahn ◽  
Sang Ah Yi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Span ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Werner Syndrome ◽  
Genetic Disorder ◽  
Dna Helicase ◽  
Premature Aging ◽  
Lamin A ◽  
Short Life Span

AbstractWerner syndrome (WRN) is a rare progressive genetic disorder, caused by functional defects in WRN protein and RecQ4L DNA helicase. Acceleration of the aging process is initiated at puberty and the expected life span is approximately the late 50 s. However, a Wrn-deficient mouse model does not show premature aging phenotypes or a short life span, implying that aging processes differ greatly between humans and mice. Gene expression analysis of WRN cells reveals very similar results to gene expression analysis of Hutchinson Gilford progeria syndrome (HGPS) cells, suggesting that these human progeroid syndromes share a common pathological mechanism. Here we show that WRN cells also express progerin, an abnormal variant of the lamin A protein. In addition, we reveal that duplicated sequences of human WRN (hWRN) from exon 9 to exon 10, which differ from the sequence of mouse WRN (mWRN), are a natural inhibitor of progerin. Overexpression of hWRN reduced progerin expression and aging features in HGPS cells. Furthermore, the elimination of progerin by siRNA or a progerin-inhibitor (SLC-D011 also called progerinin) can ameliorate senescence phenotypes in WRN fibroblasts and cardiomyocytes, derived from WRN-iPSCs. These results suggest that progerin, which easily accumulates under WRN-deficient conditions, can lead to premature aging in WRN and that this effect can be prevented by SLC-D011.

scholarly journals Functional mapping of androgen receptor enhancer activity

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chia-Chi Flora Huang ◽  
Shreyas Lingadahalli ◽  
Tunc Morova ◽  
Dogancan Ozturan ◽  
Eugene Hu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Binding Sites ◽  
Gene Promoters ◽  
Strongly Correlated ◽  
Enhancer Activity ◽  
Drive Gene Expression ◽  
In Vitro Cell Lines ◽  
Drive Gene

Abstract Background Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10–100× more binding sites than differentially expressed genes. It is unclear how or if these excess binding sites impact gene transcription. Results To characterize the regulatory logic of AR-mediated transcription, we generated a locus-specific map of enhancer activity by functionally testing all common clinical AR binding sites with Self-Transcribing Active Regulatory Regions sequencing (STARRseq). Only 7% of AR binding sites displayed androgen-dependent enhancer activity. Instead, the vast majority of AR binding sites were either inactive or constitutively active enhancers. These annotations strongly correlated with enhancer-associated features of both in vitro cell lines and clinical prostate cancer samples. Evaluating the effect of each enhancer class on transcription, we found that AR-regulated enhancers frequently interact with promoters and form central chromosomal loops that are required for transcription. Somatic mutations of these critical AR-regulated enhancers often impact enhancer activity. Conclusions Using a functional map of AR enhancer activity, we demonstrated that AR-regulated enhancers act as a regulatory hub that increases interactions with other AR binding sites and gene promoters.

scholarly journals Fluorescent antibodies and lectins stain intracellular structures in fixed cells treated with nonionic detergent.

1978 ◽  
Vol 26 (4) ◽  
pp. 251-257 ◽  
Author(s):  
P Laurila ◽  
I Virtanen ◽  
J Wartiovaara ◽  
S Stenman
Keyword(s):  
Binding Sites ◽  
Human Fibroblasts ◽  
T Antigen ◽  
Similar Distribution ◽  
Sv40 T Antigen ◽  
Con A ◽  
Acetone Treatment ◽  
Nonionic Detergent ◽  
Detergent Treatment ◽  
Scanning Electron

Nonionic detergent (NP40) treatment of paraformaldehyde-fixed normal and SV40-transformed human fibroblasts resulted in intracellular penetration of two chosen fluorescent antibodies and Concanavalin A (Con A). After the detergent treatment nuclear SV40 T antigen, cytoplasmic fibronectin glycoprotein and Con A binding sites could be visualized in fluorescence microscopy. The lowest NP40 concentration which made fixed cells permeable was 0.05%. The morphology of cells was preserved better by this new method than by conventional fixation methods, such as acetone treatment. In scanning electron microscopy the surface of the fixed NP40-treated cells had only small rugosities and fine pores. The subsurface cytoskeleton especially was well preserved and had a more distinct fine structure. The improved morphology made it possible to detect a similar distribution of fibronectin and Con A binding sites in the perinuclear endoplasmic reticulum regions.

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