Srinjan Basu
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View article: Intrinsic mechanotransduction during apical constriction licenses lineage competence in pluripotent stem cells
Intrinsic mechanotransduction during apical constriction licenses lineage competence in pluripotent stem cells Open
To acquire the capacity for multi-lineage differentiation, pluripotent stem cells must undergo a transition from naïve pluripotency to lineage competency. This transition requires epithelialization and changes in nuclear architecture. We s…
View article: A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation
A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation Open
The chromatin regulator MLL2 (KMT2B) is the primary histone 3 lysine 4 (H3K4) trimethyltransferase acting at bivalent promoters in embryonic stem cells (ESCs) and is required for differentiation toward neuroectoderm. Here, we demonstrate t…
View article: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD
Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD Open
To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer–promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensi…
View article: H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function Open
Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, …
View article: Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" Open
3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03…
View article: Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" Open
3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03…
View article: Data from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
Data from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer Open
The polarity protein complex Par6/atypical protein kinase (aPKC)/Cdc42 regulates polarization processes during epithelial morphogenesis, astrocyte migration, and axon specification. We, as well as others, have shown that this complex is al…
View article: Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer Open
Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
View article: Data from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
Data from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer Open
The polarity protein complex Par6/atypical protein kinase (aPKC)/Cdc42 regulates polarization processes during epithelial morphogenesis, astrocyte migration, and axon specification. We, as well as others, have shown that this complex is al…
View article: Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer Open
Supplementary Figures 1-6 from The Polarity Protein Par6 Induces Cell Proliferation and Is Overexpressed in Breast Cancer
View article: Editorial: Imaging Approaches to Unravel Chromatin Organization and Nuclear Dynamics
Editorial: Imaging Approaches to Unravel Chromatin Organization and Nuclear Dynamics Open
EDITORIAL article Front. Mol. Biosci., 20 May 2022Sec. Biophysics https://doi.org/10.3389/fmolb.2022.929370
View article: H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function Open
Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Many epigenetic repression mechanisms are known to silence TE transcription. However, TEs are upregulated during early development, neuronal lineag…
View article: Enhancer-Promoter Communication: It’s Not Just About Contact
Enhancer-Promoter Communication: It’s Not Just About Contact Open
Cis -regulatory elements such as enhancers can be located even a million base pairs away from their cognate promoter and yet modulate gene transcription. Indeed, the 3D organisation of chromatin enables the establishment of long-range enha…
View article: RNA, Genome Output and Input
RNA, Genome Output and Input Open
RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA a…
View article: Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics
Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics Open
Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) compl…
View article: MOESM13 of Citrullination of HP1Îł chromodomain affects association with chromatin
MOESM13 of Citrullination of HP1Îł chromodomain affects association with chromatin Open
Additional file 13: Table S3. List of RT-PCR primers used in this study
View article: MOESM3 of Citrullination of HP1γ chromodomain affects association with chromatin
MOESM3 of Citrullination of HP1γ chromodomain affects association with chromatin Open
Additional file 3: Table S1. Raw BLI data. Raw BLI data of GST, GST-HP1γWT, R38/9A and R38/9K proteins at different concentrations to H3K9me3(1–16) and H3(1–16) unmethylated peptides
View article: MOESM7 of Citrullination of HP1γ chromodomain affects association with chromatin
MOESM7 of Citrullination of HP1γ chromodomain affects association with chromatin Open
Additional file 7: Table S2. STP data of single replicates. This file contains a summary of all biological replicates of analysed STP data of mESCs expressing HP1γWT, R38/9A or I165K mutant proteins cultured in the presence or absence of L…
View article: Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols
Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols Open
Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforwar…
View article: Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols
Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols Open
Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforwar…
View article: Research data supporting "Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device"
Research data supporting "Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device" Open
Electrical impedance measurements for mouse embryonic stem cells (mESCs) were performed to study the embryonic stem cell differentiation process. The electrical frequency response (e.g. impedance magnitude and phase) of individual stem cel…
View article: Research data supporting "Dynamic monitoring of single cell lysis in an impedance-based microfluidic device"
Research data supporting "Dynamic monitoring of single cell lysis in an impedance-based microfluidic device" Open
Real-time impedance measurements of mouse embryonic stem cells (mESCs) during the process of cell membrane lysis were performed, and the changes in the electrical properties of cells during this process were quantitatively tracked over tim…
View article: Research data supporting "A microfluidic platform for trapping, releasing and super-resolution imaging of single cells"
Research data supporting "A microfluidic platform for trapping, releasing and super-resolution imaging of single cells" Open
Particles and cells were trapped and released using a microfluidic device. The device enabled the trapping of single particles with a trapping efficiency of greater than 95%, and allowed for single particles and cells to be trapped, releas…