Searching the Resource Information Network

Our searching services are busy right now. Please try again later

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes

MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation.

Xiao Hu | Zongzhi Z Liu | Xinyue Chen | Vincent P Schulz | Abhishek Kumar | Amaleah A Hartman | Jason Weinstein | Jessica F Johnston | Elisa C Rodriguez | Anna E Eastman | Jijun Cheng | Liz Min | Mei Zhong | Christopher Carroll | Patrick G Gallagher | Jun Lu | Martin Schwartz | Megan C King | Diane S Krause | Shangqin Guo
Nature communications | 2019

Actin cytoskeleton is well-known for providing structural/mechanical support, but whether and how it regulates chromatin and cell fate reprogramming is far less clear. Here, we report that MKL1, the key transcriptional co-activator of many actin cytoskeletal genes, regulates genomic accessibility and cell fate reprogramming. The MKL1-actin pathway weakens during somatic cell reprogramming by pluripotency transcription factors. Cells that reprogram efficiently display low endogenous MKL1 and inhibition of actin polymerization promotes mature pluripotency activation. Sustained MKL1 expression at a level seen in typical fibroblasts yields excessive actin cytoskeleton, decreases nuclear volume and reduces global chromatin accessibility, stalling cells on their trajectory toward mature pluripotency. In addition, the MKL1-actin imposed block of pluripotency can be bypassed, at least partially, when the Sun2-containing linker of the nucleoskeleton and cytoskeleton (LINC) complex is inhibited. Thus, we unveil a previously unappreciated aspect of control on chromatin and cell fate reprogramming exerted by the MKL1-actin pathway.

Pubmed ID: 30979898

Associated grants

  • Agency: NCATS NIH HHS, United States
    Id: UL1 TR001863
  • Agency: NIDDK NIH HHS, United States
    Id: U54 DK106857
  • Agency: NIDDK NIH HHS, United States
    Id: R01 DK094934
  • Agency: NIGMS NIH HHS, United States
    Id: R01 GM129308
  • Agency: NIDDK NIH HHS, United States
    Id: P01 DK032094
  • Agency: NIGMS NIH HHS, United States
    Id: DP2 GM123507

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.

This is a list of tools and resources that we have found mentioned in this publication.


DAVID (tool)

RRID:SCR_001881

Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

View all literature mentions

Addgene (tool)

RRID:SCR_002037

Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

View all literature mentions

Gene Set Enrichment Analysis (tool)

RRID:SCR_003199

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

View all literature mentions

Picard (tool)

RRID:SCR_006525

Java toolset for working with next generation sequencing data in the BAM format.

View all literature mentions

Imaris (tool)

RRID:SCR_007370

Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition.

View all literature mentions

Millipore (tool)

RRID:SCR_008983

An Antibody supplier

View all literature mentions

HOMER (tool)

RRID:SCR_010881

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

View all literature mentions

DiffBind (tool)

RRID:SCR_012918

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

View all literature mentions

Abcam (tool)

RRID:SCR_012931

A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.

View all literature mentions

DESeq2 (tool)

RRID:SCR_015687

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

View all literature mentions

Deeptools (tool)

RRID:SCR_016366

Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.

View all literature mentions

BioAnalyzer 2100 (tool)

RRID:SCR_019715

2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of biomolecules. The 2100 Bioanalyzer instrument, together with the 2100 Expert Software and Bioanalyzer assays, provide highly precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use.

View all literature mentions

C57BL/6-Tg(Thy1-SNCA*E35K*E46K*E61K)3798Nuber/J (tool)

RRID:IMSR_JAX:032799

Mus musculus with name C57BL/6-Tg(Thy1-SNCA*E35K*E46K*E61K)3798Nuber/J from IMSR.

View all literature mentions

NIH 3T3 (tool)

RRID:CVCL_0594

Cell line NIH 3T3 is a Spontaneously immortalized cell line with a species of origin Mus musculus

View all literature mentions