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Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells.

Cell stem cell | 2017

Replicating Lgr5+ stem cells and quiescent Bmi1+ cells behave as intestinal stem cells (ISCs) in vivo. Disrupting Lgr5+ ISCs triggers epithelial renewal from Bmi1+ cells, from secretory or absorptive progenitors, and from Paneth cell precursors, revealing a high degree of plasticity within intestinal crypts. Here, we show that GFP+ cells from Bmi1GFP mice are preterminal enteroendocrine cells and we identify CD69+CD274+ cells as related goblet cell precursors. Upon loss of native Lgr5+ ISCs, both populations revert toward an Lgr5+ cell identity. While active histone marks are distributed similarly between Lgr5+ ISCs and progenitors of both major lineages, thousands of cis elements that control expression of lineage-restricted genes are selectively open in secretory cells. This accessibility signature dynamically converts to that of Lgr5+ ISCs during crypt regeneration. Beyond establishing the nature of Bmi1GFP+ cells, these findings reveal how chromatin status underlies intestinal cell diversity and dedifferentiation to restore ISC function and intestinal homeostasis.

Pubmed ID: 28648363 RIS Download

Associated grants

  • Agency: NIDDK NIH HHS, United States
    Id: R01 DK081113
  • Agency: NIDDK NIH HHS, United States
    Id: U01 DK103152
  • Agency: NIDDK NIH HHS, United States
    Id: P30 DK034854
  • Agency: NIDDK NIH HHS, United States
    Id: U01 DK085532
  • Agency: NIDDK NIH HHS, United States
    Id: F32 DK103453
  • Agency: NCI NIH HHS, United States
    Id: P50 CA127003

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


Intestinal Stem Cell Consortium (tool)

RRID:SCR_001555

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh.

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New England Biolabs (tool)

RRID:SCR_013517

An Antibody supplier

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Bowtie 2 (tool)

RRID:SCR_016368

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

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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.

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FEV (C-18) (antibody)

RRID:AB_2231629

This polyclonal targets FEV (C-18)

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Chromogranin A antibody (antibody)

RRID:AB_301704

This polyclonal targets Chromogranin A antibody

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H3K27ac-dmelanogaster (antibody)

RRID:AB_2614979

This unknown targets H3K27ac

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GFP (B-2) (antibody)

RRID:AB_627695

This monoclonal targets GFP (B-2)

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BrdU (antibody)

RRID:AB_609568

This unknown targets

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B6.129P2-Lgr5tm1(cre/ERT2)Cle/J (organism)

RRID:IMSR_JAX:008875

Mus musculus with name B6.129P2-Lgr5tm1(cre/ERT2)Cle/J from IMSR.

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BKa.Cg-Ptprcb Bmi1 Thy1/J (organism)

RRID:IMSR_JAX:017351

Mus musculus with name BKa.Cg-Ptprcb Bmi1 Thy1/J from IMSR.

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B6.129S7-Atoh1tm3Hzo/J (organism)

RRID:IMSR_JAX:008681

Mus musculus with name B6.129S7-Atoh1tm3Hzo/J from IMSR.

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Gene Set Enrichment Analysis (software resource)

RRID:SCR_003199

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

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HOMER (software resource)

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++.

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Integrative Genomics Viewer (software resource)

RRID:SCR_011793

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

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BEDTools (software resource)

RRID:SCR_006646

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

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MACS (software resource)

RRID:SCR_013291

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

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DESeq (software resource)

RRID:SCR_000154

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

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HTSeq (software resource)

RRID:SCR_005514

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

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Bowtie (software resource)

RRID:SCR_005476

Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.

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TopHat (software resource)

RRID:SCR_013035

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

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