Evidence map›Paper›PMID 37310625›Full record

ReviewMethods in molecular biology (Clifton, N.J.)2023

Epigenetic and Transcriptional Dynamics of Notch Program in Intestinal Differentiation.

Shahadat Rahman, Xi Lan, Christopher Terranova, Rayan El-Kholdi, Omer H Yilmaz, Chia-Wei Cheng

Abstract readReview
PubMed Publisher
In one paragraph

Review in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Shahadat Rahman *Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA.
Xi Lan *Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
Christopher TerranovaGenomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Rayan El-KholdiColumbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA.
Omer H YilmazKoch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
Chia-Wei ChengColumbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA. cc4688@cumc.columbia.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The equilibrium between stem cell self-renewal and differentiation followed by proper lineage specification of progenitor cells is considered imperative for maintaining intestinal homeostasis. In the hierarchical model, intestinal differentiation is defined by the stepwise acquisition of lineage-specific mature cell features, where Notch signaling and lateral inhibition instructively regulate the cell-fate decisions. Recent studies reveal a broadly permissive intestinal chromatin underlies the lineage plasticity and adaptation to diet mediated by Notch transcriptional program. Here, we review the conventional understanding of Notch programming in intestinal differentiation and describe how new data from epigenetic and transcriptional analyses may refine or revise the current view. We provide instructions on sample preparation and data analysis and explain how to use ChIP-seq and scRNA-seq in combination of lineage tracing assay to determine the dynamics of Notch program and intestinal differentiation in the context of dietary and metabolic regulation of cell-fate decisions.

Indexed as

AcclimatizationEpigenomicsBiological AssayCell DifferentiationEpigenesis, GeneticCell-fate decisionsChIP-seqNotchscRNA-seq

Identifiers

PMID37310625

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.