Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 7 de 7
Filter
Add more filters










Database
Language
Publication year range
1.
Nat Neurosci ; 22(6): 897-908, 2019 06.
Article in English | MEDLINE | ID: mdl-31086315

ABSTRACT

Developmental programs that generate the astonishing neuronal diversity of the nervous system are not completely understood and thus present a major challenge for clinical applications of guided cell differentiation strategies. Using direct neuronal programming of embryonic stem cells, we found that two main vertebrate proneural factors, Ascl1 and neurogenin 2 (Neurog2), induce different neuronal fates by binding to largely different sets of genomic sites. Their divergent binding patterns are not determined by the previous chromatin state, but are distinguished by enrichment of specific E-box sequences that reflect the binding preferences of the DNA-binding domains. The divergent Ascl1 and Neurog2 binding patterns result in distinct chromatin accessibility and enhancer activity profiles that differentially shape the binding of downstream transcription factors during neuronal differentiation. This study provides a mechanistic understanding of how transcription factors constrain terminal cell fates, and it delineates the importance of choosing the right proneural factor in neuronal reprogramming strategies.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , Chromatin/metabolism , Nerve Tissue Proteins/metabolism , Neurogenesis/physiology , Neurons/cytology , Animals , Cell Differentiation/physiology , Embryonic Stem Cells , Humans , Neurons/metabolism
2.
PLoS Comput Biol ; 13(10): e1005795, 2017 Oct.
Article in English | MEDLINE | ID: mdl-29049320

ABSTRACT

Genomic loci with regulatory potential can be annotated with various properties. For example, genomic sites bound by a given transcription factor (TF) can be divided according to whether they are proximal or distal to known promoters. Sites can be further labeled according to the cell types and conditions in which they are active. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between the labels; e.g. if regulatory sites specific to a given cell type are also more likely to be promoter-proximal, it is difficult to assess whether motifs identified in that set of sites are associated with the cell type or associated with promoters. In order to meet this challenge, we developed SeqUnwinder, a principled approach to deconvolving interpretable discriminative sequence features associated with overlapping annotation labels. We demonstrate the novel analysis abilities of SeqUnwinder using three examples. Firstly, SeqUnwinder is able to unravel sequence features associated with the dynamic binding behavior of TFs during motor neuron programming from features associated with chromatin state in the initial embryonic stem cells. Secondly, we characterize distinct sequence properties of multi-condition and cell-specific TF binding sites after controlling for uneven associations with promoter proximity. Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines.


Subject(s)
Molecular Sequence Annotation , Regulatory Sequences, Nucleic Acid/genetics , Software , Transcription Factors/metabolism , Binding Sites , Cell Line , Cell Lineage/genetics , Chromatin/genetics , Chromatin/metabolism , Computational Biology/methods , Deoxyribonuclease I/genetics , Deoxyribonuclease I/metabolism , Embryonic Stem Cells/cytology , Embryonic Stem Cells/metabolism , Gene Expression Regulation , Genetic Loci , High-Throughput Nucleotide Sequencing , Humans , Promoter Regions, Genetic , Transcription Factors/genetics
3.
Cell Stem Cell ; 20(2): 205-217.e8, 2017 02 02.
Article in English | MEDLINE | ID: mdl-27939218

ABSTRACT

Direct cell programming via overexpression of transcription factors (TFs) aims to control cell fate with the degree of precision needed for clinical applications. However, the regulatory steps involved in successful terminal cell fate programming remain obscure. We have investigated the underlying mechanisms by looking at gene expression, chromatin states, and TF binding during the uniquely efficient Ngn2, Isl1, and Lhx3 motor neuron programming pathway. Our analysis reveals a highly dynamic process in which Ngn2 and the Isl1/Lhx3 pair initially engage distinct regulatory regions. Subsequently, Isl1/Lhx3 binding shifts from one set of targets to another, controlling regulatory region activity and gene expression as cell differentiation progresses. Binding of Isl1/Lhx3 to later motor neuron enhancers depends on the Ebf and Onecut TFs, which are induced by Ngn2 during the programming process. Thus, motor neuron programming is the product of two initially independent transcriptional modules that converge with a feedforward transcriptional logic.


Subject(s)
Cellular Reprogramming/genetics , Chromatin/metabolism , Embryonic Stem Cells/cytology , Motor Neurons/cytology , Transcription, Genetic , Animals , DNA/metabolism , Embryonic Stem Cells/metabolism , Enhancer Elements, Genetic/genetics , Genetic Loci , Mice , Models, Biological , Motor Neurons/metabolism , Nucleotide Motifs/genetics , Promoter Regions, Genetic/genetics , Protein Binding/genetics , Sequence Analysis, RNA , Single-Cell Analysis , Time Factors , Transcription Factors/metabolism
4.
Mol Cell ; 62(1): 79-91, 2016 Apr 07.
Article in English | MEDLINE | ID: mdl-27058788

ABSTRACT

Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.


Subject(s)
Enhancer Elements, Genetic , Hepatocyte Nuclear Factor 3-alpha/metabolism , Hepatocyte Nuclear Factor 3-beta/metabolism , Hepatocyte Nuclear Factor 3-gamma/metabolism , Nucleosomes/metabolism , Animals , Histones/metabolism , Liver/metabolism , Mice , Nucleosomes/genetics , Organ Specificity , Promoter Regions, Genetic , Transcription, Genetic
5.
PLoS Comput Biol ; 10(3): e1003501, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24675637

ABSTRACT

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.


Subject(s)
Computational Biology/methods , Homeodomain Proteins/chemistry , Amino Acid Motifs , Animals , Artificial Intelligence , Bayes Theorem , Binding Sites , CDX2 Transcription Factor , Cell Line , Chromatin Immunoprecipitation , Cluster Analysis , Embryonic Stem Cells/cytology , Genome , Homeodomain Proteins/metabolism , Mice , Protein Binding , Sequence Analysis, DNA
6.
Metabolites ; 3(2): 347-72, 2013 May 14.
Article in English | MEDLINE | ID: mdl-24957996

ABSTRACT

Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on "guilt-by-association" relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

7.
Plant Physiol ; 160(2): 846-67, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22837360

ABSTRACT

Drought stress affects cereals especially during the reproductive stage. The maize (Zea mays) drought transcriptome was studied using RNA-Seq analysis to compare drought-treated and well-watered fertilized ovary and basal leaf meristem tissue. More drought-responsive genes responded in the ovary compared with the leaf meristem. Gene Ontology enrichment analysis revealed a massive decrease in transcript abundance of cell division and cell cycle genes in the drought-stressed ovary only. Among Gene Ontology categories related to carbohydrate metabolism, changes in starch and Suc metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in Suc transporter function, with no comparable changes occurring in the leaf meristem. Abscisic acid (ABA)-related processes responded positively, but only in the ovaries. Related responses suggested the operation of low glucose sensing in drought-stressed ovaries. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion and the relative robustness of dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. Our working hypothesis involves signaling events associated with increased ABA levels, decreased glucose levels, disruption of ABA/sugar signaling, activation of programmed cell death/senescence through repression of a phospholipase C-mediated signaling pathway, and arrest of the cell cycle in the stressed ovary at 1 d after pollination. Increased invertase levels in the stressed leaf meristem, on the other hand, resulted in that tissue maintaining hexose levels at an "unstressed" level, and at lower ABA levels, which was correlated with successful resistance to drought stress.


Subject(s)
Droughts , Flowers/metabolism , Gene Expression Regulation, Plant , Meristem/metabolism , Plant Leaves/metabolism , Zea mays/genetics , Abscisic Acid/pharmacology , Adaptation, Physiological , Cell Cycle Checkpoints , Cell Death , Cell Division , Flowers/genetics , Flowers/physiology , Genes, Plant , Glucose/metabolism , Meristem/genetics , Phenotype , Plant Leaves/genetics , Plant Leaves/physiology , RNA Splice Sites , RNA, Plant/genetics , Seeds/genetics , Seeds/metabolism , Sequence Analysis, RNA , Signal Transduction , Stress, Physiological , Transcriptome , Type C Phospholipases/genetics , Type C Phospholipases/metabolism , Zea mays/metabolism , Zea mays/physiology
SELECTION OF CITATIONS
SEARCH DETAIL
...