HNF4A Regulates the Formation of Hepatic Progenitor Cells from Human iPSC-Derived Endoderm by Facilitating Efficient Recruitment of RNA Pol II

Elucidating the molecular basis of cell differentiation will advance our understanding of organ development and disease. We have previously established a protocol that efficiently produces cells with hepatocyte characteristics from human induced pluripotent stem cells. We previously used this cell differentiation model to identify the transcription factor hepatocyte nuclear factor 4 α (HNF4A) as being essential during the transition of the endoderm to a hepatic fate. Here, we sought to define the molecular mechanisms through which HNF4A controls this process. By combining HNF4A chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) analyses at the onset of hepatic progenitor cell formation with transcriptome data collected during early stages of differentiation, we identified genes whose expression is directly dependent upon HNF4A. By examining the dynamic changes that occur at the promoters of these HNF4A targets we reveal that HNF4A is essential for recruitment of RNA polymerase (RNA pol) II to genes that are characteristically expressed as the hepatic progenitors differentiate from the endoderm.

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Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

Scientific Reports ◽

10.1038/s41598-021-87262-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Aisajan Mamat ◽

Kuerban Tusong ◽

Juan Xu ◽

Peng Yan ◽

Chuang Mei ◽

...

Keyword(s):

Cell Differentiation ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Cell Formation ◽

Parenchyma Cell ◽

Lignin Biosynthesis ◽

Cell Content ◽

Stone Cell ◽

Fruit Samples

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

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In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

10.1101/776542 ◽

2019 ◽

Author(s):

Rodrigo G. Arzate-Mejía ◽

Angel Josué Cerecedo-Castillo ◽

Georgina Guerrero ◽

Mayra Furlan-Magaril ◽

Félix Recillas-Targa

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Regulation Of Gene Expression ◽

Topological Defects ◽

Rna Pol Ii ◽

Pol Ii ◽

Domain Boundaries ◽

Topologically Associated Domains ◽

Genetic Sequences

AbstractThe molecular mechanisms responsible for Topologically Associated Domains (TADs) formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by Architectural Proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence on the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.

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Sequential Histone Modifications at Hoxd4 Regulatory Regions Distinguish Anterior from Posterior Embryonic Compartments

Molecular and Cellular Biology ◽

10.1128/mcb.24.18.8090-8103.2004 ◽

2004 ◽

Vol 24 (18) ◽

pp. 8090-8103 ◽

Cited By ~ 48

Author(s):

Mojgan Rastegar ◽

Laila Kobrossy ◽

Erzsebet Nagy Kovacs ◽

Isabel Rambaldi ◽

Mark Featherstone

Keyword(s):

Rna Polymerase Ii ◽

Histone Modifications ◽

Chromatin Immunoprecipitation ◽

Gene Activation ◽

Open Chromatin ◽

Rna Pol Ii ◽

Regulatory Regions ◽

Pol Ii ◽

Embryonic Tissues ◽

Intervening Sequences

ABSTRACT Hox genes are differentially expressed along the embryonic anteroposterior axis. We used chromatin immunoprecipitation to detect chromatin changes at the Hoxd4 locus during neurogenesis in P19 cells and embryonic day 8.0 (E8.0) and E10.5 mouse embryos. During Hoxd4 induction in both systems, we observed that histone modifications typical of transcriptionally active chromatin occurred first at the 3′ neural enhancer and then at the promoter. Moreover, the sequential distribution of histone modifications between E8.0 and E10.5 was consistent with a spreading of open chromatin, starting with the enhancer, followed by successively more 5′ intervening sequences, and culminating at the promoter. Neither RNA polymerase II (Pol II) nor CBP associated with the inactive gene. During Hoxd4 induction, CBP and RNA Pol II were recruited first to the enhancer and then to the promoter. Whereas the CBP association was transient, RNA Pol II remained associated with both regulatory regions. Histone modification and transcription factor recruitment occurred in posterior, Hox-expressing embryonic tissues, but never in anterior tissues, where such genes are inactive. Together, our observations demonstrate that the direction of histone modifications at Hoxd4 mirrors colinear gene activation across Hox clusters and that the establishment of anterior and posterior compartments is accompanied by the imposition of distinct chromatin states.

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Angiotensin II biphasically regulates cell differentiation in human iPSC-derived kidney organoids

AJP Renal Physiology ◽

10.1152/ajprenal.00134.2021 ◽

2021 ◽

Vol 321 (5) ◽

pp. F559-F571

Author(s):

Stacy M. Yanofsky ◽

Courtney M. Dugas ◽

Akemi Katsurada ◽

Jiao Liu ◽

Zubaida Saifudeen ◽

...

Keyword(s):

Cell Differentiation ◽

Angiotensin Ii ◽

Induced Pluripotent Stem Cell ◽

Human Kidney ◽

Developmental Potential ◽

Novel Strategy ◽

Induced Pluripotent ◽

Human Ipsc ◽

Kidney Organoids

This study demonstrates angiotensin II exertion of biphasic effects on cell differentiation through distinct mediatory roles of angiotensin II type 1 receptor and type 2 receptor in human induced pluripotent stem cell-derived kidney organoids, providing a novel strategy to establish and further characterize the developmental potential of the human kidney organoids.

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Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

10.1101/2020.07.25.220095 ◽

2020 ◽

Author(s):

A.I. Garrido-Godino ◽

I. Gupta ◽

F. Gutiérrez-Santiago ◽

A.B. Martínez-Padilla ◽

A. Alekseenko ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Mrna Stability ◽

Molecular Mechanisms ◽

Rna Binding ◽

Large Population ◽

Dependent Manner ◽

Mrna Synthesis ◽

Rna Pol Ii ◽

Pol Ii ◽

The Stability

ABSTRACTGene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analyzed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

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Transcriptome Analysis of Induced Pluripotent Stem Cell (iPSC)-derived Pancreatic β-like Cell Differentiation

Cell Transplantation ◽

10.1177/0963689717720281 ◽

2017 ◽

Vol 26 (8) ◽

pp. 1380-1391 ◽

Cited By ~ 5

Author(s):

Yan Huang ◽

Jian Wan ◽

Yibing Guo ◽

Shajun Zhu ◽

Yao Wang ◽

...

Keyword(s):

Cell Differentiation ◽

Time Course ◽

Molecular Mechanisms ◽

Induced Pluripotent Stem Cell ◽

Rna Seq ◽

Β Cells ◽

Β Cell ◽

Induced Pluripotent ◽

Selective Differentiation ◽

Differentiation Period

Diabetes affects millions of people worldwide, and β-cell replacement is one of the promising new strategies for treatment. Induced pluripotent stem cells (iPSCs) can differentiate into any cell type, including pancreatic β cells, providing a potential treatment for diabetes. However, the molecular mechanisms underlying the differentiation of iPSC-derived β cells have not yet been fully elucidated. Here, we generated pancreatic β-like cells from mouse iPSCs using a 3-step protocol and performed deep RNA sequencing to get a transcriptional landscape of iPSC-derived pancreatic β-like cells during the selective differentiation period. We then focused on the differentially expressed genes (DEGs) during the time course of the differentiation period, and these genes underwent Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In addition, gene-act networks were constructed for these DEGs, and the expression of pivotal genes detected by quantitative real-time polymerase chain reaction was well correlated with RNA sequence (RNA-seq). Overall, our study provides valuable information regarding the transcriptome changes in β cells derived from iPSCs during differentiation, elucidates the biological process and pathways underlying β-cell differentiation, and promotes the identification and functional analysis of potential genes that could be used for improving functional β-cell generation from iPSCs.

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