Raja Jothi
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View article: GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors
GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors Open
View article: Additional file 6 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors
Additional file 6 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors Open
Additional file 6: Table S2. A Lists of genes binding GLIS3, NKX2.1, and/or PAX8 as indicated (within 5 kb from TSS). ChIP-Seq analysis was performed with thyroid glands from mouse fed an LID. G+N+P+, G+N+P−, etc. are defined as described …
View article: Additional file 5 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors
Additional file 5 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors Open
Additional file 5: Table S1. List of primers used in ChIP Q-PCR.
View article: Additional file 7 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors
Additional file 7 of GLIS3 regulates transcription of thyroid hormone biosynthetic genes in coordination with other thyroid transcription factors Open
Additional file 7: Table S3. Lists of genes binding GLIS3, NKX2.1, PAX8, and/or FOXE1 as indicated (within 5 kb from TSS). ChIP-Seq analysis was performed with rat thyrocyte PCCl3 cells. G+N+P+, G+N+P−, etc. are defined as described in “Re…
View article: Decoding the function of bivalent chromatin in development and cancer
Decoding the function of bivalent chromatin in development and cancer Open
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells (ES…
View article: Bivalent chromatin protects reversibly repressed genes from irreversible silencing
Bivalent chromatin protects reversibly repressed genes from irreversible silencing Open
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells, bi…
View article: Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes
Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes Open
Polycomb group (PcG) proteins control organism development by regulating the expression of developmental genes. Transcriptional regulation by PcG proteins is achieved, at least partly, through the PRC2-mediated methylation on lysine 27 of …
View article: INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development
INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development Open
The master transcription factors play integral roles in the pluripotency transcription circuitry of embryonic stem cells (ESCs). How they selectively activate expression of the pluripotency network while simultaneously repressing genes inv…
View article: Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning
Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning Open
The developmental potential of cells, termed pluripotency, is highly dynamic and progresses through a continuum of naive, formative and primed states. Pluripotency progression of mouse embryonic stem cells (ESCs) from naive to formative an…
View article: NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region
NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region Open
View article: Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency Open
View article: GLIS3 Transcriptionally Activates WNT Genes to Promote Differentiation of Human Embryonic Stem Cells into Posterior Neural Progenitors
GLIS3 Transcriptionally Activates WNT Genes to Promote Differentiation of Human Embryonic Stem Cells into Posterior Neural Progenitors Open
Anterior–posterior (A–P) specification of the neural tube involves initial acquisition of anterior fate followed by the induction of posterior characteristics in the primitive anterior neuroectoderm. Several morphogens have been implicated…
View article: Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency Open
SUMMARY Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the inter…
View article: NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region
NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region Open
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y,…
View article: An Optimal Job Scheduling Algorithm for Cloud Environment using Enhanced Hyper-Heuristic Approach
An Optimal Job Scheduling Algorithm for Cloud Environment using Enhanced Hyper-Heuristic Approach Open
View article: GLIS3 is indispensable for TSH/TSHR-dependent thyroid hormone biosynthesis and follicular cell proliferation
GLIS3 is indispensable for TSH/TSHR-dependent thyroid hormone biosynthesis and follicular cell proliferation Open
Deficiency in Krüppel-like zinc finger transcription factor GLI-similar 3 (GLIS3) in humans is associated with the development of congenital hypothyroidism. However, the functions of GLIS3 in the thyroid gland and the mechanism by which GL…
View article: Intragenic Enhancers Attenuate Host Gene Expression
Intragenic Enhancers Attenuate Host Gene Expression Open
View article: CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State
CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State Open
Poly(A) tail length and mRNA deadenylation play important roles in gene regulation. However, how they regulate embryonic development and pluripotent cell fate is not fully understood. Here we present evidence that CNOT3-dependent mRNA dead…
View article: mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes
mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes Open
View article: KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis
KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis Open
Mass spectrometry (MS)‐based quantitative phosphoproteomics has become a key approach for proteome‐wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, wh…
View article: Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates
Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates Open
View article: Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates
Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates Open
View article: Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data Open
Motivation: Protein phosphorylation is a post-translational modification that underlines various aspects of cellular signaling. A key step to reconstructing signaling networks involves identification of the set of all kinases and their sub…
View article: Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data Open
Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics …
View article: DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis
DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis Open
Mammary stem/progenitor cells (MaSCs) maintain self-renewal of the mammary epithelium during puberty and pregnancy. DNA methylation provides a potential epigenetic mechanism for maintaining cellular memory during self-renewal. Although DNA…