scholarly journals Identifying DNA Sequence Motifs of Pdx-1 and NeuroD1 Transcription Factors

10.29007/sfxr ◽  
2019 ◽  
Author(s):  
Hassan Aldarwish ◽  
David Keller ◽  
Elena Harris
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Beta Cells ◽  
Type I Diabetes ◽  
Motif Finding ◽  
Type I ◽  
Sequence Motifs ◽  
Regulate Gene Expression ◽  
Treatment Of Diabetes ◽  
Dna Sequence Motifs

Diabetes is a disease reported to be the 8th leading cause of death across the world. Nearly 38 million people worldwide have Type I diabetes caused by a dysfunction of beta cells that impairs insulin production. A better understanding of mechanisms related to gene expression in beta cells might help in the development of novel strategies for the effective treatment of diabetes. Two known transcription factors, Pdx-1 and NeuroD1, are shown to regulate gene expression in beta cells. Recently gene targets that are regulated by both Pdx-1 and NeuroD1 have been identified experimentally [7]. However, the motifs for this set of genes have not been found yet. Here we undertake the task of finding statistically overrepresented motifs in genes regulated by Pdx-1 and NeuroD1. The challenge of this project is to identify statistically significant pairs of motifs: one motif of each pair is for Pdx-1 and the other for NeuroD1. Commonly known motif-finding methods are usually restricted to finding a set of potential candidates, each of which is a single motif.

scholarly journals Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

2019 ◽  
Vol 70 (19) ◽  
pp. 5355-5374 ◽  
Author(s):  
Dandan Zang ◽  
Jingxin Wang ◽  
Xin Zhang ◽  
Zhujun Liu ◽  
Yucheng Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Heat Shock ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Ion Homeostasis ◽  
Cellulose Synthase ◽  
Regulate Gene Expression ◽  
E Box ◽  
Regulate Gene

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

scholarly journals Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

Gene expression of type I phospholipase A2in pancreatic beta cells

FEBS Letters ◽  
1991 ◽  
Vol 295 (1-3) ◽  
pp. 110-112 ◽  
Author(s):  
S. Metz ◽  
D. Holmes ◽  
R.P. Robertson ◽  
W. Leitner ◽  
B. Draznin
Keyword(s):  
Gene Expression ◽  
Beta Cells ◽  
Pancreatic Beta Cells ◽  
Type I

Bone inflammation and altered gene expression with type I diabetes early onset

2009 ◽  
Vol 218 (3) ◽  
pp. 575-583 ◽  
Author(s):  
Katherine J. Motyl ◽  
Sergiu Botolin ◽  
Regina Irwin ◽  
Daniel M. Appledorn ◽  
Tejas Kadakia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Onset ◽  
Type I Diabetes ◽  
Type I ◽  
Altered Gene Expression ◽  
Altered Gene ◽  
Bone Inflammation

scholarly journals Genome wide analysis of the transcriptional profiles in different regions of the developing rice grains

2020 ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular in different contributions of grain tissues to these process, are not understood. Main text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

scholarly journals Differentially expressed Maf family transcription factors, c-Maf and MafA, activate glucagon and insulin gene expression in pancreatic islet alpha- and beta-cells

2004 ◽  
Vol 32 (1) ◽  
pp. 9-20 ◽  
Author(s):  
K Kataoka ◽  
S Shioda ◽  
K Ando ◽  
K Sakagami ◽  
H Handa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Line ◽  
Beta Cells ◽  
Cell Lines ◽  
Promoter Activity ◽  
Insulin Gene ◽  
Insulinoma Cell ◽  
Insulin Gene Expression ◽  
Glucagon And Insulin

A basic-leucine zipper transcription factor, MafA, was recently identified as one of the most important transactivators of insulin gene expression. This protein controls the glucose-regulated and pancreatic beta-cell-specific expression of the insulin gene through a cis-regulatory element called RIPE3b/MARE (Maf-recognition element). Here, we show that MafA expression is restricted to beta-cells of pancreatic islets in vivo and in insulinoma cell lines. We also demonstrate that c-Maf, another member of the Maf family of transcription factors, is expressed in islet alpha-cells and in a glucagonoma cell line (alphaTC1), but not in gamma- and delta-cells. An insulinoma cell line, betaTC6, also expressed c-Maf, albeit at a low level. Chromatin immunoprecipitation assays demonstrated that Maf proteins associate with insulin and glucagon promoters in beta- and alpha-cell lines, respectively. c-Maf protein stimulated glucagon promoter activity in a transient luciferase assay, and activation of the glucagon promoter by c-Maf was more efficient than by the other alpha-cell-enriched transcription factors, Cdx2, Pax6, and Isl-1. Furthermore, inhibition of c-Maf expression in alphaTC1 cells by specific short hairpin RNA resulted in marked reduction of the glucagon promoter activity. Thus, c-Maf and MafA are differentially expressed in alpha- and beta-cells where they regulate glucagon and insulin gene expression, respectively.

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