Identification of ATAC-Seq Derived Open Chromatin Regions to Modulate Tissue Specific Gene Regulation in Pennycress (Thlaspi arvense)

2020 ◽  
Author(s):  
KRISHAN RAI
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Open Chromatin ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Thlaspi Arvense

scholarly journals A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation

2021 ◽  
Author(s):  
Isabel Regadas ◽  
Olle Dahlberg ◽  
Roshan Vaid ◽  
Oanh Ho ◽  
Sergey Belikov ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Chromatin Signature ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Histone 3

scholarly journals A Unique Histone 3 Lysine 14 Chromatin Signature Underlies Tissue-Specific Gene Regulation

2020 ◽  
Author(s):  
Isabel Regadas ◽  
Olle Dahlberg ◽  
Roshan Vaid ◽  
Oanh Ho ◽  
Sergey Belikov ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Chromatin Signature ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Histone 3

scholarly journals Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression

2020 ◽  
Author(s):  
Mitra Ansariola ◽  
Valerie N. Fraser ◽  
Sergei A. Filichkin ◽  
Maria G. Ivanchenko ◽  
Zachary A. Bright ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Open Chromatin ◽  
Transcription Start ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Tissue Specific Gene ◽  
Specific Gene Expression

AbstractAcross tissues, gene expression is regulated by a combination of determinants, including the binding of transcription factors (TFs), along with other aspects of cellular state. Recent studies emphasize the importance of both genetic and epigenetic states – TF binding sites and binding site chromatin accessibility have emerged as potentially causal determinants of tissue specificity. To investigate the relative contributions of these determinants, we constructed three genome-scale datasets for both root and shoot tissues of the same Arabidopsis thaliana plants: TSS-seq data to identify Transcription Start Sites, OC-seq data to identify regions of Open Chromatin, and RNA-seq data to assess gene expression levels. For genes that are differentially expressed between root and shoot, we constructed a machine learning model predicting tissue of expression from chromatin accessibility and TF binding information upstream of TSS locations. The resulting model was highly accurate (over 90% auROC and auPRC), and our analysis of model contributions (feature weights) strongly suggests that patterns of TF binding sites within ∼500 nt TSS-proximal regions are predominant explainers of tissue of expression in most cases. Thus, in plants, cis-regulatory control of tissue-specific gene expression appears to be primarily determined by TSS-proximal sequences, and rarely by distal enhancer-like accessible chromatin regions. This study highlights the exciting future possibility of a native TF site-based design process for the tissue-specific targeting of plant gene promoters.

scholarly journals Corrigendum: Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene

RNA ◽  
2021 ◽  
Vol 27 (10) ◽  
pp. 1291-1291
Author(s):  
Bastian Fromm ◽  
Marcel Tarbier ◽  
Oliver Smith ◽  
Emilio Mármol-Sánchez ◽  
Love Dalén ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Tissue Specific ◽  
Tissue Specific Gene

scholarly journals A unique H3K4me2 profile marks tissue-specific gene regulation

2010 ◽  
Vol 20 (11) ◽  
pp. 1493-1502 ◽  
Author(s):  
A. Pekowska ◽  
T. Benoukraf ◽  
P. Ferrier ◽  
S. Spicuglia
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Tissue Specific ◽  
Tissue Specific Gene
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