scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

scholarly journals Identification and characterization of Hoxa9 binding sites in hematopoietic cells

Blood ◽  
2012 ◽  
Vol 119 (2) ◽  
pp. 388-398 ◽  
Author(s):  
Yongsheng Huang ◽  
Kajal Sitwala ◽  
Joel Bronstein ◽  
Daniel Sanders ◽  
Monisha Dandekar ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Binding Sites ◽  
Enhancer Activity ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
P300 Binding ◽  
Histone H3k4

The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.

scholarly journals Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11034
Author(s):  
Bidisha Bhowal ◽  
Annapurna Bhattacharjee ◽  
Kavita Goswami ◽  
Neeti Sanan-Mishra ◽  
Sneh L. Singla-Pareek ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Gene Families ◽  
Pcr Analysis ◽  
Tryptophan Decarboxylase ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Suitable Target

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

scholarly journals Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 366
Author(s):  
Rungaroon Suksamran ◽  
Treenut Saithong ◽  
Chinae Thammarongtham ◽  
Saowalak Kalapanulak
Keyword(s):  
Transcriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Gene Families ◽  
Cellular Processes ◽  
Nuclear Factor Y ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation ◽  
Genome Wide Study

Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.

scholarly journals Genome-wide study of methotrexate clearance replicates SLCO1B1

Blood ◽  
2013 ◽  
Vol 121 (6) ◽  
pp. 898-904 ◽  
Author(s):  
Laura B. Ramsey ◽  
John C. Panetta ◽  
Colton Smith ◽  
Wenjian Yang ◽  
Yiping Fan ◽  
...  
Keyword(s):  
Genetic Variations ◽  
Genome Wide ◽  
A Genome ◽  
Key Points ◽  
Genome Wide Study

Key Points A genome-wide study of the association of over 5 million SNPs with methotrexate clearance in 1279 patients treated with HDMTX in multicenter COG trials 9904 and 9905. We replicated the finding that inherited variations in SLCO1B1 are the most important genetic variations influencing methotrexate clearance.

scholarly journals A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk

BMC Genetics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 24 ◽  
Author(s):  
Samuel G Younkin ◽  
Robert B Scharpf ◽  
Holger Schwender ◽  
Margaret M Parker ◽  
Alan F Scott ◽  
...  
Keyword(s):  
Cleft Lip ◽  
De Novo ◽  
Candidate Locus ◽  
Genome Wide ◽  
A Genome ◽  
Cleft Lip Palate ◽  
Genome Wide Study

scholarly journals Investigation of 95 variants identified in a genome-wide study for association with mortality after acute coronary syndrome

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Thomas M Morgan ◽  
John A House ◽  
Sharon Cresci ◽  
Philip Jones ◽  
Hooman Allayee ◽  
...  
Keyword(s):  
Acute Coronary Syndrome ◽  
Coronary Syndrome ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Study
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