scholarly journals Long-distance regulation of Add2 pre-mRNA3′end processing

RNA Biology ◽  
2013 ◽  
Vol 10 (4) ◽  
pp. 516-527 ◽  
Author(s):  
Mirjana Nedeljkovic ◽  
Luisa Costessi ◽  
Alessandra Iaconcig ◽  
Fabiola Porro ◽  
Andrés F. Muro
Keyword(s):  
Long Distance ◽  
Distance Regulation

Long-distance regulation of shoot gravitropism by Cyclophilin 1 in tomato (Solanum lycopersicum) plants

Planta ◽  
2020 ◽  
Vol 252 (4) ◽  
Author(s):  
Ziv Spiegelman ◽  
Or Broshi ◽  
Amit Shahar ◽  
Sumita Omer ◽  
Hagit Hak ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Long Distance ◽  
Shoot Gravitropism ◽  
Distance Regulation

scholarly journals TOO MUCH LOVE, a Novel Kelch Repeat-Containing F-box Protein, Functions in the Long-Distance Regulation of the Legume–Rhizobium Symbiosis

2013 ◽  
Vol 54 (4) ◽  
pp. 433-447 ◽  
Author(s):  
Masahiro Takahara ◽  
Shimpei Magori ◽  
Takashi Soyano ◽  
Satoru Okamoto ◽  
Chie Yoshida ◽  
...  
Keyword(s):  
Long Distance ◽  
Protein Functions ◽  
F Box Protein ◽  
Distance Regulation

scholarly journals Regulation of TCR δ and α repertoires by local and long-distance control of variable gene segment chromatin structure

2005 ◽  
Vol 202 (4) ◽  
pp. 467-472 ◽  
Author(s):  
Abbas Hawwari ◽  
Michael S. Krangel
Keyword(s):  
Chromatin Structure ◽  
Genetic Locus ◽  
Gene Segment ◽  
Chromatin Accessibility ◽  
Small Subset ◽  
Double Positive ◽  
Long Distance ◽  
Variable Gene ◽  
Distance Regulation ◽  
Variable Gene Segment

Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4−CD8− (double negative [DN]) and CD4+CD8+ (double positive [DP]) thymocytes, respectively. TcraTcrd locus variable gene segments are subject to complex regulation. Only a small subset of ∼100 variable gene segments contributes substantially to the adult TCRδ repertoire. Moreover, although most contribute to the TCRα repertoire, variable gene segments that are Jα proximal are preferentially used during primary Tcra recombination. We investigate the role of local chromatin accessibility in determining the developmental pattern of TcraTcrd locus variable gene segment recombination. We find variable gene segments to be heterogeneous with respect to acetylation of histones H3 and H4. Those that dominate the adult TCRδ repertoire are hyperacetylated in DN thymocytes, independent of their position in the locus. Moreover, proximal variable gene segments show dramatic increases in histone acetylation and germline transcription in DP thymocytes, a result of super long-distance regulation by the Tcra enhancer. Our results imply that differences in chromatin accessibility contribute to biases in TcraTcrd locus variable gene segment recombination in DN and DP thymocytes and extend the distance over which the Tcra enhancer can regulate chromatin structure to a remarkable 525 kb.

scholarly journals HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

2019 ◽  
Author(s):  
Pavel P. Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D. Gregory ◽  
...  
Keyword(s):  
High Resolution ◽  
Cell Line ◽  
Cell Lines ◽  
Dna Looping ◽  
Open Chromatin ◽  
Fine Scale ◽  
Long Distance ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Distance Regulation

AbstractMost regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically-interacting elements such as enhancers, insulators, or promoters. To map these elements and interactions, we developed HIPPIE2 which analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify fine-scale physically-interacting regions (PIRs). Unlike standard genome binning approaches (e.g., 10K-1Mbp bins), HIPPIE2 dynamically calls physical locations of PIRs with better precision and higher resolution based on the pattern of restriction events and relative locations of interacting sites inferred from the sequencing readout.We applied HIPPIE2 to in situ Hi-C datasets across 6 human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE and Roadmap functional genomic data. HIPPIE2 detected 1,042,738 distinct PIRs across cell lines, with high resolution (average PIR length of 1,006bps) and high reproducibility (92.3% in GM12878 replicates). 32.8% of PIRs were shared among cell lines. PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8M significant intrachromosomal PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50,608 interactions were enhancer–promoter interactions and were enriched for 33 TFs (31 in enhancers/29 in promoters), several of which are known to mediate DNA looping/long-distance regulation. 29 TFs were enriched in >1 cell line and 4 were cell line-specific. These findings demonstrate that the dynamic approach used in HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) characterizes PIR–PIR interactions with high resolution and reproducibility.

scholarly journals Localization of the 3′ IgH Locus Elements that Effect Long-Distance Regulation of Class Switch Recombination

Immunity ◽  
2001 ◽  
Vol 15 (2) ◽  
pp. 187-199 ◽  
Author(s):  
Eric Pinaud ◽  
Ahmed Amine Khamlichi ◽  
Caroline Le Morvan ◽  
Mireille Drouet ◽  
Valérie Nalesso ◽  
...  
Keyword(s):  
Class Switch Recombination ◽  
Long Distance ◽  
Class Switch ◽  
Igh Locus ◽  
Distance Regulation

scholarly journals The economy of chromosomal distances in bacterial gene regulation

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Eda Cakir ◽  
Annick Lesne ◽  
Marc-Thorsten Hütt
Keyword(s):  
Transcriptional Regulatory Network ◽  
Real Space ◽  
Regulator Gene ◽  
Long Distance ◽  
Circular Chromosome ◽  
Chromosomal Structure ◽  
Bacterial Gene ◽  
Condensed Representation ◽  
Transcriptional Regulatory ◽  
Distance Regulation

AbstractIn the transcriptional regulatory network (TRN) of a bacterium, the nodes are genes and a directed edge represents the action of a transcription factor (TF), encoded by the source gene, on the target gene. It is a condensed representation of a large number of biological observations and facts. Nonrandom features of the network are structural evidence of requirements for a reliable systemic function. For the bacterium Escherichia coli we here investigate the (Euclidean) distances covered by the edges in the TRN when its nodes are embedded in the real space of the circular chromosome. Our work is motivated by ’wiring economy’ research in Computational Neuroscience and starts from two contradictory hypotheses: (1) TFs are predominantly employed for long-distance regulation, while local regulation is exerted by chromosomal structure, locally coordinated by the action of structural proteins. Hence long distances should often occur. (2) A large distance between the regulator gene and its target requires a higher expression level of the regulator gene due to longer reaching times and ensuing increased degradation (proteolysis) of the TF and hence will be evolutionarily reduced. Our analysis supports the latter hypothesis.

scholarly journals Long-Distance Regulation of Fetal Vδ Gene Segment TRDV4 by the Tcrd Enhancer

2011 ◽  
Vol 187 (5) ◽  
pp. 2484-2491 ◽  
Author(s):  
Bingtao Hao ◽  
Michael S. Krangel
Keyword(s):  
Gene Segment ◽  
Long Distance ◽  
Distance Regulation

scholarly journals Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1

2018 ◽  
Vol 4 (2) ◽  
pp. e1701729 ◽  
Author(s):  
Robert-Jan Palstra ◽  
Elisa de Crignis ◽  
Michael D. Röling ◽  
Thomas van Staveren ◽  
Tsung Wai Kan ◽  
...  
Keyword(s):  
Long Distance ◽  
Allele Specific ◽  
Isoform Switching ◽  
Distance Regulation ◽  
Hiv 1
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