Cargando…

A comprehensive map of preferentially located motifs reveals distinct proximal cis-regulatory sequences in plants

Identification of cis-regulatory sequences controlling gene expression is an arduous challenge that is being actively explored to discover key genetic factors responsible for traits of agronomic interest. Here, we used a genome-wide de novo approach to investigate preferentially located motifs (PLMs...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rozière, Julien, Guichard, Cécile, Brunaud, Véronique, Martin, Marie-Laure, Coursol, Sylvie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2022
Materias:	Plant Science
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9597372/ https://www.ncbi.nlm.nih.gov/pubmed/36311095 http://dx.doi.org/10.3389/fpls.2022.976371

Ejemplares similares

Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome
por: Huang, Jia-Hsin, et al.
Publicado: (2018)

Using hexamers to predict cis-regulatory motifs in Drosophila
por: Chan, Bob Y, et al.
Publicado: (2005)

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize
por: Cuello, Clément, et al.
Publicado: (2019)

MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
por: Kato, Mamoru, et al.
Publicado: (2007)

A new framework for identifying cis-regulatory motifs in prokaryotes
por: Li, Guojun, et al.
Publicado: (2011)

Characterization of Putative cis-Regulatory Elements in Genes Preferentially Expressed in Arabidopsis Male Meiocytes
por: Li, Junhua, et al.
Publicado: (2014)

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation
por: Bernard, Virginie, et al.
Publicado: (2010)

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
por: Boeva, Valentina, et al.
Publicado: (2007)

CompMoby: Comparative MobyDick for detection of cis-regulatory motifs
por: Chaivorapol, Christina, et al.
Publicado: (2008)

Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes
por: Li, Guojun, et al.
Publicado: (2010)

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva
por: Tretina, Kyle, et al.
Publicado: (2016)

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
por: Ivan, Andra, et al.
Publicado: (2008)

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
por: Wilczynski, Bartek, et al.
Publicado: (2009)

MotifClick: prediction of cis-regulatory binding sites via merging cliques
por: Zhang, Shaoqiang, et al.
Publicado: (2011)

Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation
por: Rouault, Hervé, et al.
Publicado: (2014)

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses
por: Liu, Bingqiang, et al.
Publicado: (2016)

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
por: Vardhanabhuti, Saran, et al.
Publicado: (2007)

Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons
por: Liu, Rui, et al.
Publicado: (2009)

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria
por: Sun, Eric I, et al.
Publicado: (2013)

Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis
por: Barkoulas, Michalis, et al.
Publicado: (2016)

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes
por: Liu, Bingqiang, et al.
Publicado: (2016)

Dichotomous cis-regulatory motifs mediate the maturation of the neuromuscular junction by retrograde BMP signaling
por: Vuilleumier, Robin, et al.
Publicado: (2022)

Identification of cis-regulatory modules encoding temporal dynamics during development
por: Potier, Delphine, et al.
Publicado: (2014)

Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis
por: Cao, Chensi, et al.
Publicado: (2016)

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data
por: Zhang, Shuangquan, et al.
Publicado: (2021)

GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer
por: Kumegawa, Kohei, et al.
Publicado: (2022)

NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks
por: Wei, Zheng, et al.
Publicado: (2023)

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element
por: Barrière, Antoine, et al.
Publicado: (2011)

MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs
por: Hu, Jianfei, et al.
Publicado: (2008)

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs
por: Girgis, Hani Z, et al.
Publicado: (2012)

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms
por: Yang, Peng, et al.
Publicado: (2014)

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest
por: Wang, Xin, et al.
Publicado: (2018)

A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation
por: Donohue, Laura K.H., et al.
Publicado: (2022)

Preferential targeting of i-motifs and G-quadruplexes by small molecules
por: Debnath, Manish, et al.
Publicado: (2017)

Cis-regulatory control of corticospinal system development and evolution
por: Shim, Sungbo, et al.
Publicado: (2012)

OncoCis: annotation of cis-regulatory mutations in cancer
por: Perera, Dilmi, et al.
Publicado: (2014)

Finding subtypes of transcription factor motif pairs with distinct regulatory roles
por: Bais, Abha Singh, et al.
Publicado: (2011)

Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana
por: Back, Georg, et al.
Publicado: (2021)

Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
por: Shepherdson, James L., et al.
Publicado: (2023)

Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution
por: Yokoyama, Ken Daigoro, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_cmj59cf9n09g68350ml3535kju