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ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments

2019 Nucleic Acids Research  
from DNA-binding experiments in Human and Arabidopsis (Arabidopsis thaliana).  ...  ReMap ( aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators  ...  Indeed, the ReMap database shows an unprecedented landscape of the human regulatory abundance and complexity constituted by 165M binding regions forming 1.7M CRMs.  ... 
doi:10.1093/nar/gkz945 pmid:31665499 pmcid:PMC7145625 fatcat:n4ve2kjtk5grnmzihal2kqkxdy

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Fayrouz Hammal, Pierre de Langen, Aurélie Bergon, Fabrice Lopez, Benoit Ballester
2021 Nucleic Acids Research  
ReMap ( aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse  ...  In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species.  ...  Plant group for their help with the Human, Mouse, Fly and Arabidopsis track hubs.  ... 
doi:10.1093/nar/gkab996 pmid:34751401 pmcid:PMC8728178 fatcat:k2zuwebeizfk5khhm5funirbfi

GTRD: an integrated view of transcription regulation

Semyon Kolmykov, Ivan Yevshin, Mikhail Kulyashov, Ruslan Sharipov, Yury Kondrakhin, Vsevolod J Makeev, Ivan V Kulakovskiy, Alexander Kel, Fedor Kolpakov
2020 Nucleic Acids Research  
The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and  ...  With the latest release, the database has reached a new level of data integration.  ...  recognition of TFBSs; (iii) human and mouse cistromes, the maps of putative cis-regulatory regions bound by TFs, as an early approach to the construction of meta-clusters (41); (iv) MSigDB (34) includes  ... 
doi:10.1093/nar/gkaa1057 pmid:33231677 fatcat:krekihbvl5hv7pkont2kzepjne

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

Mirko Ronzio, Federico Zambelli, Diletta Dolfini, Roberto Mantovani, Giulio Pavesi
2020 Frontiers in Genetics  
However, while pipelines and best practices have been established for the analysis of a single experiment, there is still no consensus on the best way to perform an integrated analysis of multiple datasets  ...  We present here a computational pipeline for this task, that integrates peak summit colocalization, a novel statistical framework for the evaluation of its significance, and motif enrichment analysis.  ...  The integration of peak and summit overlap with a sequence analysis method developed specifically for the analysis of ChIP-Seq regions also permits the characterization of the recruitment rules on DNA  ... 
doi:10.3389/fgene.2020.00072 pmid:32153638 pmcid:PMC7046753 fatcat:evrqxbr5czftvdi465tjm6yuwe

Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation

Mo-Xian Chen, Fu-Yuan Zhu, Bei Gao, Kai-Long Ma, Youjun Zhang, Alisdair R. Fernie, Xi Chen, Lei Dai, Neng-Hui Ye, Xue Zhang, Yuan Tian, Di Zhang (+3 others)
2020 Zenodo  
In addition, a large number of fusion and intergenic transcripts have been observed.  ...  Parallel short-read RNA sequencing indicated that lrRNA_seq has a superior capacity for the identification of longer transcripts.  ...  Proteogenomics is an analytical approach to integrate genomic, transcriptomic, and proteomic data for comprehensive analysis.  ... 
doi:10.5281/zenodo.3692372 fatcat:k5te2si4h5aslbehi76crudyju

MethReg: estimating the regulatory potential of DNA methylation in gene transcription [article]

Tiago C. Silva, Juan I. Young, Eden R. Martin, Xi Chen, Lily Wang
2021 bioRxiv   pre-print
AbstractEpigenome-wide association studies (EWAS) often detect a large number of differentially methylated sites or regions, many are located in distal regulatory regions.  ...  Here we present MethReg, an R/Bioconductor package that analyzes matched DNA-methylation and gene-expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize  ...  Cheneby J, Menetrier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez F, Ballester B: ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis  ... 
doi:10.1101/2021.02.18.431696 fatcat:42h55iig6jfhfirixkvhszf2nu

Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Beoung Hun Lee, Suhn K. Rhie
2021 Epigenetics & Chromatin  
AbstractEpigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements.  ...  Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.  ...  Authors' contributions BL and SKR wrote the article. All authors read and approved the final manuscript.  ... 
doi:10.1186/s13072-021-00390-y pmid:33741028 pmcid:PMC7980343 fatcat:dgtydqgyhjgxdni34kedgzw3wy

Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

Quan Zou, Pengwei Xing, Leyi Wei, Bin Liu
2018 RNA: A publication of the RNA Society  
To the best of our knowledge, our work is the first attempt to use word embedding and deep neural networks for m 6 A prediction from mRNA sequences.  ...  Using four deep neural networks, we developed a model inferred from a larger sequence shifting window that can predict m 6 A accurately and robustly.  ...  Based on information from MeRIP-seq experiments, comprehensive databases of m 6 A modification have been built to help researchers determine the locations and effects of these modifications Xuan et al  ... 
doi:10.1261/rna.069112.118 pmid:30425123 fatcat:km4p6nn77fbjfnpc4hultke73e

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila [article]

Yi Liao, Xinwen Zhang, Mahul Chakraborty, J.J. Emerson
2020 bioRxiv   pre-print
the formation and maintenance of TADs via 3D cis-regulatory interactions commonly found within long genes.  ...  To decipher the evolutionary significance of TADs, we de novo assembled the genome of D. pseudoobscura and created a high-resolution (~800 bp) Hi-C contact map to annotate TADs.  ...  Acknowledgements This work was funded by the National Institutes of Health (R01GM123303), National Science Foundation (IOS-1656260), and startup funding from the University of California, Irvine to J.J.E  ... 
doi:10.1101/2020.05.13.094516 fatcat:7iv65xcokjfilh3j5txaqo72ua

Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast [article]

Yaqing Zhang, David Kuster, Tobias Schmidt, Daniel Kirrmaier, Gabriele Nübel, David Ibberson, Vladimir Benes, Hans Hombauer, Michael Knop, Andres Jäschke
2020 biorxiv/medrxiv   pre-print
Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate  ...  The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids.  ...  The data supporting the findings of this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.  ... 
doi:10.1101/2020.04.28.065920 fatcat:2xagakhf6rgonf34bvmimhpu6u

Discovery of Anthocyanin Biosynthetic Pathway in Cosmos caudatus Kunth. Using Omics Analysis

Darvien Gunasekaran, Noor Idayu Tahir, Muhamad Afiq Akbar, Syazwani Basir, Ismanizan Ismail, Noraini Talip, Ahmad Bazli Ramzi, Syarul Nataqain Baharum, Normah Mohd Noor, Hamidun Bunawan
2021 Agronomy  
This study correlated multi-omics data that will help integrate systems biology and synthetic biology, for a detailed understanding of the molecular mechanism and characterization of the anthocyanin biosynthesis  ...  Among the interesting compounds are the anthocyanins that possess a dual role; an antioxidant and natural colorant.  ...  Acknowledgments: Sequencing and assembly was done at TheragenEtex Bio Institute, Republic of Korea.  ... 
doi:10.3390/agronomy11040661 fatcat:aclvn7i7lbfj3c5jo3rw5i4zie

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Dongmei Yin, Changmian Ji, Qingxin Song, Wanke Zhang, Xingguo Zhang, Kunkun Zhao, Charles Y. Chen, Chuantang Wang, Guohao He, Zhe Liang, Xingli Ma, Zhongfeng Li (+16 others)
2019 Advanced Science  
A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported.  ...  Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts.  ...  [45, 51] Arabidopsis MNT/ARF2, an ortholog of peanut ARF2, is a negative regulator of seed size and weight by repressing cell division and organ growth.  ... 
doi:10.1002/advs.201901672 pmid:32099754 pmcid:PMC7029647 fatcat:cen73bala5esvhpwr6ocnghvbq

Linking cis-regulatory regions using transcription factor binding signatures

Kang, Yueming (Michelle)
Linking cooperatively functioning cis-regulatory elements (CREs), specifically enhancers and promoters, is a challenging task.  ...  TF-binding signatures are binary string representations (e.g. 0011001...), where each position indicates binding ("1") or not ("0") of a TF to a CRE.  ...  Wyeth Wasserman for giving me the chance to work on this project and for all of his patience, support and encouragement throughout my  ... 
doi:10.14288/1.0392001 fatcat:66zfifigbnc2lnjk4xabj6luw4

ENHANCing the limb: from micro- to macro-evolution [article]

Joao Castro, Universitaet Tuebingen, Universitaet Tuebingen, Nordheim, Alfred (Prof. Dr.)
One especially relevant class of cis-regulatory elements are enhancers.  ...  Understanding the molecular basis of the diverse morphological forms found within and across species is a longstanding goal in evolutionary biology.  ...  Hughes, Variation in homeodomain DNA binding revealed by high-resolution analysis of P. L. Crotwell, P. M.  ... 
doi:10.15496/publikation-43086 fatcat:prkxypd2xvb2lot3fdmrt6ohva

BNA Festival of Neuroscience 2019

2019 Brain and Neuroscience Advances  
An n of 6 will be used for experiments.  ...  Statistical analysis will be performed using unpaired T-tests and/or One-way analysis of variance (ANOVA) with an appropriate post-hoc test.  ...  sequence differs from the original DNA.  ... 
doi:10.1177/2398212819855490 fatcat:y4b5r7rpdnblzoxvb2crpzqhee
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