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Chapter 10 Genomic Identification of Regulatory Elements by Evolutionary Sequence Comparison and Functional Analysis [chapter]

Gabriela G. Loots
2008 Advances in Genetics  
Phylogenetic footprinting is a method for identifying highly conserved DNA motifs present in a multiple sequence alignment.  ...  encoded in noncoding DNA.  ... 
doi:10.1016/s0065-2660(07)00010-7 pmid:18282510 pmcid:PMC2882178 fatcat:ikp33rs4qvanpkjf2cp4ze7lny

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting

A. Sosinsky, B. Honig, R. S. Mann, A. Califano
2007 Proceedings of the National Academy of Sciences of the United States of America  
Together, they can identify large regulatory elements (e.g., enhancers) as evolutionarily conserved order-independent clusters of short conserved motifs.  ...  The functional annotation of the nonprotein-coding DNA of eukaryotic genomes is a problem of central importance.  ...  We thank Oliver Hobert for careful reading of and critical remarks on the paper.  ... 
doi:10.1073/pnas.0701614104 pmid:17395715 pmcid:PMC1851073 fatcat:4pivyglrhfcj3dwt3n27fkzchi

Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome

Martina Tassinari, Sara N Richter, Paolo Gandellini
2021 Nucleic Acids Research  
This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression.  ...  Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids  ...  Figure 6 . 6 rG4s within lncRNAs influence the interaction between lncRNAs and their targets. (A) Nascent NEAT1 transcripts bind to the NONO proteins through conserved rG4 motifs.  ... 
doi:10.1093/nar/gkab127 pmid:33721024 fatcat:ryexbnqc5rglhi4v6smqj2sy7y

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms

Sierra S. Nishizaki, Alan P. Boyle
2017 Trends in Genetics  
We discuss several leading methods for annotating noncoding variants and how they can be integrated into research pipelines in hopes that they will be broadly applied in future GWAS analyses.  ...  Noncoding SNPs, which represent the majority of GWAS SNPs, present a particular challenge.  ...  Author manuscript; available in PMC 2017 August 11.  ... 
doi:10.1016/j.tig.2016.10.008 pmid:27939749 pmcid:PMC5553318 fatcat:btgssc32xvhc3hz53xlcilurxa

Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease

Timothy J. Cherry, Marty G. Yang, David A. Harmin, Peter Tao, Andrew E. Timms, Miriam Bauwens, Rando Allikmets, Evan M. Jones, Rui Chen, Elfride De Baere, Michael E. Greenberg
2020 Proceedings of the National Academy of Sciences of the United States of America  
We took advantage of the retina, a well-characterized region of the CNS known to be affected by pathogenic variants in CREs, to establish a roadmap for characterizing regulatory variation in the human  ...  This comprehensive analysis of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, and retinal pigment  ...  Liesl Strand and James Gillespie provided technical assistance with the luciferase assay for the 5q14.3 enhancer. Sinisa Hrvatin provided indepth assistance with the single-nuc-RNA-sequencing.  ... 
doi:10.1073/pnas.1922501117 pmid:32265282 fatcat:cly2lgnfwvfoxhzywxkc72oiwy

A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants

Jan Van de Velde, Michiel Van Bel, Dries Van Eechoutte, Klaas Vandepoele
2016 Plant Physiology  
The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.  ...  Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help  ...  DNA sequences that are not actively transcribed and that are conserved across a large number of related species are called conserved noncoding sequences (CNSs).  ... 
doi:10.1104/pp.16.00821 pmid:27261064 pmcid:PMC4972296 fatcat:4xwrkzh4bvhj7ih6aikmpmdh4q

Advanced Topics in Bioinformatics and Computational Biology [chapter]

Bailin Hao, Chunting Zhang, Yixue Li, Hao Li, Liping Wei, Minoru Kanehisa, Luhua Lai, Runsheng Chen, Nikolaus Rajewsky, Michael Q. Zhang, Jingdong Han, Rui Jiang (+2 others)
2013 Basics of Bioinformatics  
For example, in a living cell, DNA-binding proteins are believed to be in a balance between the bound and unbound states, thus introducing uncertainties in protein-DNA interactions.  ...  The Z-curve is a unique three-dimensional curve representation for a given DNA sequence in the sense that each can be uniquely reconstructed given the other.  ... 
doi:10.1007/978-3-642-38951-1_12 fatcat:z5w7u5xeprhw5a65it476q4x4e

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

Martin Kircher, Chenling Xiong, Beth Martin, Max Schubach, Fumitaka Inoue, Robert J. A. Bell, Joseph F. Costello, Jay Shendure, Nadav Ahituv
2019 Nature Communications  
The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome.  ...  These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and comprise a rich dataset for the further development  ...  Acknowledgements We thank current and previous members of the Ahituv, Kircher, and Shendure laboratories, as well as Daniela Witten, Greg Cooper, and Franklin Huang, for valuable discussions and feedback  ... 
doi:10.1038/s41467-019-11526-w pmid:31395865 pmcid:PMC6687891 fatcat:sowv6na6czghtk23m4t4kitbr4

A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes

L A Gossett, D J Kelvin, E A Sternberg, E N Olson
1989 Molecular and Cellular Biology  
Oligomers corresponding to the region of the mlc-1/3 enhancer, which encompasses this conserved sequence, bound MEF-2 and competed for its binding to the mck enhancer.  ...  A 10-bp sequence, which was shown by DNase I footprinting and diethyl pyrocarbonate interference to interact directly with MEF-2, was identified within the rat and human mck enhancers, the rat myosin light-chain  ...  Rosenthal for providing us with the mlc-113 DNA fragment for use in gel retardation assays. We also thank S. Hauschka and J. Buskin for communicating results prior to publication.  ... 
doi:10.1128/mcb.9.11.5022 pmid:2601707 pmcid:PMC363654 fatcat:mq44suveojbmhnfaj673cka7w4

Identification and Computational Analysis of Gene Regulatory Elements

Leila Taher, Leelavati Narlikar, Ivan Ovcharenko
2015 Cold Spring Harbor Protocols  
Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements  ...  Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences.  ...  , noncoding) DNA.  ... 
doi:10.1101/pdb.top083642 pmid:25561628 pmcid:PMC5885252 fatcat:qdzm42aypzdz5askrohbwnswny

Emerging Properties and Functional Consequences of Noncoding Transcription

Ryan Ard, Robin C Allshire, Sebastian Marquardt
2017 Genetics  
Indeed, this alternative mechanism might better explain how low-abundance lncRNAs transcribed from noncoding DNA function in organisms.  ...  Eukaryotic genomes are rich in transcription units encoding "long noncoding RNAs" (lncRNAs).  ...  By capturing native RNAPII-DNA-RNA complexes from chromatin and sequencing, the 39-most nucleotide of RNAPII-associated RNAs, NET-seq (native elongating transcript sequencing) visualizes active transcription  ... 
doi:10.1534/genetics.117.300095 pmid:28978770 pmcid:PMC5629311 fatcat:2kmosoh2pne6nlgviocz57u7ti

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini
2015 Briefings in Bioinformatics  
Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics.  ...  In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants.  ...  R.S. would like to thank National Centre for Biological Sciences (TIFR) for infrastructural support.  ... 
doi:10.1093/bib/bbv084 pmid:26494363 pmcid:PMC6078163 fatcat:xeldhpluhjajnnatu44secmb3u

piRNAQuest: searching the piRNAome for silencers

Arijita Sarkar, Ranjan Maji, Sudipto Saha, Zhumur Ghosh
2014 BMC Genomics  
Overall, piRNAQuest will serve as a useful resource for exploring human, mouse and rat piRNAome.  ...  Further, expression profile for piRNA in different tissues and from different developmental stages has been provided.  ...  We thank MadhushreeKamak and YogendraBhaskar (summer trainees) for their contribution towards building the database.  ... 
doi:10.1186/1471-2164-15-555 pmid:24997126 pmcid:PMC4227290 fatcat:o3tfgreo2vf2rdo3a53rmbkpcu

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

Daniel Ryan, Laura Jenniches, Sarah Reichardt, Lars Barquist, Alexander J. Westermann
2020 Nature Communications  
Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source.  ...  Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research.  ...  Thanks to the Core Unit Systems Medicine in Würzburg, particularly to Tobias Heckel, Sascha Dietrich, and Elena Katzowitsch, for support with cDNA library preparation and RNA-seq, to Falk Ponath for help  ... 
doi:10.1038/s41467-020-17348-5 pmid:32678091 pmcid:PMC7366714 fatcat:ge533m3ys5heto22dy6adon3yq

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

Leeban Yusuf, Matthew C. Heatley, Joseph P.G. Palmer, Henry J. Barton, Christopher R. Cooney, Toni I. Gossmann
2020 Genome Research  
Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological  ...  We identify 1434 protein-coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution.  ...  Acknowledgments We thank Sangeet Lamichhaney for providing F ST data on the Darwin finch populations and Victor Soria-Carrasco, Gavin Thomas, and Jon Slate for constructive comments at earlier stages of  ... 
doi:10.1101/gr.255752.119 pmid:32269134 pmcid:PMC7197477 fatcat:uz4cyhjwmrhzjbc6iwtxwzgeje
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