Differences in local genomic context of bound and unbound motifs

Loren HansenDavid Landsman


Understanding gene regulation is a major objective in molecular biology research. Frequently, transcription is driven by transcription factors (TFs) that bind to specific DNA sequences. These motifs are usually short and degenerate, rendering the likelihood of multiple copies occurring throughout the genome due to random chance as high. Despite this, TFs only bind to a small subset of sites, thus prompting our investigation into the differences between motifs that are bound by TFs and those that remain unbound. Here we constructed vectors representing various chromatin- and sequence-based features for a published set of bound and unbound motifs representing nine TFs in the budding yeast Saccharomyces cerevisiae. Using a machine learning approach, we identified a set of features that can be used to discriminate between bound and unbound motifs. We also discovered that some TFs bind most or all of their strong motifs in intergenic regions. Our data demonstrate that local sequence context can be strikingly different around motifs that are bound compared to motifs that are unbound. We concluded that there are multiple combinations of genomic features that characterize bound or unbound motifs.


Dec 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·B J Andrews, L A Moore
Oct 20, 1988·Nature·M Ptashne
Jan 1, 1996·Molecular and Cellular Biology·J W Fickett
Feb 12, 1998·Nucleic Acids Research·D MeierhansR K Allemann
Jun 17, 1998·Nucleic Acids Research·S H LeemH Araki
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Apr 3, 2003·Genome Research·Alexander P LifanovDmitri A Papatsenko
Jun 26, 2003·Nucleic Acids Research·Martin C FrithZhiping Weng
Jun 26, 2003·Nucleic Acids Research·Mathieu Blanchette, Martin Tompa
Apr 28, 2004·The Journal of Biological Chemistry·Nicholas A KentJane Mellor
May 8, 2004·Nature Reviews. Genetics·Wyeth W Wasserman, Albin Sandelin
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Jun 18, 2005·Bioinformatics·Kannan TharakaramanJohn L Spouge
Aug 27, 2005·Cell·Dmitry K PokholokRichard A Young
Mar 3, 2006·Bioinformatics·Victor Trevino, Francesco Falciani
Apr 8, 2006·Nature Biotechnology·Patrik D'haeseleer
May 16, 2006·PLoS Computational Biology·Zhihua ZhangRunsheng Chen
Jun 27, 2007·BMC Bioinformatics·Shouyong PengPeter J Park
Aug 28, 2007·Bioinformatics·Yvan SaeysPedro Larrañaga
Sep 18, 2007·Nature Genetics·William LeeCorey Nislow
Nov 13, 2008·Systems and Synthetic Biology·Dustin T HollowayCharles Delisi
Nov 20, 2008·Bioinformatics·Xiaohui XiePierre Baldi
Nov 26, 2008·Cold Spring Harbor Symposia on Quantitative Biology·K S ZaretT Sekiya
Dec 20, 2008·IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society·Xu-Ying LiuZhi-Hua Zhou
Jan 23, 2009·Genome Research·Cong ZhuMartha L Bulyk

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

KIF1A Associated Neurological Disorder

KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.