List of Top 25

Articles of
Bioinformatics
Oct - Dec 2014

Sr. No

Title

1
A 3D Map
of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Library Information
Services,
Islamabad.
Summary
We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell
types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We
find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with
distinct patterns of histone marks and segregate into six subcompartments. We identify 10,000 loops. These
loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across
cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop
anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs facing one
another. The inactive X chromosome splits into two massive domains and contains large loops anchored at
CTCF-binding repeats.
2

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging
Summary
Signals in many biological processes can be amplified by recruiting multiple copies of regulatory proteins to a
site of action. Harnessing this principle, we have developed a protein scaffold, a repeating peptide array termed
SunTag, which can recruit multiple copies of an antibody-fusion protein. We show that the SunTag can recruit up
to 24 copies of GFP, thereby enabling long-term imaging of single protein molecules in living cells. We also use
the SunTag to create a potent synthetic transcription factor by recruiting multiple copies of a transcriptional
activation domain to a nuclease-deficient CRISPR/Cas9 protein and demonstrate strong activation of
endogenous gene expression and re-engineered cell behavior with this system. Thus, the SunTag provides a
versatile platform for multimerizing proteins on a target protein scaffold and is likely to have many applications
in imaging and controlling biological outputs.

A Proteome-Scale Map of the Human Interactome Network

Cell, Volume 159, Issue 5, November 2014, Pages 1212-1226
Rolland, T.; Tasan, M.; Charloteaux, B.; Pevzner, Samuel J.; Zhong, Q.; Sahni, N.; Yi, S.; Lemmens, I.; Fontanillo,
C.; Mosca, R.; Kamburov, A.; Ghiassian, Susan D.; Yang, X.; Ghamsari, L.; Balcha, D.; Begg, Bridget E.; Braun, P.;
Brehme, M.; Broly, Marti
Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut
Summary
To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice
with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and
estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut;
their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success.
1
Cohousing mice harboring these xenomicrobiota
or a mouse cecal microbiota, along with germ-free
bystanders, revealed the success of particular bacterial taxa in invading guts with established communities
and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-