: Isolation and sequencing of
genomic DNA "bound" by a specific transcription factor,
covalently modified histone, or other nuclear
protein. This methodology provides genome-wide maps
of factor binding. Most of HOMER's routines cater to
the analysis of ChIP-Seq data.
Treatment of nuclei with a restriction enzyme such as
DNase I will result in cleavage of DNA at accessible
regions. Isolation of these regions and their
detection by sequencing allows the creation of DNase
hypersensitivity maps, providing information about which
regulatory elements are accessible in the genome.
Micrococcal Nuclease (MNase) is a restriction enzyme that
degrades genomic DNA not wrapped around histones.
The remaining DNA represents nucleosomal DNA, and can be
sequencing to reveal nucleosome positions along the
genome. This method can also be combined with ChIP
to map nucleosomes that contain specific histone
Extraction, fragmentation, and sequencing of RNA
populations within a sample. The replacement for
gene expression measurements by microarray. There
are many variants on this, such as Ribo-Seq (isolation of
ribosomes translating RNA), small RNA-Seq (to identify
of nascent RNA. Transcription is halted, nuclei are
isolated, labeled nucleotides are added back, and
transcription briefly restarted resulting in labeled RNA
molecules. These newly created, nascent RNAs are
isolated and sequenced to reveal "rates of transcription"
as opposed to the total number of stable transcripts
measured by normal RNA-seq.
: Genomic interaction assay for understanding
genome 3D structure. This assay is much more
specialized - For more information about how to use HOMER
to analyze Hi-C data, check out the Hi-C analysis section
Unsolicited advice: If you are going to perform RNA-Seq,
use a protocol for STRAND-SPECIFIC
RNA-Seq. Why would you throw away the strand
More Unsolicited advice: Run controls!!!
Yet More Unsolicited advice: Be careful about GC-bias!!