EMBOSS: marscan


Program marscan

Function

Finds MAR/SAR sites in nucleic sequences

Description

Matrix/scaffold attachment regions (MARs/SARs) are genomic elements thought to delineate the structural and functional organisation of the eukaryotic genome. Originally, MARs and SARs were identified through their ability to bind to the nuclear matrix or scaffold. Binding cannot be assigned to a unique sequence element, but is dispersed over a region of several hundred base pairs. These elements are found flanking a gene or a small cluster of genes and are located often in the vicinity of cis-regulatory sequences. This has led to the suggestion that they contribute to higher order regulation of transcription by defining boundaries of independently controlled chromatin domains. There is indirect evidence to support this notion. In transgenic experiments MARs/SARs dampen position effects by shielding the transgene from the effects of the chromatin structure at the site of integration. Furthermore, they may act as boundary elements for enhancers, restricting their long range effect to only the promoters that are located in the same chromatin domain.

marscan finds a bipartite sequence element that is unique for a large group of eukaryotic MARs/SARs. This MAR/SAR recognition signature (MRS) comprises two individual sequence elements that are <200 bp apart and may be aligned on positioned nucleosomes in MARs. The MRS can be used to correctly predict the position of MARs/SARs in plants and animals, based on genomic DNA sequence information alone. Experimental evidence from the analysis of >300 kb of sequence data from several eukaryotic organisms show that wherever a MRS is observed in the DNA sequence, the corresponding genomic fragment is a biochemically identifiable SAR.

The MRS is a bipartite sequence element that consists of two individual sequences of 8 (AATAAYAA) and 16 bp (AWWRTAANNWWGNNNC) within a 200 bp distance from each other. One mismatch is allowed in the 16 bp pattern. The patterns can occur on either strand of the DNA with respect to each other. The 8 bp and the 16 bp sites can overlap.

Where there are many possible MRS sites caused by many 8 bp and/or 16 bp pattern sites located within 200 bp of each other, then only the 8 bp site and the 16 bp site that occur closest to each other are reported.

Once a MRS has been reported, no more sites will be looked for within 200 bp of that site. This reduces (but maybe will not totally eliminate) over-reporting of the clusters of MRS's that tend to occur within a MAR/SAR.

Not all SARs contain a MRS. Analysis of >300 kb of genomic sequence from a variety of eukaryotic organisms shows that the MRS faithfully predicts 80% of MARs and SARs, suggesting that at least one other type of MAR/SAR may exist which does not contain a MRS.

Usage

Here is a sample session with marscan:

% marscan
marscan
Finds MAR/SAR sites in nucleic sequences
Input sequence(s): EMBL:u01317
Output file [hsfau1.marscan]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outf]              featout    File for output of MAR/SAR recognition
                                  signature (MRS) regions. This contains
                                  details of the MRS in normal GFF format. The
                                  MRS consists of two recognition sites, one
                                  of 8 bp and one of 16 bp on either sense
                                  strand of the genomic DNA, within 200 bp of
                                  each other.

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
[-outf]
(Parameter 2)
File for output of MAR/SAR recognition signature (MRS) regions. This contains details of the MRS in normal GFF format. The MRS consists of two recognition sites, one of 8 bp and one of 16 bp on either sense strand of the genomic DNA, within 200 bp of each other. Writeable feature table unknown.gff
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Normal genomic DNA USA.

Output file format

It writes a standard GFF (Gene Feature Format) file.

The output from the above example is:


##gff-version 0.0
##date 2001-02-21
##sequence-region HSHBB 0 0
HSHBB   marscan misc_signal     2242    2458    1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=2451..2458. 16bp pattern = 2242..2257"
HSHBB   marscan misc_signal     17654   17730   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=17723..17730. 16bp pattern = 17654..17669"
HSHBB   marscan misc_signal     40956   41123   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=40956..40963. 16bp pattern = 41108..41123"
HSHBB   marscan misc_signal     42232   42248   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=42232..42239. 16bp pattern = 42233..42248"
HSHBB   marscan misc_signal     47834   47966   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=47959..47966. 16bp pattern = 47834..47849"
HSHBB   marscan misc_signal     65112   65146   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=65139..65146. 16bp pattern = 65112..65127"
HSHBB   marscan misc_signal     65947   65963   1.0     .       .       note "MAR/SAR recognition site (MRS). 8bp pattern=65947..65954. 16bp pattern = 65948..65963"

Data files

None.

Notes

None.

References

The method for finding the MAR/SAR sites is described in:

van Drunen CM., Sewalt RGAB., Oosterling RW., Weisbeek PJ., Smeekens SCM. and van Driel R. "A bipartite sequence element associated with matrix/scaffold attachment regions" Nucleic Acids Research. 1999. Vol 27, No. 14, pp. 2924-2930

The original paper on MASs/SARs is:

Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp. 223-232.

Warnings

It does not check that the DNA input seequnce is genomic or not.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
dregregular expression search of a nucleotide sequence
fuzznucNucleic acid pattern search
fuzztranProtein pattern search after translation
getorfFinds and extracts open reading frames (ORFs)
plotorfPlot potential open reading frames
showorfPretty output of DNA translations
wobbleWobble base plot

Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

History

Written (Jan 2001) - Gary Williams.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments