EMBOSS: marscan

| ## 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:HSHBB
    Output file [hshbb.marscan]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outfile]           report     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
[-outfile] (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. | Report file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Normal genomic DNA USA.

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default marscan writes a GFF (Gene Feature Format) report file.

The output from the above example is:

    ##gff-version 2.0
    ##date 2002-04-04
    ##Type DNA HSHBB
    HSHBB	marscan	misc_signal	2242	2458	0.000	+	.	Sequence "HSHBB.1" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 2451" ; note "*end8bp 2458" ; note "*start16bp 2242" ; note "*end16bp 2257"
    HSHBB	marscan	misc_signal	17654	17730	0.000	+	.	Sequence "HSHBB.2" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 17723" ; note "*end8bp 17730" ; note "*start16bp 17654" ; note "*end16bp 17669"
    HSHBB	marscan	misc_signal	40956	41123	0.000	+	.	Sequence "HSHBB.3" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 40956" ; note "*end8bp 40963" ; note "*start16bp 41108" ; note "*end16bp 41123"
    HSHBB	marscan	misc_signal	42232	42248	0.000	+	.	Sequence "HSHBB.4" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 42232" ; note "*end8bp 42239" ; note "*start16bp 42233" ; note "*end16bp 42248"
    HSHBB	marscan	misc_signal	47834	47966	0.000	+	.	Sequence "HSHBB.5" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 47959" ; note "*end8bp 47966" ; note "*start16bp 47834" ; note "*end16bp 47849"
    HSHBB	marscan	misc_signal	65112	65146	0.000	+	.	Sequence "HSHBB.6" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65139" ; note "*end8bp 65146" ; note "*start16bp 65112" ; note "*end16bp 65127"
    HSHBB	marscan	misc_signal	65947	65963	0.000	+	.	Sequence "HSHBB.7" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65947" ; note "*end8bp 65954" ; note "*start16bp 65948" ; note "*end16bp 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 name | Description
--- | ---
dreg | regular expression search of a nucleotide sequence
fuzznuc | Nucleic acid pattern search
fuzztran | Protein pattern search after translation
getorf | Finds and extracts open reading frames (ORFs)
plotorf | Plot potential open reading frames
showorf | Pretty output of DNA translations
wobble | Wobble base plot

## Author(s)

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

## History

Written (Jan 2001) - Gary Williams.

Changed output file to standard EMBOSS report format (April 2002) - Peter Rice

## Target users

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

## Comments