The question is not so much about distance, but rather if the (potential) regulation depends on a physical link between the ncRNA gene and the target genes. If the ncRNA spreads along the chromatin fibre (http://www.ncbi.nlm.nih.gov/pubmed/18988810) or uses intra-chromosomal looping towards the target promoter (http://www.ncbi.nlm.nih.gov/pubmed/23417068), it's considered 'in cis'. If the ncRNA difuses to its target locus, which may be on a different chromosome (as proposed in http://www.ncbi.nlm.nih.gov/pubmed/17604720), it can be considered 'in trans'.

In this paper, they used ChIP and qRT-PCR to answer a similar question

Article Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Medi...

In our paper we detect unique gene expression and the location of specific gene transcripts in vivo with PCR sensitivity and specificity...FASEB J 27:712-724. The questions are how many gene transcripts can one microRNA regulate?

The question is not so much about distance, but rather if the (potential) regulation depends on a physical link between the ncRNA gene and the target genes. If the ncRNA spreads along the chromatin fibre (http://www.ncbi.nlm.nih.gov/pubmed/18988810) or uses intra-chromosomal looping towards the target promoter (http://www.ncbi.nlm.nih.gov/pubmed/23417068), it's considered 'in cis'. If the ncRNA difuses to its target locus, which may be on a different chromosome (as proposed in http://www.ncbi.nlm.nih.gov/pubmed/17604720), it can be considered 'in trans'.

A short answer for the “cis-regualtion” is to check whether it is overlapped with other neighbor genes to form a natural antisense sense transcript. See “http://www.ncbi.nlm.nih.gov/pubmed/22378763"

There are several mechanisms for cis regulation by ncRNA. The budding yeast model has several examples. Mostly regulation in cis requires chromatin modifying complexes, especially methyltransferases and deacetylases. The RNA itself might either dislodge TFIID or bind to the p300 to inactivate it. These is a recent report in Nature from the Sheikhattar lab (Nature 2013 494:p497) about activating ncRNAs.

1. Kim T, Buratowski S: Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. Cell 2009, 137:259–272.

2. Kung JT, Colognori D, Lee JT: Long noncoding RNAs: past, present, and future. Genetics 2013, 193:651–669.

3. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F: Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 2007, 131:706–717.

4. Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F: Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 2009, 23:1534–1545.

5. Martens JA, Wu PY, Winston F: Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 2005, 19:2695–2704.

6. Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA: Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 2011, 25:29–40.

7. van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A: Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 2012, 150:1170–1181.

8. Hongay CF, Grisafi PL, Galitski T, Fink GR: Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006, 127:735–745.

9. Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR: Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 2009, 106:18321–18326.

10. Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M: A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol Cell 2008, 32:685–695.

Hope this helps!

i worked on Human enhancers and thier function as cis regulatory elements ..........i dnt knw the complete detail of your project ..may be i be helpfull to u

Usually not more than 250kb even if it can be a bigger distance

http://www.nature.com/nsmb/journal/v20/n3/full/nsmb.2496.html

A recent review came out in BMC Biology 2013, 11:59. Might be a good start for you. Here it is.

There is a paper . They developed a method termed as ChIRP,that chould detect the specific lncRNAs with bound protein and DNA sequences. It would be useful for you.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21963238

It sounds like your primary question is what these ncRNAs are doing in your experimental condition, and the hypothesis about cis-regulation is more of a logical starting point than an end-goal by itself. If you're interested, my lab has developed methods to predict function for ncRNA based upon transcriptional network analysis (initial paper PMID: 19447786). Given either names or chromosome coordinates of the ncRNAs in question, we could check if we have enough data to predict function.

I'm not sure whether this paper (published in Science) can give you some idea. http://www.sciencemag.org/content/340/6132/619.abstract