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  Fri May 31 11:41:50 2019 -0700
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 <H2>Overview</H2>
 
 <div class="figure" style="  float: right;  width: 30%; min-width: 450px; border: 
   thin silver solid ; margin: 0.5em; padding: 0.5em">
   <p><img src="../images/laminB1Super.gif" alt="Nuclear Lamina and Chromosomal Organization"  >
   <p style="text-align: center;">
 Model of chromosome organization in interphase, summarizing the main results
 presented in this paper. Large, discrete chromosomal domains are dynamically
 associated (double arrows) with the nuclear lamina, and demarcated by putative
 insulator elements that include CTCF binding sites, promoters that are oriented
 away from the lamina, and CpG islands (Fig. S1, Guelen <EM>et al.</EM>, 2008).
 </div>
 
 <P>
 The architecture of human chromosomes in interphase nuclei is
 still largely unknown. Microscopy studies have indicated that specific
 regions of chromosomes are located in close proximity to the
 nuclear lamina (NL, a dense fibrillar network associated with the inner face 
 of the nuclear envelope). 
 This has led to the idea that certain genomic elements may be attached to the 
 NL, which may contribute to
 the spatial organization of chromosomes inside the nucleus.
 This track represents a high-resolution map of genome-NL interactions in human 
 Tig3 lung fibroblasts, 
 as determined by the DamID technique. 
 </P>
 
 <h3> NKI LaminB1 track </h3>
 <P>
 The LaminB1 track shows a high resolution
 map of the interaction sites of the entire genome with
 Lamin B1, (a key NL component) in human fibroblasts.
 This map shows that genome-lamina interactions occur through more than 1,300 
 sharply defined large domains 0.1-10 megabases in size. 
 Microscopy evidence indicates that most of these domains are preferentially 
 located at nuclear periphery. 
 These lamina associated domains (LADs) are characterized by low gene-expression
 levels,
 indicating that LADs represent a repressive chromatin environment. 
 The borders of LADs are demarcated by the insulator
 protein CTCF, by promoters that are oriented away from
 LADs, or by CpG islands, suggesting possible mechanisms of
 LAD confinement. 
 Taken together, these results demonstrate that
 the human genome is divided into large, discrete domains that are
 units of chromosome organization within the nucleus (see Guelen <EM>et al.</EM>, 
 2008).
 </P>
 
 <h3> NKI LADs track </h3>
 <P> The LADs track shows Lamina Associated Domains, or LADs, based on a 
 genome-wide DamID profile of LaminB1 (above). 
 For the definition of LADs, the full-genome lamin B1 DamID data set was
 binarized by setting tiling array probes with positive DamID log ratios to 1 and
 otherwise to 21. Next, a two-step algorithm was used to identify LADs. First,
 sharp transitions were identified with a sliding edge filter, which calculates the
 difference in average binary values in two windows of 99 neighbouring probes
 immediately left and right of a queried probe. The cutoff for this difference was
 chosen such that the number of edges detected in randomly permuted data sets
 was less than 5% of the number of edges detected in the original lamin B1 data
 set. Second, pairs of adjacent 'left' and 'right' edges were identified that together
 enclosed a region of arbitrary size with at least 70% of the enclosed probes
 reporting a positive log2 ratio. A total of 1,344 regions fulfilled these criteria
 and were termed LADs. In 20 randomly permuted data sets, fewer than 13
 domains were identified by the same criteria. Note that there are also
 lamin-B1-positive domains flanked by one or two gradual or irregular transitions.
 Because it is difficult to define the borders of such domains precisely, these 
 'fuzzy' domains are not analyzed here. 
 (see Guelen <EM>et al.</EM>, 2008).
 </P>
 
 <H2>Display Conventions and Configuration</H2>
 
 <P> The LaminB1 wiggle track values range from -6.602 to 5.678 and were 
 normalized so have a median of 0 and standard deviation of 1.037.  The 
 default vertical viewing range for the wiggle track was chosen from -2 
 to 2 because  this is roughly +/- 2 standard deviations.
 </P>
 
 <P> For an example region see genomic location: 
 <a href="/cgi-bin/hgTracks?db=hg18&amp;position=chr4%3A35000001-45000000&amp;laminB1Super=show&laminB1Lads=full&laminB1=full">chr4:35,000,001-45,000,000</a> (Fig 1, Guelen <EM>et al.</EM>, 2008).
 </P>
 
 
 <H2>Methods</H2> 
 
 <P> The DamID technique was applied to generate a high-resolution map of NL 
 interactions for the entire human genome. 
 DamID is based on targeted adenine methylation of DNA sequences that interact 
 in vivo with a protein of interest. 
 </P>
 
 <P> DamID was performed with lentiviral transduction as described
 (Guelen <EM>et al.</EM>, 2008). In short, a fusion protein consisting
 of Escherichia coli DNA adenine methyltransferase (Dam) fused to human
 LaminB1 was introduced into cultured Tig3 human lung fibroblasts. 
 Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. 
 Here, the LaminB1-Dam fusion protein incorporates
 in the nuclear lamina, as verified by immunofluorescence
 staining. Hence, the sequences near the nuclear lamina are marked with
 a unique methylation tag. The adenine methylation pattern was detected with 
 genomic tiling arrays. 
 Unfused Dam was used as a
 reference (http://research.nki.nl/vansteensellab/DamID.htm). The data
 shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.
 </P>
 
 <P> Sample labelling and hybridizations were performed by NimbleGen
 Inc., on a set of 8 custom-designed oligonucleotide arrays, with a median
 probe spacing of ~750 bp. All probes recognize unique (non-repetitive) sequences. 
 The raw data was log2 transformed and loess
 normalized. Between array median/scale normalization was based on 6979
 probes common to all arrays. Replicate arrays were averaged and the
 full data set normalized to genome-wide median.
 </P>
 
 <H2>Verification</H2>
 
 <P> The data are based on two independent biological replicates. 
 Fluorescence in situ hybridization microscopy confirmed 
 that most of the LaminB1 associated regions are preferentially located at 
 the nuclear periphery. 
 The array platform, the <A HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8854"
 TARGET = _BLANK>raw 
 and normalized data</A> have been deposited at the NCBI Gene Expression Omnibus 
 (GEO) (https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE8854.
 </P>
 
 <H2>Credits</H2>
 
 <P> The data for this track were generated by Lars Guelen, Ludo Pagie,
-and Bas van Steensel at the <a href="http://research.nki.nl/vansteensellab/"
+and Bas van Steensel at the <a href="https://chromatingenomics.org/"
 target="_blank">Van Steensel Lab</a>, Netherlands Cancer Institute.
 </P>
 
 <H2>References</H2>
 <p>
 Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de
 Laat W <em>et al</em>.
 <a href="https://www.nature.com/articles/nature06947" target="_blank">
 Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions</a>.
 <em>Nature</em>. 2008 Jun 12;453(7197):948-51.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18463634" target="_blank">18463634</a>
 </p>