Loops Of Lampbrush Chromosomes Research Articles

The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.

Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying mechanisms of global transcriptome up-regulation. Here, we obtained a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs. For a number of protein-coding genes, we visualized their nascent transcripts on the lateral loops of lampbrush chromosomes by RNA-FISH. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes and is characterized by a broad expression pattern. We also present the first high-throughput transcriptome characterization of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and long terminal repeat (LTR) containing retrotransposable elements. Transcription of tandem repeat arrays was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs is initiated at adjacent LTR elements. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is required for synthesizing large amounts of transferred to the embryo maternal RNA for thousands of genes.

Association of modified cytosines and the methylated DNA-binding protein MeCP2 with distinctive structural domains of lampbrush chromatin

The lampbrush chromosomes (LBCs) of the amphibian oocyte are the largest known chromosomes and offer the unique opportunity to visualize the distinctive closed and open chromatin structural domains with an unprecedented spatial resolution. In this study we investigated the association of DNA methylation and proteins interpreting methylation state, such as MeCP2, with LBCs. We expressed HA-tagged MeCP2 in Xenopus laevis oocytes, and we observed that while it predominantly targeted the transcriptionally inactive chromomeres, a minor fraction of HA-MeCP2 also associated with many of the transcriptionally active lateral loops of LBCs. We further demonstrated that the association of MeCP2 with LBCs is directly determined by its 5-methylcytosine-binding domain. We then defined the distribution of 5-methylcytosines (5mC) by immunostaining Xenopus and axolotl LBCs and confirmed the pattern suggested by the expression of HA-MeCP2 targeting of intense staining of the chromomeres and of many loop bases. In addition, we found that short interstitial regions of the active transcriptional units could be clearly stained for 5mC. Interestingly, these 5mC-positive regions corresponded precisely to segments of active transcription units from which RNA polymerase II and nascent transcripts were simultaneously absent. Together, these data support a model presenting MeCP2 as both a transcriptional repressor and activator.

Modifications of lampbrush chromosome structure of the European domestic goose <i>Anser anser</i>

Abstract. Lampbrush chromosomes (LBCs) represent a new model in avian cytogenetics and are increasingly more often used in poultry chromosome analyses. Additionally, lampbrush chromosomes are considered as model structures in the study of transcription regulation. Changes in transcription activity are reflected as modifications of LBC morphological structure and associated with physiological processes in the organism. The aim of the present study was to compare transcriptional activity of the first five lampbrush macrochromosomes and ZW sex lampbrush bivalents sampled from the oocytes of geese prior to and after the reproductive period. The respective bivalents sampled before and after reproduction have similar sizes but differ in morphological structure. Side loops of lampbrush chromosomes are sites of transcription activity. The activity varies according to the loop size. As the loops become more prominent, the activity grows and vice versa. Lampbrush chromosomes sampled after reproduction have smaller side loops. On the other hand, inactive chromomeres become prominent in the chromosomes. Marker loops are the last structures to be degraded after the end of reproduction. Consequently, they are used for identifying particular bivalents at different stages of cellular transcriptional activity.

Morphological manifestation of unique DNA segments in human meiotic prophase I

The commercial sample of human DNA fragment from the choromosome 17 was used as the probe for FISH to study of the mode of its attachment to the lateral elements of synaptonemal complex (SC) in human spermatocytes. It was a 160 kb probe from the band 17p1.2, containing RAI1 gene with D17S620 marker (the probe for deletion causing Smith-Magenis syndrome). The probe made lateral chromatin protrusions, contacting with SC stained with anty-SYCP3. Different morphological configuration of lateral chromatin protrusions where observed. They depended on substages of meiotic prophase I. At zygotene, FISH probe form two sticks, c. a. 6 micro long, which was perpendicular to SC longitudinal axe, one stick at each SC side. At early pachytene, each stick transforms into a globule, one globule at each SC side again. At late pachytene each globule transformed into two crumbly globules containing short threads and clumps. At diplotene, globules finally transformed into thin DNA (chromatin) loops up to 10 micro long from the base to top with periodical thickenings (beads) along their length. As the result of this dynamics of transformation, two chromatin loops with beads were found on each side of SC of the chromosome 17. These loops most probably were the loops of sister chromatides, the full set of chromatide loops at the particular SC (bivalent) site being four in number, i. e. representing of two pair of chromatides. This study is the first one in which lateral chromatin loops in human mail meiotic prophase I are visualized as true open loop instead of that usually postulated "loops" after observation of condensed road-like or brush-like chromatin protrusion attached to the lateral elements of synaptonemal complexes. Open configuration of the loops, presumably, depends on activation of transcription during late pachytene-early diplotene. They resemble lateral loops of mini lampbrush chromosomes.

Chicken lampbrush chromosomes: Transcription of tandemly repetitive DNA sequences

The transcribed part of the genome includes both protein-coding sequences and a variety of sequences with unknown functions. Amphibian and avian lampbrush chromosomes represent a convenient experimental system for studying cell functions and the regulation of transcription of protein-noncoding DNA. Taking lumpy loops formed on chicken (Gallusgallus domesticus) chromosome 2 at the lampbrush stage as an example, we applied an approach allowing RNA sources to be identified in the lateral loops of lampbrush chromosomes. This approach involves a bioinformatic analysis of data from the chicken genome sequencing project and a high-resolution mapping of transcripts on microsurgically isolated bivalents. As a result, a novel tandemly repetitive DNA sequence, LL2R (lumpy loop 2 repeat), of approximately 440 bp in size was identified in the chicken genome, its transcripts taking part in the formation of lumpy loops with a massive RNP matrix on chromosome 2 in growing oocytes.

TBP2 is a substitute for TBP in Xenopus oocyte transcription

BackgroundTATA-box-binding protein 2 (TBP2/TRF3) is a vertebrate-specific paralog of TBP that shares with TBP a highly conserved carboxy-terminal domain and the ability to bind the TATA box. TBP2 is highly expressed in oocytes whereas TBP is more abundant in embryos.ResultsWe find that TBP2 is proteolytically degraded upon meiotic maturation; after germinal vesicle breakdown relatively low levels of TBP2 expression persist. Furthermore, TBP2 localizes to the transcriptionally active loops of lampbrush chromosomes and is recruited to a number of injected promoters in oocyte nuclei. Using an altered binding specificity mutant reporter system we show that TBP2 promotes RNA polymerase II transcription in vivo. Intriguingly, TBP, which in oocytes is undetectable at the protein level, can functionally replace TBP2 when ectopically expressed in oocytes, showing that switching of initiation factors can be driven by changes in their expression. Proteolytic degradation of TBP2 is not required for repression of transcription during meiotic maturation, suggesting a redundant role in this repression or a role in initiation factor switching between oocytes and embryos.ConclusionThe expression and transcriptional activity of TBP2 in oocytes show that TBP2 is the predominant initiation factor in oocytes, which is substituted by TBP on a subset of promoters in embryos as a result of proteolytic degradation of TBP2 during meiotic maturation.

The chromosome field

The distribution of seven different chromosomal properties is described. Non-disjunction of B chromosomes in seven species of Gramineae shows a very regular location which depends on the position of the kinetochore and the telomeres. This property is one of the best examples of the interactions extending along the length of the chromosome, demonstrating how the chromosome field determines the location and expression of a specific genetic property. In rye, the distance between the kinetochore and the locus of non-disjunction comprises about 78 times 106 nucleotide pairs. This means that the effect of the centromere extends along the chromosomal DNA for at least this distance. Chiasmata in Fritillaria meleagris show an optimal distribution which also appears at a constant distance from the kinetochore. The kinetochore—chiasmata distance is about 2.5 μm. irrespective of arm-length. The “fluffy” loops of lampbrush chromosomes of Ambystoma also have a similar distribution as well as the Giemsa banding patterns described in the Triturus species. The distribution of four other chromosome properties, including chromosome breaks in humans, is described and its relation to the interactions established within the chromosome field is discussed.

Studies on the loops of amphibian lampbrush chromosomes during the phase of retraction

Flannery, A.V. and Hill, R.S. 1987. Studies on the loops of amphibian chromosomes during the phase of retraction. —Herediras 106: 209–218. Lund, Sweden. ISSN 0018–0661. Received August 8, 1986 The process of loop retraction in lampbrush chromosomes of Triturus cristastus carnifex, during oocyte maturation, has been investigated by studying the morphology of the loops isolated under different monovalent cation conditions, using a combination of light and electron microscopy. When lampbrush chromosomes bearing retracted loops were prepared in buffer containing reduced levels of monovalent cations (0.7 mM), the mean axial loop length was increased by at least 2.5 times over the mean length of loops prepared under ionic conditions which stabilize normal lampbrush structure (i.e., 70 mM cations). This cation-dependent change in loop structure indicates that the retracted appearance of the loops in maturing oocytes involves the folding of the loop axis. RNA transcription appears to continue during retraction since ribonucleo-protein transcripts are clearly present on the loop axes at all ionic concentrations used and in Miller spreading studies. In Miller spreading preparations, however, the density of transcripts is clearly less in transcription units from retracted loops. Direct evidence concerning the structure of the loop axis at cation concentrations of 0.7 mM and above has not been obtained because the axis remains obscured by RNP transcript under these conditions. However, a model is proposed which accounts for the folding of the loop axis and its simultaneous transcription by RNA polymerases.

RNA helicase p54 (DDX6) is a shuttling protein involved in nuclear assembly of stored mRNP particles.

Previously, we showed that an integral component of stored mRNP particles in Xenopus oocytes, Xp54, is a DEAD-box RNA helicase with ATP-dependent RNA-unwinding activity. Xp54 belongs to small family of helicases (DDX6) that associate with mRNA molecules encoding proteins required for progress through meiosis. Here we describe the nucleocytoplasmic translocation of recombinant Xp54 in microinjected oocytes and in transfected culture cells. We demonstrate that Xp54 is present in oocyte nuclei, its occurrence in both soluble and particle-bound forms and its ability to shuttle between nucleus and cytoplasm. Translocation of Xp54 from the nucleus to the cytoplasm appears to be dependent on the presence of a leucine-rich nuclear export signal (NES) and is blocked by leptomycin B, a specific inhibitor of the CRM1 receptor pathway. However, the C-terminal region of Xp54 can act to retain the protein in the cytoplasm of full-grown oocytes and culture cells. Cytoplasmic retention of Xp54 is overcome by activation of transcription. That Xp54 interacts directly with nascent transcripts is shown by immunostaining of the RNP matrix of lampbrush chromosome loops and co-immunoprecipitation with de novo-synthesized RNA. However, we are unable to show that nuclear export of this RNA is affected by either treatment with leptomycin B or mutation of the NES. We propose that newly synthesized Xp54 is regulated in its nucleocytoplasmic distribution: in transcriptionally quiescent oocytes it is largely restricted to the cytoplasm and, if imported into the nucleus, it is rapidly exported again by the CRM1 pathway. In transcriptionally active oocytes, it binds to a major set of nascent transcripts, accompanies mRNA sequences to the cytoplasm by an alternative export pathway and remains associated with masked mRNA until the time of translation activation at meiotic maturation and early embryonic cell division.

Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function.

The lampbrush chromosomes and assorted nuclear bodies of amphibian and avian oocytes provide uniquely advantageous and amenable experimental material for cell biologists to study the structure and function of the eukaryotic nucleus, and in particular to address the processes of nuclear gene expression. Recent findings discussed here include the molecular analysis of the actively elongating RNA polymerase complexes associated with lampbrush chromosome loops and of the association between loop nascent transcripts and RNA processing components. In addition, several types of chromosome structure that do not outwardly resemble simple extended loops and that may house novel nuclear functions have recently been studied in detail. Among these a type of chromosomal body that can also exist free in the oocyte nucleus, the Cajal body, has been shown to possess a range of characteristics that suggest it is involved in the assembly of macromolecular complexes required for gene expression. Homologous structures have also been described in somatic nuclei. Fundamental aspects of the looped organization exhibited by lampbrush as well as other chromosomes have also been addressed, most notably by the application of a technique for de-novo chromosome assembly.

The I protein of the heterogeneous nuclear ribonucleoprotein complex is a novel dog nuclear autoantigen.

In eukaryotic cells, heterogeneous nuclear RNA is associated with a set of abundant nuclear proteins to form complex ribonucleoprotein structures (hnRNP). Autoantibodies to hnRNP G protein have been previously reported in German shepherd dogs with lupus-like syndrome. In the present study, we describe the characterization of a novel antigen recognized by a serum from a schnauzer dog with a non-erosive polyarthritis. The autoantibodies give, by indirect immunofluorescence, a nuclear pattern with staining close to one of the nucleoli. Immunoblotting and immunoprecipitation data reveal that the autoantigens are in fact two closely related basic proteins (average pI 8.7) with apparent molecular weights of 56 kDa (p56) and 59 kDa (p59). The results of immunoprecipitation with anti-hnRNP antibodies and DNA affinity column chromatography strongly suggest that these autoantigens correspond to hnRNP I proteins. This point was confirmed by cloning and sequencing a cDNA clone encoding the complete sequence of the antigens. In addition, we found that anti-hnRNP I antibodies preferentially stain certain loops of the Pleurodeles waltl lampbruch chromosomes. These data, added to previous ones on anti-p43/hnRNP G protein in German shepherd dogs with lupus-like syndrome, confirm the interest of this category of antibodies to hnRNP proteins in autoimmune disorders.

Strukturdifferenzierungen in Y-chromosom von Drosophila hydei: the unique morphology of the Y chromosomal lampbrush loops Threads results from 'coaxial shells' formed by different satellite-specific subregions within megabase-sized transcripts.

The results of pulsed-field gel electrophoresis (PFGE) analysis and two-colour transcript fluorescence in situ hybridization (FISH) for the three Threads-specific DNA satellites YLII, YLI and rally are in support of long-range clustering of these sequence families within the subterminal region on the long arm of the Y chromosome of Drosophila hydei. On the basis of the linear arrangement of at least four extended clusters of satellite-specific sequences, the loop morphology of wild-type and several mutant Threads can be explained by assumption of a single Threads-specific transcription unit comprising about 5.1 Mb of repetitive DNA located between the Pseudonucleolus and the Nucleolus organizer. Transcription is unidirectional from the Pseudonucleolus towards the terminally located Nucleolus organizer. Transcripts most likely start in front of or within the 3.2 Mb region of YLII-related sequences, pass through subsequent blocks of 1.2 and 0.3 Mb of YLI- and rally-related sequences, respectively, and cease within the region of a smaller block of YLI-related repeats. The megabase-sized transcripts remain physically linked to the DNA axis and their extended satellite-specific regions form coaxial clouds or shells around the central DNA axis. In this way each cluster of earlier-transcribed sequences generates a cloud or shell on top of the later-transcribed ones. According to this model of 'satellite-specific coaxial shells' the tube-like morphology and other peculiarities of the Y chromosomal lampbrush loops Threads can be explained as a result of satellite-specific RNA superstructures and/or formation of extended ribonucleoprotein (RNP) complexes between clusters of satellite-specific transcripts and specific proteins. On the basis of this model the specific morphology of several Threads mutants can be interpreted as the result of large interstitial or terminal deletions that alter the total length of the Threads-specific transcription unit without exerting other major effects on principal features of the transcription process along the Threads.

Localization of a high molecular weight form of DNA topoisomerase I in amphibian oocytes.

Xenopus oocytes express a 165 kDa variant of DNA topoisomerase I (topo I) as opposed to the canonical 110 kDa form of somatic cells (Richard and Bogenhagen, Dev. Biol. 146: 4-11, 1991). By immunofluorescence microscopy using variant-specific antibodies we show that this high molecular weight form is associated with lampbrush chromosome loops and the inner regions of the amplified nucleoli. Inhibition of topo I-activity by either Camptothecin-treatment or microinjection of neutralizing antibodies resulted in loop retraction and the condensation of chromosomes and amplified nucleoli. These data indicate that the oocyte-specific 165 kDa form of topo I is involved in transcriptional processes mediated by RNA polymerase I and II and is therefore functionally equivalent to the somatic cell 110 kDa counterpart.

A zinc-binding domain is required for targeting the maternal nuclear protein PwA33 to lampbrush chromosome loops.

In oocytes of the newt Pleurodeles waltl, the maternal nuclear protein PwA33 occurs on the lampbrush chromosomes and in some nucleoplasmic particles of the germinal vesicle. PwA33 is a modular protein and we used site-directed mutagenesis to alter the sequences encoding two metal-binding regions, the C3HC4 (or RING finger) and B-box motifs. Several mutant clones were generated and their synthetic transcripts were injected into Pleurodeles oocytes for in vivo analysis. In the oocyte, all translation products localized in the germinal vesicle. Proteins encoded by RING finger mutant clones were distributed in a pattern identical to that of the wild type protein, but when His266 of the B-box was mutated, PwA33 failed to localize in the lampbrush chromosomes and the nucleoplasmic particles. Using an in vitro colorimetric assay, we demonstrated that PwA33 is a zinc-binding protein and that mutations in the RING finger and B-Box altered its metal-binding properties. The RING finger motif bound two Zn2+ ions and the binding ratios of several mutants were consistent with the tertiary structure recently proposed for this motif. The B-box coordinated one Zn2+ and this binding was inhibited by the His266 mutation. The failure of the His266 mutation to bind zinc and to localize properly within the germinal vesicle suggests that an intact B-box is required for normal functioning of the PwA33 protein in the oocyte.

Localization of antigens PwA33 and La on lampbrush chromosomes and on nucleoplasmic structures in the oocyte of the urodele Pleurodeles waltl: Light and electron microscopic immunocytochemical studies

Monoclonal antibodies A33/22 and La11G7 have been used to study the distribution of the corresponding antigens, PwA33 and La, on the lampbrush chromosome loops and nucleoplasmic structures of P. waltl oocytes, using immunofluorescence, confocal laser scanning microscopy and immunogold labeling. The results obtained with these antibodies have been compared with those obtained with the Sm-antigen-specific monoclonal antibody Y12. All these monoclonal antibodies (mAbs) labeled the matrices of the majority of normal loops along their whole length. Nucleoplasmic RNP granules showed a strong staining with the mAbs La11G7 and Y12 throughout their mass, but with the mAb A33/22, they showed only a weak peripheral labeling in the form of patches on their surface. This patchy labeling was confirmed by confocal laser scanning microscopy. Electron microscopy revealed that this patchy labeling might be due to a hitherto undescribed type of submicroscopic granular structure, around 100 nm in either dimension, formed by 10-nm particles. Such granules were observed either attached to the RNP granules or free in the nucleoplasm, but rarely in relation with the normal loop matrices. These 100-nm granules may have a role in the movement of proteins and snRNPs inside the oocyte nuclei for storage, recycling, and/or degradation. Our results also suggest that all the microscopically visible free RNP granules of the nucleoplasm of P. waltl oocytes correspond to B snurposomes. The granules forming the B (globular) loops showed a labeling pattern similar to that of B snurposomes; their possible relationship is discussed.

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Constitutive expression of a somatic heat-inducible hsp70 gene during amphibian oogenesis

We isolated and characterized a sequence coding for heat-shock protein 70 (HSP70) of the amphibian Pleurodeles waltl. Results from S1 nuclease protection assays led us to conclude that an hsp70 gene, strictly inducible in somatic cells during heat shock, is constitutively active during oogenesis. By quantitative northern and western blot analysis, we showed that both hsp70 mRNA and HSP70-related protein levels increased in oocytes from stage II to stage VI under physiological conditions. Furthermore, by in situ hybridization to the nascent transcripts of lampbrush chromosome loops, we provided evidence for a clear-cut relationship between this increase in hsp70 mRNA and transcriptional activity during the lampbrush stage of oogenesis. These results strongly suggest that hsp70 genes are actively transcribed throughout oogenesis. HSP70-related proteins localized in the cytoplasm of young oocytes are progressively transferred to the nucleus in the course of oogenesis and preferentially accumulated in the nuclei of some stage VI oocytes.

Snurposomes and Coiled Bodies

In the GV of amphibian oocytes, the splicing snRNPs (U1, U2, U4, U5, and U6) occur on most of the lampbrush chromosome loops in association with the nascent transcripts. They also occur in thousands of small extrachromosomal bodies (1-4 microns in diameter) designated B snurposomes. U7 snRNA, which is involved in processing the 3' end of histone pre-mRNAs, occurs in a few dozen extrachromosomal bodies (1-20 microns in diameter) called C snurposomes. C snurposomes often have B snurposomes attached to their surface and B-like inclusions; these compound structures are known as spheres or sphere organelles. One or two sphere organelles are attached to the lampbrush chromosomes at the histone gene loci. Two snRNAs (or snoRNAs) known to be involved in pre-rRNA processing (U3 and U8) occur in the 1000 or so extrachromosomal nucleoli of the GV. We looked for a snurposome that might contain U3 and U8 but not rDNA or rRNA. We were unable to find such a snurposome, but we did identify a hitherto unrecognized population of minute nucleoli in the size range of B snurposomes. Prenucleolar bodies in telophase/early interphase nuclei meet the definition of a pre-rRNA snurposome in that they contain U3 snoRNA and fibrillarin (and probably other processing components) but lack rDNA and do not synthesize rRNA. The structures previously identified as prenucleolar bodies in pronuclei formed in vitro in Xenopus egg extracts share many components with coiled bodies from HeLa nuclei.(ABSTRACT TRUNCATED AT 250 WORDS)

Assembly and localization of the U1-specific snRNP C protein in the amphibian oocyte.

To study the intranuclear localization of the U1-specific snRNP C protein and its assembly into U1 snRNPs, we injected transcripts encoding a myc-tagged C protein into amphibian oocytes. The distribution of protein translated from the injected RNA was essentially the same in continuous and pulse-label experiments. In both cases the C protein localized within the germinal vesicle in those structures known to contain U1 snRNPs, namely the lampbrush chromosome loops and hundreds of extrachromosomal granules called snurposomes. Oocytes were also injected with an antisense oligodeoxynucleotide that caused truncation of U1 snRNA at the 5' end. In these oocytes, myc-tagged C protein localized normally in the germinal vesicle and could be immunoprecipitated together with truncated U1 snRNA. These experiments suggest that the C protein can enter the germinal vesicle on its own and there associate with previously assembled U1 snRNPs. In transfected tissue culture cells, the myc-tagged C protein localized within the nucleus in a speckled pattern similar to that of endogenous U1 snRNPs.

Transcription on lampbrush chromosome loops in the absence of U2 snRNA.

The five small nuclear RNAs (snRNAs) involved in splicing occur on the loops of amphibian lampbrush chromosomes and in hundreds to thousands of extrachromosomal granules called B snurposomes. To assess the role of these snRNAs during transcription and to explore possible relationships between the loops and B snurposomes, we injected single-stranded antisense oligodeoxynucleotides (oligos) against U1 and U2 snRNA into toad and newt oocytes. As shown before, antisense U1 and U2 oligos caused truncation of U1 and complete destruction of U2 snRNAs, respectively. However, injection of any oligo, regardless of sequence, brought on dramatic cytological changes, including shortening of the chromosomes and retraction of the lateral loops, with concomitant shutdown of polymerase II transcription, as well as disappearance of some or all of the B snurposomes. When injected oocytes were incubated for 12 h or longer in physiological saline, these changes were reversible; that is, the chromosomes lengthened, transcription (detected by 3H-UTP incorporation) resumed on newly extended lateral loops, and B snurposomes reappeared. In situ hybridization showed that loops and B snurposomes had negligible amounts of U2 snRNA after recovery from injection of the anti-U2 oligo, whereas these structures had normal levels of U2 snRNA after recovery from a control oligo. Thus, the morphological integrity of B snurposomes and lampbrush chromosome loops is not dependent on the presence of U2 snRNA. Because transcription occurs in the absence of U2 snRNA, we conclude that splicing is not required for transcription on lampbrush chromosome loops.