The “CTCF code” hypothesis posits that CTCF pleiotropic functions are driven by recognition of diverse sequences through combinatorial use of its 11 zinc fingers (ZFs). This model, however, is ...supported by in vitro binding studies of a limited number of sequences. To study CTCF multivalency in vivo, we define ZF binding requirements at ∼50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. ZFs 4–7 anchor CTCF to ∼80% of targets containing the core motif. Nonconserved flanking sequences are recognized by ZFs 1–2 and ZFs 8–11 clusters, which also stabilize CTCF broadly. Alternatively, ZFs 9–11 associate with a second phylogenetically conserved upstream motif at ∼15% of its sites. Individually, ZFs increase overall binding and chromatin residence time. Unexpectedly, we also uncovered a conserved downstream DNA motif that destabilizes CTCF occupancy. Thus, CTCF associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.
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•Genome-wide maps of 11 CTCF zinc finger mutants in B lymphocytes•Zinc finger mutations differentially affect CTCF binding and nuclear mobility•CTCF uses zinc finger clusters to recognize DNA sequence diversity•DNA sequences flanking the core motif modulate CTCF binding
CTCF is a nuclear architectural protein that binds to thousands of highly diverse sequences in eukaryotes. The current hypothesis, known as the “CTCF code,” proposes that CTCF binds DNA targets through combinatorial use of its 11 zinc fingers (ZFs). This model, however, is mostly supported by in vitro binding studies. By expressing ZF mutants in B lymphocytes, Resch, Casellas, and colleagues now present genome-wide maps of CTCF multivalency. They show that CTCF reads sequence diversity by relying on well-defined ZF clusters.
While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron ...microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator’s structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
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•A genetic, functional, and structural analysis of mammalian Mediator is provided•Contacts between a conserved core and the tail impact mMED-Pol II interaction•Loss of non-essential mMED subunits affects promoters linked to multiple enhancers•Cohesin is required to tether regulatory DNA; mMED and Pol II are not
A structurally-conserved Mediator promotes and controls interactions between enhancers and promoters but is not itself necessary to tether these elements.
In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by ...topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements.
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•Chromosome loop anchors bound by CTCF and Cohesin are vulnerable to DNA breaks•Breaks are transcription independent, mediated by TOP2B and correlate with cohesin•Translocation breakpoint regions in various cancers are enriched at loop anchors•Chromosome folding and topological stress relief go hand in hand
Chromatin assembly into higher-order structures generates torsional stress that makes chromosome loop anchor regions more vulnerable to topoisomerase 2-mediated DNA breaks.
The RAG endonuclease initiates Igh locus V(D)J recombination in progenitor (pro)-B cells
. Upon binding a recombination centre-based J
, RAG scans upstream chromatin via loop extrusion, potentially ...mediated by cohesin, to locate Ds and assemble a DJ
-based recombination centre
. CTCF looping factor-bound elements (CBEs) within IGCR1 upstream of Ds impede RAG scanning
; however, their inactivation allows scanning to proximal V
s, where additional CBEs activate rearrangement and impede scanning any further upstream
. Distal V
utilization is thought to involve diffusional access to the recombination centre following large-scale Igh locus contraction
. Here we test the potential of linear RAG scanning to mediate distal V
usage in G1-arrested v-Abl pro-B cell lines
, which undergo robust D-to-J
but little V
-to-DJ
rearrangements, presumably owing to lack of locus contraction
. Through an auxin-inducible approach
, we degraded the cohesin component RAD21
or CTCF
in these G1-arrested lines. Degradation of RAD21 eliminated all V(D)J recombination and interactions associated with RAG scanning, except for reecombination centre-located DQ52-to-J
joining, in which synapsis occurs by diffusion
. Remarkably, while degradation of CTCF suppressed most CBE-based chromatin interactions, it promoted robust recombination centre interactions with, and robust V
-to-DJ
joining of, distal V
s, with patterns similar to those of 'locus-contracted' primary pro-B cells. Thus, downmodulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG scanning across the 2.7-Mb Igh locus.
A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. ...As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.
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•ChIA-PET is used to characterize the regulome of primary mouse cells•Broadly expressed genes change their enhancer landscape during development•The dynamics of CpG methylation mirrors changes in the enhancer landscape•Most transcription factors bind to cell-specific and constitutively active enhancers
Promoters of genes expressed in a wide range of tissues associate with a changing enhancer landscape as cells progress in development. The turning on and off of enhancers correlates with the extent of promoter activity and is mirrored by CpG methylation levels.
The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two ...loci—almost always bound by CTCF and cohesin—lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.
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•We track the 4D Nucleome during cohesin loss and recovery, with 10 kb/20 min resolution•After cohesin loss, loop domains disappear; effects on transcription are modest•During cohesin recovery, loop domains form in minutes, consistent with fast extrusion•Superenhancers form loops, interchromosomal links, and higher-order hubs
Mapping the nucleome in 4D during cohesin loss and recovery reveals that cohesin degradation eliminates loop domains but has only modest transcriptional consequences.
Activation-induced cytidine deaminase (AID) converts cytosine into uracil to initiate somatic hypermutation (SHM) and class switch recombination (CSR) of antibody genes. In addition, this enzyme ...produces DNA lesions at off-target sites that lead to mutations and chromosome translocations. However, AID is mostly cytoplasmic, and how and exactly when it accesses nuclear DNA remains enigmatic. Here, we show that AID is transiently in spatial contact with genomic DNA from the time the nuclear membrane breaks down in prometaphase until early G1, when it is actively exported into the cytoplasm. Consistent with this observation, the immunoglobulin (Igh) gene deamination as measured by uracil accumulation occurs primarily in early G1 after chromosomes decondense. Altering the timing of cell cycle-regulated AID nuclear residence increases DNA damage at off-target sites. Thus, the cell cycle-controlled breakdown and reassembly of the nuclear membrane and the restoration of transcription after mitosis constitute an essential time window for AID-induced deamination, and provide a novel DNA damage mechanism restricted to early G1.
Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via ...transcription-dependent cytidine deamination of single-stranded DNA targets. Though largely specific for immunoglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. How AID is recruited to off-targets has been a long-standing mystery. Based on deep GRO-seq studies of mouse and human B lineage cells activated for CSR or SHM, we report that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge. Moreover, we found that such AID-targeting “convergent” transcription arises from antisense transcription that emanates from super-enhancers within sense transcribed gene bodies. Our findings provide an explanation for AID off-targeting to a small subset of mostly lineage-specific genes in activated B cells.
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•AID off-target activity is associated with sense/antisense convergent transcription•AID off-targeting occurs within intragenic SEs in mouse and human B lineage cells•Strongly convergently transcribed intragenic SEs are predominant AID off-targets•Ectopically expressed AID in fibroblasts targets convergently transcribed SEs
Activation-induced cytidine deaminase (AID) off-target activities are frequently promoted by “convergent” sense/antisense transcription that emanates from super-enhancers within transcribed gene bodies, suggesting that super-enhancers may target oncogenes for translocations in cancer.
To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that ...integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and ...prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.
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•Single-stranded DNA (ssDNA) is a common feature of mammalian genome•The pattern of ssDNA reactivity reveals different non-B DNA structures•Non-B DNA formation drives chromatin reorganization•Non-B DNA formation is coupled to specific transcriptome output
Potassium permanganate footprinting combined with high-throughput sequencing revealed abundant formation of “melted bubbles,” Z-DNA, quadruplex, and other non-B DNA structures in mouse and human cells. Non-B DNA formation is dramatically coupled with chromatin reorganization and particular transcription programs, indicating high regulatory potential of non-B DNA structures across a mammalian genome.
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