Chromatin Reprogramming Research Articles

Function of histone demethylasehistone lysine-specific demethylase 1A in tumor initiation and progression

As a member of the histone lysine-specific demethylase family, KDM1A plays a pivotal role in biological processes including signal transduction, chromatin reprogramming, embryo development, hematopoiesis, glucose and lipid metabolism. Recently, increasing studies and clinical evidences suggest that the expression of KDM1A is related to initiation and development of tumors and plays a key role in regulating of initiation and development of tumors, such as prostate cancer, breast cancer, lung cancer and liver cancer. KDM1A binds to distinct complexes and mediates different downstream signaling pathways. However, KDM1A often plays an oncogenic role in the initiation and development of tumors. Based on the current literatures, we describe the latest research of KDM1A in the initiation and progression of various tumors, and summarize its mechanism of actions, to provide clues for cancer therapy.

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF

SummarySpecialized regulatory T (Treg) cells accumulate and perform homeostatic and regenerative functions in nonlymphoid tissues. Whether common precursors for nonlymphoid-tissue Treg cells exist and how they differentiate remain elusive. Using transcription factor nuclear factor, interleukin 3 regulated (Nfil3) reporter mice and single-cell RNA-sequencing (scRNA-seq), we identified two precursor stages of interleukin 33 (IL-33) receptor ST2-expressing nonlymphoid tissue Treg cells, which resided in the spleen and lymph nodes. Global chromatin profiling of nonlymphoid tissue Treg cells and the two precursor stages revealed a stepwise acquisition of chromatin accessibility and reprogramming toward the nonlymphoid-tissue Treg cell phenotype. Mechanistically, we identified and validated the transcription factor Batf as the driver of the molecular tissue program in the precursors. Understanding this tissue development program will help to harness regenerative properties of tissue Treg cells for therapy.

P01 - Chromatin reprogramming as an adaptation mechanism in prostate cancer

P01 - Chromatin reprogramming as an adaptation mechanism in prostate cancer

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation.

Facultative heterochromatin forms and reorganizes in response to external stimuli. However, how the initial establishment of such a chromatin state is regulated in cell-cycle-arrested cells remains unexplored. Mouse gonocytes are arrested male germ cells, at which stage the genome-wide DNA methylome forms. Here, we discovered transiently accessible heterochromatin domains of several megabases in size in gonocytes and named them differentially accessible domains (DADs). Open DADs formed in gene desert and gene cluster regions, primarily at transposons, with the reprogramming of histone marks, suggesting DADs as facultative heterochromatin. De novo DNA methylation took place with two waves in gonocytes: the first region specific and the second genome-wide. DADs were resistant to the first wave and their opening preceded the second wave. In addition, the higher-order chromosome architecture was reorganized with less defined chromosome compartments in gonocytes. These findings suggest that multiple layers of chromatin reprogramming facilitate de novo DNA methylation.

MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation

Actin cytoskeleton is well-known for providing structural/mechanical support, but whether and how it regulates chromatin and cell fate reprogramming is far less clear. Here, we report that MKL1, the key transcriptional co-activator of many actin cytoskeletal genes, regulates genomic accessibility and cell fate reprogramming. The MKL1-actin pathway weakens during somatic cell reprogramming by pluripotency transcription factors. Cells that reprogram efficiently display low endogenous MKL1 and inhibition of actin polymerization promotes mature pluripotency activation. Sustained MKL1 expression at a level seen in typical fibroblasts yields excessive actin cytoskeleton, decreases nuclear volume and reduces global chromatin accessibility, stalling cells on their trajectory toward mature pluripotency. In addition, the MKL1-actin imposed block of pluripotency can be bypassed, at least partially, when the Sun2-containing linker of the nucleoskeleton and cytoskeleton (LINC) complex is inhibited. Thus, we unveil a previously unappreciated aspect of control on chromatin and cell fate reprogramming exerted by the MKL1-actin pathway.

Abstract OT1-01-03: The WinPro study: A window of opportunity study of endocrine therapy with and without prometrium in postmenopausal women with early stage hormone receptor-positive breast cancer

Abstract Background There is bidirectional interplay between PR and ER in human breast cancers (Lim et al, Endo Rel Can 2016). There is evidence for a reprogramming of ER chromatin binding sites with 470 genes differentially regulated by dual treatment with estrogen plus progestogen compared to estrogen alone in breast cancer cell lines (Mohammed et al, Nature 2015). Functionally, there was an additive anti-cancer effect with the addition of natural progesterone to endocrine therapy in preclinical breast cancer models. Trial Design This is a phase II multi-site, randomised, open-label, three-arm, study in 200 postmenopausal women with early-stage ER+, PR+, HER2-negative breast cancer. Eligible patients will be randomised 1:1:1 to receive 14 days of intervention with either letrozole 2.5mg PO daily (arm 1), letrozole 2.5mg + prometrium 300mg PO daily (arm 2) or tamoxifen 20mg + prometrium 300mg PO daily (arm 3), between diagnosis of breast cancer and definite surgery. Australian Clinical Trials Registry: ACTRN1261800092813 Eligibility Criteria Inclusion Criteria a) Histologically confirmed ER+ and PR+ breast cancers (≥10% positive staining cells) b) HER2/CEP17 ratio of <2 and mean HER2 copy number <6 (ASCO CAP 2013 guidelines) c) Tumour size ≥1cm on ultrasound and/or mammogram d) Aged ≥18 years Exclusion Criteria a) Currently on hormone therapies (HRT and OCP) b) Locally advanced/inoperable and inflammatory breast cancer c) Clinical evidence of metastatic disease d) Received other preoperative systemic therapies e) Nut allergy (prometrium contains peanut oil) f) Prior history of uterine cancer, deep vein thrombosis, pulmonary embolism or clotting disorder g) Women who are pregnant/breast feeding Specific Aims a) Primary Endpoint The geometric mean suppression of the centrally assessed proliferation marker Ki67, after two weeks of intervention, compared with baseline. This will be obtained by comparing the mean difference in Ki67 staining between pre and post-treated samples in each intervention arm. b) Secondary Endpoint Safety and tolerability of combination therapy (NCI-CTCAE v4.0) c) Translational Endpoints 1. Define a gene set as a predictive biomarker for a reduction in Ki67 2. Evaluate changes in the apoptotic markers Bcl-2 and Caspase 3 in the tumors following intervention 3. Evaluate changes in ER, PR, AR, FoxA1, Cyclin D1 protein and mRNA expression in the tumors following intervention Statistical Methods The IMPACT study reported a geometric mean reduction in Ki67 after 2 weeks of preoperative tamoxifen of 59.5% and anastrazole of 76% (Dowsett et al, JNCI 2007). This allows estimation of power to detect differences between Arm 1 and either Arm 2 or Arm 3 with a p-value of 0.025. For the third possible comparison of Arm 2 vs Arm 3, there is no prior evidence, therefore this as a purely exploratory comparison. With a total trial recruitment of 200 and allowing 4% dropouts, this would give 80% power to detect an improvement in Ki67 suppression from 76% in the letrozole alone control arm to 92% in either experimental arm. Accrual Present: 5 (1 site open) Target: 200 (8 sites total) Contact Information Elgene Lim, MBBS, FRACP, PhD. e.lim@garvan.com.au Citation Format: Carson E, Segara D, Parker A, O'Toole S, Coates A, Mann B, Lindeman G, Tilley W, Lim E. The WinPro study: A window of opportunity study of endocrine therapy with and without prometrium in postmenopausal women with early stage hormone receptor-positive breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT1-01-03.

Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer.

Tumor evolution is based on the ability to constantly mutate and activate different pathways under the selective pressure of targeted therapies. Epigenetic alterations including those of the chromatin structure are associated with tumor initiation, progression and drug resistance. Many cancers, including prostate cancer, present enlarged nuclei, and chromatin appears altered and irregular. These phenotypic changes are likely to result from epigenetic dysregulation. High-throughput sequencing applied to bulk samples and now to single cells has made it possible to study these processes in unprecedented detail. It is therefore timely to review the impact of chromatin relaxation and increased DNA accessibility on prostate cancer growth and drug resistance, and their effects on gene expression. In particular, we focus on the contribution of chromatin-associated proteins such as the bromodomain-containing proteins to chromatin relaxation. We discuss the consequence of this for androgen receptor transcriptional activity and briefly summarize wider gain-of-function effects on other oncogenic transcription factors and implications for more effective prostate cancer treatment.

Generation of directly reprogrammed human endothelial cells derived from fibroblast using ultrasound

Physical microenvironment plays an important role in determining cellular reprogramming. In this study, we first generated directly reprogrammed human dermal fibroblasts (HDFs) into endothelial cells (ECs) mediated by environmental transition-guided cellular reprogramming (e/Entr) using ultrasound and characterized e/Entr. Ultrasound stimulus was introduced to ECs culture media and HDFs and induced into ECs-like cells. We performed microarray, RT-PCR, protein analysis, matrigel plug assay and e/Entr were transplanted into ischemic hindlimb mice model. Here we show that the activation of MAPK signaling pathways and the modulation of histone proteins such as Hp1-α, H3K27me3 and H3K4me3 in e/Entr contribute to the changes in chromatin configuration and reprogramming. Microarray data demonstrated that e/Entr highly expressed genes associated with ECs transcription factors and angiogenesis. In addition, the transplantation of e/Entr into hindlimb ischemia showed a high recovery of blood perfusion, limb salvage and e/Entr contributed to the formation of new vessels. In conclusion, the present study provided the first evidence that ultrasound reprogramming can induce postnatal cells to functional ECs. Therefore, our data suggest that physical stimulus-mediated reprogramming is a highly effective and safe strategy for the novel therapeutic alternatives.

P-08 - Chromatin reprogramming as adaptation mechanism in advanced prostate cancer

P-08 - Chromatin reprogramming as adaptation mechanism in advanced prostate cancer

Genomic insights into chromatin reprogramming to totipotency in embryos.

The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.

Rad9a is involved in chromatin decondensation and post-zygotic embryo development in mice.

Zygotic chromatin undergoes extensive reprogramming immediately after fertilization. It is generally accepted that maternal factors control this process. However, little is known about the underlying mechanisms. Here we report that maternal RAD9A, a key protein in DNA damage response pathway, is involved in post-zygotic embryo development, via a mouse model with conditional depletion of Rad9a alleles in oocytes of primordial follicles. Post-zygotic losses originate from delayed zygotic chromatin decondensation after depletion of maternal RAD9A. Pronucleus formation and DNA replication of most mutant zygotes are therefore deferred, which subsequently trigger the G2/M checkpoint and arrest development of most mutant zygotes. Delayed zygotic chromatin decondensation could also lead to increased reabsorption of post-implantation mutant embryos. In addition, our data indicate that delayed zygotic chromatin decondensation may be attributed to deferred epigenetic modification of histone in paternal chromatin after fertilization, as fertilization and resumption of secondary meiosis in mutant oocytes were both normal. More interestingly, most mutant oocytes could not support development beyond one-cell stage after parthenogenetic activation. Therefore, RAD9A may also play an important role in maternal chromatin reprogramming. In summary, our data reveal an important role of RAD9A in zygotic chromatin reprogramming and female fertility.

3187 - The Role of E Protein Heterodimer Partner Switching in Determining Chromatin Landscape and T Cell Fate Commitment in Mouse Early T Cell Development

For hematopoietic precursors establishing their T cell identity in mouse thymus, a key question is how the precise coordination of key transcription factors activates the T lineage program and shuts off the precursor program. To identify the key regulatory changes in a non-biased way, we profiled the global chromatin accessibility changes during the T lineage commitment process using ATAC-seq. Many regulatory elements that became accessible during commitment were highly enriched for E protein heterodimer E2A-HEB binding motifs. Using E protein inhibitor ID2 to block the E2A-HEB activity in a committed pro-T cell line, we observed that E2A-HEB is indispensable to maintain the chromatin accessibility of T cell specific elements and to activate their associated T cell genes. Paradoxically, E2A-HEB expression levels are nearly constant throughout the developmental process, and ID2 level is nearly absent. We therefore have tried to identify the mechanism that must be counteracting E2A-HEB activity before commitment, specifically testing the precursor-specific form of E2A heterodimer, E2A-Lyl1, and its cofactor Lmo2. Forced expression of Lmo2 and Lyl1 in primary early committed T cells induces closing of commitment specific sites and loss of T lineage commitment, evident by the downregulation of T cell gene expression, including Bcl11b, Rag1 and Cd3e. More strikingly, it shows dramatic backward chromatin and transcriptome reprogramming to a precursor-like state, with the reopening of precursor-specific sites and the reactivation of many precursor genes including PU.1, Bcl11a, c-Kit. These results indicate that in precursors, E2A-Lyl1-Lmo2 can not only establish the precursor specific chromatin landscape and activate precursor genes, but can also strongly compete against existing HEB proteins and suppress E2A-HEB activity on initiating T lineage program. Our work suggests that the E2A heterodimer partner switching during early T cell development is crucial in determining T lineage progression through regulating the chromatin landscape both before and after commitment. Our work also suggests new strategies of hematopoietic reprogramming.

Real-time observation of nucleoplasmin-mediated DNA decondensation and condensation reveals its specific functions as a chaperone

Fertilization requires decondensation of promatine-condensed sperm chromatin, a dynamic process serving as an attractive system for the study of chromatin reprogramming. Nucleoplasmin is a key factor in regulating nucleosome assembly as a chaperone during fertilization process. However, knowledge on nucleoplasmin in chromatin formation remains elusive. Herein, magnetic tweezers (MT) and a chromatin assembly system were used to study the nucleoplasmin-mediated DNA decondensation/condensation at the single-molecular level in vitro. We found that protamine induces DNA condensation in a stepwise manner. Once DNA was condensed, nucleoplasmin, polyglutamic acid, and RNA could remove protamine from the DNA at different rates. The affinity binding of the different polyanions with protamine suggests chaperone-mediated chromatin decondensation activity occurs through protein–protein interactions. After decondensation, both RNA and polyglutamic acid prevented the transfer of histones onto the naked DNA. In contrast, nucleoplasmin is able to assist the histone transfer process, even though it carries the same negative charge as RNA and polyglutamic acid. These observations imply that the chaperone effects of nucleoplasmin during the decondensation/condensation process may be driven by specific spatial configuration of its acidic pentamer structure, rather than by electrostatic interaction. Our findings offer a novel molecular understanding of nucleoplasmin in sperm chromatin decondensation and subsequent developmental chromatin reprogramming at individual molecular level.

Abstract 1478: Gene-selective recruitment of NuRD drives chromatin reprogramming in cancer cells

Abstract ATP-dependent chromatin remodelers are frequently mutated in cancers. However, the molecular basis of the association between mutations in specific remodeler subunits and particular types of cancer is poorly understood. To understand how remodelers are targeted in a cell-type specific manner, we aim to explore the mechanisms of the Nucleosome Remodeling and Deacetylase (NURD) complex during cancer progression. We recently showed that DOC1-dependent recruitment of NuRD reveals antagonism with SWI/SNF during epithelial-mesenchymal transition in oral cancer cells (Mohd-Sarip et al., 2017). It is instructive to compare the function of DOC1 in oral squamous cell carcinomas (OSCCs) with that of the SWI/SNF subunit SMARCB1/hSNF5 in malignant rhabdoid tumors (MRTs). MRTs are an extremely aggressive pediatric cancer caused by the loss of SMARCB1 (Kia et al., 2008). Although the loss of DOC1 in OSCCs or that of SMARCB1 in MRTs generates opposite epigenetic states of their target genes, in both cases, this is caused by failed remodeler recruitment. The loss of a single subunit, such as DOC1 or SMARCB1, does not abrogate all other remodeler functions. We suggest that subunit-dependent gene selection is a major cause of the association between the loss of specific remodeler subunits and particular types of cancer. Our results emphasize that gene control involves a dynamic equilibrium between opposing chromatin modulating enzymes rather than a static chromatin state. Disturbances in this balance can initiate a cascade of chromatin reprogramming events that drives oncogenesis. Such an intertwined system of epigenetic regulation suggests therapeutic strategies aimed at restoring the balance between antagonistic activities. Prompted by these findings, we will present an inclusive view of the protein regulatory network in order to gain a wholesome understanding of the molecular transactions and dynamic composition of NuRD complexes in specific cancer types. These were identified by immunopurifications using in-house antibodies followed by mass spectrometry. Our proteomic studies of the NuRD complex in flies (Reddy et al., 2010) and HeLa nuclear extracts suggest that mammalian NuRD share the same subunits with flies. Upon closer inspection, we found unanticipated novel interacting partners of NuRD and that they are altered in specific cancers namely prostate, pancreatic and ovarian. This will be followed by confirmation of the interactomes using cell-based and biochemistry assays in combination with genome-wide approaches, as well as potentially leading to the characterization of novel targets of NuRD. These findings will represent the types of multiprotein NuRD-like complexes that can form during cancer progression and how they are targeted to chromatin. Citation Format: Adone Mohd-Sarip, Diana Zatreanu, Jeroen A. Demmers, C Peter Verrijzer. Gene-selective recruitment of NuRD drives chromatin reprogramming in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1478.

Can Reprogramming of Overall Epigenetic Memory and Specific Parental Genomic Imprinting Memory within Donor Cell-Inherited Nuclear Genome be a Major Hindrance for the Somatic Cell Cloning of Mammals? – A Review

Abstract Successful cloning of animals by somatic cell nuclear transfer (SCNT) requires epigenetic transcriptional reprogramming of the differentiated state of the donor cell nucleus to a totipotent embryonic ground state. It means that the donor nuclei must cease its own program of gene expression and restore a particular program of the embryonic genome expression regulation that is necessary for normal development. Transcriptional activity of somatic cell-derived nuclear genome during embryo pre- and postimplantation development as well as foetogenesis is correlated with the frequencies for spatial remodeling of chromatin architecture and reprogramming of cellular epigenetic memory. This former and this latter process include such covalent modifications as demethylation/re-methylation of DNA cytosine residues and acetylation/deacetylation as well as demethylation/re-methylation of lysine residues of nucleosomal core-derived histones H3 and H4. The main cause of low SCNT efficiency in mammals turns out to be an incomplete reprogramming of transcriptional activity for donor cell-descended genes. It has been ascertained that somatic cell nuclei should undergo the wide DNA cytosine residue demethylation changes throughout the early development of cloned embryos to reset their own overall epigenetic and parental genomic imprinting memories that have been established by re-methylation of the nuclear donor cell-inherited genome during specific pathways of somatic and germ cell lineage differentiation. A more extensive understanding of the molecular mechanisms and recognition of determinants for epigenetic transcriptional reprogrammability of somatic cell nuclear genome will be helpful to solve the problems resulting from unsatisfactory SCNT effectiveness and open new possibilities for common application of this technology in transgenic research focused on human biomedicine.

12 DOC1-dependent recruitment of NURD reveals antagonism with SWI/SNF during epithelial-mesenchymal transition in oral cancer cells

IntroductionThe molecular basis of the association between mutations in specific remodeler subunits and particular types of cancer is poorly understood. To understand how remodelers are targeted in a cell-type specific manner, we aim to explore the mechanisms of the Nucleosome Remodelling and Deacetylase (NURD) complex during cancer progression. Loss of the NURD subunit Deleted in Oral Cancer 1 (DOC1) is associated with human oral squamous cell carcinomas (OSCCs). Here, we show that restoration of DOC1 expression in OSCCs leads to a reversal of Epithelial-mesenchymal transition (EMT).Material and methodsWe examined DOC1 expression in normal and cancerous tongue tissue with immunohistochemistry. Besides, 4 different human OSCC cell lines were examined using immunofluorescence and immunoblotting. To study its role in these cells, we re-expressed DOC1 and utilised shRNA-mediated knockdowns (remodelers, EMT regulators). Subsequently we carried out proteomics, genomics, cell-based and biochemistry assays.Results and discussionsThe loss of DOC1 in oral cancer cells leads to a failure of NURD to bind and repress master transcriptional regulators of EMT. Re-expression of DOC1 in OSCC cells restores NURD recruitment to key target genes, a switch from open to closed chromatin, transcriptional repression, and reversal of EMT (MET). We speculate that, during the development of oral cancer, DOC1 is lost after the inactivation of p53 and INK4a. Our genome-wide binding site analysis showed that DOC1 is crucial for NURD recruitment to a subset of target loci; in particular, promoter regions harbouring CpG islands. DOC1-mediated NURD binding to the Twist1/2 and Zeb2 promoters leads to eviction of SWI/SNF involving nucleosome repositioning, epigenetic reprogramming, and shutdown of transcription. Binding of either SWI/SNF or NURD determines opposite epigenetic states, thereby committing OSCC cells to either EMT or MET.ConclusionRe-expression of DOC1 in OSCC cells restores the switch from open- to closed chromatin and reversal of EMT. We suggest that subunit-dependent gene selection is a major cause of the association between the loss of specific remodeler subunits and particular types of cancer. Our results emphasise that gene control involves a dynamic equilibrium between opposing chromatin modulating enzymes rather than a static chromatin state. Disturbances in this balance can initiate a cascade of chromatin reprogramming events that drives oncogenesis.

Dual Requirement of CHD8 for Chromatin Landscape Establishment and Histone Methyltransferase Recruitment to Promote CNS Myelination and Repair

Disruptive mutations in chromatin remodeler CHD8 cause autism spectrum disorders, exhibiting widespread white matter abnormalities; however, the underlying mechanisms remain elusive. We show that cell-type specific Chd8 deletion in oligodendrocyte progenitors, but not in neurons, results in myelination defects, revealing a cell-intrinsic dependence on CHD8 for oligodendrocyte lineage development, myelination and post-injury remyelination. CHD8 activates expression of BRG1-associated SWI/SNF complexes that in turn activate CHD7, thus initiating a successive chromatin remodeling cascade that orchestrates oligodendrocyte lineage progression. Genomic occupancy analyses reveal that CHD8 establishes an accessible chromatin landscape, and recruits MLL/KMT2 histone methyltransferase complexes distinctively around proximal promoters to promote oligodendrocyte differentiation. Inhibition of histone demethylase activity partially rescues myelination defects of CHD8-deficient mutants. Our data indicate that CHD8 exhibits a dual function through inducing a cascade of chromatin reprogramming and recruiting H3K4 histone methyltransferases to establish oligodendrocyte identity, suggesting potential strategies of therapeutic intervention for CHD8-associated white matter defects.

Identification and expression analysis of long noncoding RNAs in embryogenesis and larval metamorphosis of Ciona savignyi

Long noncoding RNAs (lncRNAs) play important roles in diverse developmental and pathological processes through chromatin reprogramming, cis regulation and posttranscriptional modification. They have been extensively studied in both vertebrates and invertebrates. However, the information of lncRNAs in urochordate is still lacking. In this study, we used the RNA-Seq data from three developmental stages (18, 21 and 42 hours post fertilization, hpf) of embryos and larvae in Ciona savignyi to identify candidate lncRNAs and analyze their expression profiles. A total of 29,944 unigenes were predicted as lncRNAs, five of which had hits with lncRNAs in NONCODE database. The acquired lncRNAs had an average length of 466 nt. The peaks of length, GC content and minimum free energy of the lncRNAs were significantly lower than that of the message RNAs (mRNAs). The average expression levels of lncRNAs were also lower than those of mRNAs. Among the three developmental stages, highly expressed lncRNAs concentrated in 18 hpf embryos. While, for those lncRNAs specifically up-regulated in 21 hpf embryos, their co-expressed mRNAs were enriched in GO terms of membrane, indicating these lncRNAs are involved in the regulation of luminal membrane biogenesis, and extracellular matrix secretion through membrane localized proteins during Ciona notochord tubulogenesis. The lncRNAs in 42 hpf larvae were distinct from those in 18 and 21 hpf embryos. This result is associated with the fact that swimming larvae are transiting into metamorphic juveniles at this stage, indicating lncRNAs are involved in the regulation of larval metamorphosis. Overall, our study identified a large number of lncRNAs in C. savignyi and revealed their expression characteristics and dynamics during Ciona embryogenesis and larval metamorphosis. The results will help to further understand the function of lncRNAs in chordate development and the evolution of lncRNAs.

Reprogramming of Chromatin Accessibility in Somatic Cell Nuclear Transfer Is DNA Replication Independent

SUMMARYMammalian oocytes have the ability to reset the transcriptional program of differentiated somatic cells into that of totipotent embryos through somatic cell nuclear transfer (SCNT). However, the mechanisms underlying SCNT-mediated reprogramming are largely unknown. To understand the mechanisms governing chromatin reprogramming during SCNT, we profiled DNase I hypersensitive sites (DHSs) in donor cumulus cells and one-cell stage SCNT embryos. To our surprise, the chromatin accessibility landscape of the donor cells is drastically changed to recapitulate that of the in vitro fertilization (IVF)-derived zygotes within 12 hr. Interestingly, this DHS reprogramming takes place even in the presence of a DNA replication inhibitor, suggesting that SCNT-mediated DHS reprogramming is independent of DNA replication. Thus, this study not only reveals the rapid and drastic nature of the changes in chromatin accessibility through SCNT but also establishes a DNA replication-independent model for studying cellular reprogramming.

Chromatin reprogramming in breast cancer.

Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. In this review, we describe what is currently known about the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. Emphasis has been placed on characterizing the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin in breast cancer cells. In addition, we discuss current techniques employed to study enhancer function at a genome-wide level. Further, we have noted recent advances in live cell imaging technology. These single-cell approaches enable the coupling of population-based assays with real-time studies to address many unsolved questions about SRs and chromatin dynamics in breast cancer.