Chromatin Repair Research Articles

Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β.

Single-strand breaks (SSBs) are one of the most prevalent forms of DNA damage found in the chromatinized genome and are repaired by direct single-strand break repair (SSBR) or base excision repair (BER). DNA polymerase beta (Pol β) is the primary enzyme responsible for processing the 1-nt gap intermediate in chromatin during SSBR and BER. However, the mechanism used by Pol β to process a 1-nt gap in the context of the nucleosome and chromatin remains poorly understood. Here, we use biochemical assays and cryogenic electron microscopy (cryo-EM) to determine the kinetic and structural basis of gap-filling DNA synthesis in the nucleosome by Pol β. Kinetic analysis identified that gap-filling DNA synthesis in the nucleosome by Pol β is position-dependent, where solvent exposed 1-nt gaps are processed more efficiently than histone-occluded 1-nt gaps. A series of cryo-EM structures of Pol β bound to a solvent-exposed 1-nt gap in the nucleosome reveal a global DNA sculpting mechanism for 1-nt gap recognition, which is mediated by sequential engagement of the Pol β lyase domain and polymerase domain. Finally, cryo-EM structures of Pol β bound to 1-nt gaps at two additional positions in the nucleosomal DNA define the structural basis for position-dependent nucleotide insertion in the nucleosome. This work establishes the mechanism used by Pol β for processing 1-nt gaps in the nucleosome during SSBR and BER, providing fundamental insight into DNA repair in chromatin.

The role of different subunits of INO80 remodeling complex in repair chromatin assembly in yeast <i>Saccharomyces cerevisiae</i>

Reparative chromatin assembly is an important step in maintaining genome stability. The correct assembly of chromatin is provided by histone chaperones, whose dysfunction can lead to the development of various forms of cancer and a number of hereditary diseases in humans. The effect of remodeling factors completes chromatin repair. The yeast chromatin remodeling complex INO80 plays an important role in chromatin architecture. We used induced mutagenesis and real-time PCR to study the role of INO80 in chromatin repair assembly. In double mutants ies5Δ hsm3Δ(hif1Δ), defects in the structure of nucleosomes caused by mutations hsm3Δ and hif1Δ lead to hypersensitivity of cells to UV radiation and the disappearance of hsm3- and hif1-specific mutagenesis. Double mutants carrying the nhp10Δ mutation and hsm3Δ or hif1Δ mutations were indistinguishable from a single mutant in terms of the lethal effect of UV irradiation, however, the high UV-induced mutagenesis characteristic of all mutations disappeared. Thus, we found that mutations in the genes controlling the subunits of the INO80 complex can exhibit strong interactions with mutations in histone chaperone genes. We have confirmed the hypothesis that the Him1 protein performs a chaperone function in the process of reparative chromatin assembly.

The Role of Various Subunits of the INO80 Remodeling Complex in Chromatin Repair Assembly in Yeast Saccharomyces cerevisiae

The Role of Various Subunits of the INO80 Remodeling Complex in Chromatin Repair Assembly in Yeast Saccharomyces cerevisiae

Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications

At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One crucial part of this machinery is histone posttranslational modifications, which form a flexible system, driving transient changes in chromatin, and defining particular epigenetic states. Posttranslational modifications work in concert with replication-independent histone variants further adapted for transcriptional regulation and chromatin repair. However, little is known about how such complex regulatory pathways are orchestrated and interconnected in cells. In this work, we demonstrate the utility of mass spectrometry–based approaches to explore how different epigenetic layers interact in Arabidopsis mutants lacking certain histone chaperones. We show that defects in histone chaperone function (e.g., chromatin assembly factor-1 or nucleosome assembly protein 1 mutations) translate into an altered epigenetic landscape, which aids the plant in mitigating internal instability. We observe changes in both the levels and distribution of H2A.W.7, altogether with partial repurposing of H3.3 and changes in the key repressive (H3K27me1/2) or euchromatic marks (H3K36me1/2). These shifts in the epigenetic profile serve as a compensatory mechanism in response to impaired integration of the H3.1 histone in the fas1 mutants. Altogether, our findings suggest that maintaining genome stability involves a two-tiered approach. The first relies on flexible adjustments in histone marks, while the second level requires the assistance of chaperones for histone variant replacement.

DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants.

DNA repair pathways play a critical role in genome stability, but in eukaryotic cells, they must operate to repair DNA lesions in the compact and tangled environment of chromatin. Previous studies have shown that the packaging of DNA into nucleosomes, which form the basic building block of chromatin, has a profound impact on DNA repair. In this review, we discuss the principles and mechanisms governing DNA repair in chromatin. We focus on the role of histone post-translational modifications (PTMs) in repair, as well as the molecular mechanisms by which histone mutants affect cellular sensitivity to DNA damage agents and repair activity in chromatin. Importantly, these mechanisms are thought to significantly impact somatic mutation rates in human cancers and potentially contribute to carcinogenesis and other human diseases. For example, a number of the histone mutants studied primarily in yeast have been identified as candidate oncohistone mutations in different cancers. This review highlights these connections and discusses the potential importance of DNA repair in chromatin to human health.

The Role of the RPD3 Complex of Saccharomyces cerevisiae Yeast in the Activation of UV-Induced Expression of RNR Complex Genes

Reparative chromatin assembly is an important step in maintaining the stability of the genome. Proper chromatin assembly is provided by histone chaperones. Violation of the function of these proteins can lead to the development of various forms of cancer and to a number of hereditary diseases in humans. One of the key processes in the reparative assembly of chromatin is acetylation and deacetylation of histones, complexes NuB4 and RPD3. Results presented in this work demonstrate that inactivation of Rpd3 and Sin3 subunits of the RPD3 complex blocks super activation of RNR3 gene. The phenotypes of rpd3Δ and sin3Δ mutants differ due to different activation of Rad53 kinase in these mutants, which may be due to deacetylation of Rad53 by Rpd3 deacetylase. Our findings revealed that the contribution of deacetylation of Rad53 kinase makes a significant contribution to the regulation hyperactivation RNR complex after UV irradiation. In addition, this work provides indirect evidence that the Him1 protein may participate as a histone chaperone in chromatin repair assembly.

Generation of Recombinant Nucleosomes Containing Site-Specific DNA Damage.

Eukaryotic DNA exists in chromatin, where the genomic DNA is packaged into a fundamental repeating unit known as the nucleosome. In this chromatin environment, our genomic DNA is constantly under attack by exogenous and endogenous stressors that can lead to DNA damage. Importantly, this DNA damage must be repaired to prevent the accumulation of mutations and ensure normal cellular function. To date, most in-depth biochemical studies of DNA repair proteins have been performed in the context of free duplex DNA. However, chromatin can serve as a barrier that DNA repair enzymes must navigate in order find, access, and process DNA damage in the cell. To facilitate future studies of DNA repair in chromatin, we describe a protocol for generating nucleosome containing site-specific DNA damage that can be utilized for a variety of in vitro applications. This protocol describes several key steps including how to generate damaged DNA oligonucleotides, the expression and purification of recombinant histones, the refolding of histone complexes, and the reconstitution of nucleosomes containing site-specific DNA damage. These methods will enable researchers to generate nucleosomes containing site-specific DNA damage for extensive biochemical and structural studies of DNA repair in the nucleosome.

Abstract 12715: Role of Novel Long Non-Coding RNA BAZ1A-AS1 in Neointima Formation in Human Saphenous Vein Graft Disease

Introduction: Saphenous veins (SVs) are frequently used in CABG surgery, but over 50% of the SV grafts fail in the first 10 years after surgery due to neointima formation. Long non-coding RNAs (lncRNAs) have emerged as attractive therapeutic targets and biomarkers for cardiovascular disease. However, studies on their role and mechanisms in humans are limited. This study aimed to unravel epigenetic mechanisms of neointima formation in human SVs and investigate the role of candidate lncRNAs in key vascular cell functions pertinent to neointima formation. Methods and Results: By using an ex vivo model of human SV graft disease wherein segments of human SV are incubated in tissue culture, we performed RNA-sequencing on human SV with and without neointima formation to interrogate the global transcriptomic changes, and determined 699 differentially expressed novel lncRNAs during neointimal formation. We then identified BAZ1A-antisense (AS)1 as a novel lncRNA highly upregulated during neointima formation. BAZ1A-AS1 overlaps antisense to its cis- regulatory gene, BAZ1A , which was reported to play a role in oxidative stress and DNA damage repair response. We found that one isoform of BAZ1A-AS1 primarily localizes to the nucleus of VSMCs. Interestingly, UV exposure of vascular smooth muscle cells (VSMCs) isolated from human SV induced significant upregulation of BAZ1A and BAZ1A-AS1, suggesting that BAZ1A-AS1 could be associated with chromatin repair processes activated during neointima formation. To investigate whether BAZ1A-AS1 can regulate VSMC functions pertinent to neointima formation, VSMCs were transfected with BAZ1A-AS1 antisense gapmers. Knockdown of BAZ1A-AS1 showed reduced cell proliferation and migration, and increased cell death and DNA damage in VSMCs. Furthermore, role of BAZ1A during neointima formation in vivo is currently under investigation in a carotid artery ligation model using BAZ1A knockout mice. Conclusions: We identified BAZ1A-AS1 as a novel lncRNA associated with neointima formation in human SV, and targeted inhibition of BAZ1A-AS1 or its cis-regulator gene BAZ1A could be a promising strategy for SV graft disease.

Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles

At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.

Obstacles and opportunities for base excision repair in chromatin

Most eukaryotic DNA is packaged into chromatin, which is made up of tandemly repeating nucleosomes. This packaging of DNA poses a significant barrier to the various enzymes that must act on DNA, including DNA damage response enzymes that interact intimately with DNA to prevent mutations and cell death. To regulate access to certain DNA regions, chromatin remodeling, variant histone exchange, and histone post-translational modifications have been shown to assist several DNA repair pathways including nucleotide excision repair, single strand break repair, and double strand break repair. While these chromatin-level responses have been directly linked to various DNA repair pathways, how they modulate the base excision repair (BER) pathway remains elusive. This review highlights recent findings that demonstrate how BER is regulated by the packaging of DNA into nucleosome core particles (NCPs) and higher orders of chromatin structures. We also summarize the available data that indicate BER may be enabled by chromatin modifications and remodeling.

Analysis of SMARCA4 and SMARCA2 Loss in Lung Sarcomatoid Carcinomas.

Sarcomatoid carcinomas of the lung are a group of aggressive tumors. It has been reported that losses of SMARCA4 and SMARCA2, which play a role in the repair and remodeling of chromatin, contribute to the initiation, progression, and differentiation of neoplasms. The aim of our study was to examine SMARCA4 and SMARCA2 profiles in sarcomatoid carcinomas of the lung. We screened pleomorphic carcinomas (PCs), carcinosarcomas (CSs), and pulmonary blastomas (PBs). The loss of SMARCA4 and SMARCA2 expression in the tumors was evaluated using immunohistochemical methods. The tumors were also examined to determine immunophenotype, histological tumor diagnosis, surgical resection, tumor histological component, largest tumor diameter, and lymph node metastasis status. Sixty-nine cases were screened, of which 84% were PCs, 13% were CSs, and 2.8% were PBs. In PCs components, 84.4% were biphasic and 15.5% were monophasic. The PCs showed the most frequent loss of SMARCA4 (25.8%) and SMARCA2 (44.8%). A loss of SMARCA4 and SMARCA2, respectively, was detected in 14.2% and 24.4% in both components of biphasic PCs; 12.2% and 14.2% in the sarcoma component of biphasic PCs; 0% and 8.1% in the carcinoma component of biphasic PCs; 22.2% and 33.3% in monophasic PCs; 0% and 22.2% in both components of CSs; and 0% and 22.2% in the sarcoma component of CSs. These findings demonstrate a loss of expression of SMARCA4 and SMARCA2 in pulmonary sarcomatoid carcinomas. Loss of the SMARCA complex may be caused by the heterogeneous morphological profile of sarcomatoid carcinomas, independent of tumor histopathological parameters.

Epigenetic Enabled Normal Human Cells, Lead to <i>First Cell</i>’s Unique Division System, Driving Tumorigenesis Evolution

Normal cells must become cancer-enabling before anything else occurs, according to latest literature. The goal in this mini-review is to demonstrate special tetraploidy in the enabling process. This we have shown from genomic damage, DDR (DNA Damage Response) activity with skip of mitosis leading to diploid G2 cells at the G1 border in need of chromatin repair for continued cell cycling to the special tetraploid division system. In several studies specific methylation transferase genes were activated in normal human cells in tissue fields, containing different cell growth stages of the cancerous process. Histology studies, in addition to molecular chemistry for identification of oncogenic mutational change, were a welcome change (see below). In a study on melanoma origin, DDR also showed arrested diploid cells regaining cycling from methylation transferase activity with causation of 2n melanocytes transforming to 4n melanoblasts, giving rise to epigenetic tumorigenesis enabled First Cells. Such First Cells were from Barrett’s esophagus shown to have inherited the unique division system from 4n diplochromosomal cells, first described in mouse ascites cancer cells (below). We discovered that the large nucleus prior to chromosomal division turned 90° relative to the cytoskeleton axis, and divided genome reductive to diploid, First Cells, in a perpendicular orientation to the surrounding normal cells they had originated from. This unique division system was herein shown to occur at metastasis stage, implying activity throughout the cancerous evolution. Another study showed 4-chromatid tetraploidy in development to B-cell lymphoma, and that such cancer cells also proliferated with participation of this unusual division system. Such participation has long been known from Bloom’s inherited syndrome with repair chiasmas between the four chromatids, also an in vitro observation by us. Our cytogenetic approach also revealed that they believed mitotic division in cancer cells is wrong because such cell divisions were found to be from an adaptation between amitosis and mitosis, called amitotic-mitosis. Amitosis means division without centrosomes, which has long been known from oral cancer cells, in that MOTCs (microtubule organizing center) were lacking centrioles. This observation calls for re-introduction of karyotype and cell division studies in cancer cell proliferation. It has high probability of contributing novel approaches to cancer control from screening of drugs against the amitotic-mitotic division apparatus.

The Efficiency of Global Genome-Nucleotide Excision Repair is Linked to the Fraction of Open rRNA Gene Chromatin, in Yeast.

The yeast rDNA locus is a suitable model to study nucleotide excision repair (NER) in chromatin. A portion of rRNA genes is transcribed and largely depleted of nucleosomes, the remaining genes are not transcribed and folded in nucleosomes. In G1-arrested cells, most rRNA genes do not have nucleosomes. TC-NER removes UV-induced DNA lesions from the transcribed strand of active genes. GG-NER is less efficient and removes DNA lesions from the nontranscribed strand of active genes and from the inactive genome. Different from mammalian cells, in yeast, the rRNA gene-transcribed strand is repaired by RNA polymerase-I-dependent TC-NER. The opposite nontranscribed strand is repaired faster than both strands of inactive rRNA genes. In log-phase cells, RNA polymerase-I are dislodged from the damaged transcribed strand and partially replaced by nucleosomes. Contrary to log-phase cells, in G1-phase cells few, if any, histones are deposited on the open rRNA genes during NER. In this study, we compared GG-NER efficiency in the rRNA gene coding region: without nucleosomes, partially loaded or wholly loaded with nucleosomes. The results indicate that in log-phase cells histones obstruct GG-NER, whereas in G1-phase cells GG-NER is as efficient as TC-NER.

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin.

DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.

The role of FACT in managing chromatin:disruption, assembly, or repair?

FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.

Genome-wide methylation profiles in monozygotic twins with discordance for ovarian carcinoma.

Ovarian cancer is a disease that is generally diagnosed at an advanced stage, and has poor survival. Monozygotic (MZ) twins are considered to be good research models for investigating the epigenetic changes associated with diseases. In the present study, the involvement of epigenetic mechanisms in ovarian cancer etiology were evaluated using the MZ twin model. Whole-genome methylation patterns were investigated in a BRCA1 gene mutation-carrying family comprising MZ twins, only one of whom had ovarian cancer, and other healthy siblings. Whole-genome methylation patterns were assessed in peripheral blood DNA using Infinium MethylationEPIC BeadChips on an Illumina iScan device. The hypermethylated and hypomethylated genes were detected between cases and controls in four different comparison groups in order to evaluate the differences in methylation levels according to cancer diagnosis and BRCA mutation status. The obtained results showed that the differential methylations in 12 different genes, namely PR/SET domain 6, cytochrome B5 reductase 4, ZNF714, OR52M1, SEMA4D, CHD1L, CAPZB, clustered mitochondria homolog, RB-binding protein 7, chromatin repair factor, ankyrin repeat domain 23, RIB43A domain with coiled-coils 1 and C6orf227, were associated with ovarian cancer. Biological functional analysis of the genes detected in the study using the PANTHER classification system revealed that they have roles in biological processes including ‘biologic adhesion’, ‘regulation’, ‘cellular components organization’, ‘biogenesis’, ‘immune system functioning’, ‘metabolic functioning’ and ‘localization’. Overall, the present study suggested that epigenetic differences, such as methylation status, could be used as a non-invasive biological markers for the early diagnosis and follow-up of ovarian cancer.

Characteristic of the active substance of the Saccharomyces cerevisiae preparation having radioprotective properties

В работе охарактеризованы некоторые биологические особенности радиопротекторного действия препарата двуцепочечной РНК. Обнаружено, что препарат дрожжевой РНК обладает пролонгированным радиопротекторным действием при облучении животных летальной дозой в 9.4 Гр. При облучении через 1 ч и на 4-е сутки после введения 7 мг препарата РНК выживает 100 % животных на 70-е сутки наблюдения, при облучении на 8-е и 12-е сутки – 60 % животных. Были оценены временные параметры процесса репарации двуцепочечных разрывов, индуцированных γ-лучами. Выявлено, что введение препарата РНК в момент максимального количества двуцепо- чечных разрывов, через 1 ч после облучения, снижает эффективность радиопротекторного действия по сравнению с введением за 1 ч до облучения и через 4 ч после облучения. Проведено сравнение эффективности радиозащит- ного действия штатного радиопротектора Б-190 и препарата РНК в одном эксперименте. Установлено, что препарат суммарной РНК не уступает по эффективности препарату Б-190. Выживаемость на 40-е сутки после облучения для группы мышей, получавших препарат РНК, составила 78 %, для Б-190 – 67 % животных. В ходе аналитических иссле- дований препарата суммарной РНК дрожжей обнаружилось, что препарат представляет собой смесь одноцепочеч- ной и двуцепочечной РНК. Радиопротекторными свойствами обладает только двуцепочечная РНК. При введении 160 мкг препарата двуцепочечной РНК выживает 100 % подопытных животных после абсолютно летальной дозы гамма-радиации 9.4 Гр. Установлено, что радиозащитный эффект двуцепочечной РНК зависит не от последователь- ности, а от ее двуцепочечной формы, причем для осуществления радиопротекторного действия двуцепочечная РНК должна иметь «открытые» концы молекулы. Предполагается, что радиозащитное действие препарата двуцепочеч- ной РНК связано с участием молекул РНК в корректном восстановлении поврежденного облучением хроматина в стволовых клетках крови. Сохранившие жизнеспособность стволовые гемопоэтические клетки мигрируют на пери- ферию и достигают селезенки, где активно пролиферируют. Вновь образовавшаяся клеточная популяция восстанав- ливает кроветворную и иммунную системы, что определяет выживание летально облученных животных.

Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that removes RNA polymerase (RNAP)-stalling DNA damage from the transcribed strand (TS) of active genes. TC-NER deficiency in humans is associated with the severe neurological disorder Cockayne syndrome. Initiation of TC-NER is mediated by specific factors such as the human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of the chromatin organization, is unclear. Here, we used single-nucleotide resolution UV damage mapping data to show that Rad26 and its ATPase activity is critical for TC-NER downstream of the first (+1) nucleosome in gene coding regions. However, TC-NER on the transcription start site (TSS)-proximal half of the +1 nucleosome is largely independent of Rad26, likely due to high occupancy of the transcription initiation/repair factor TFIIH in this nucleosome. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER in Rad26-deficient cells. We show that deletion of SPT4 significantly restores TC-NER across the genome in a rad26∆ mutant, particularly in the downstream nucleosomes. These data demonstrate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5 in transcribed chromatin and Rad26 mainly functions downstream of the +1 nucleosome to remove TC-NER suppression by Spt4/Spt5.

Molecular structures and mechanisms of DNA break processing in mouse meiosis.

Exonucleolytic resection, critical to repair double-strand breaks (DSBs) by recombination, is not well understood, particularly in mammalian meiosis. Here, we define structures of resected DSBs in mouse spermatocytes genome-wide at nucleotide resolution. Resection tracts averaged 1100 nt, but with substantial fine-scale heterogeneity at individual hot spots. Surprisingly, EXO1 is not the major 5' → 3' exonuclease, but the DSB-responsive kinase ATM proved a key regulator of both initiation and extension of resection. In wild type, apparent intermolecular recombination intermediates clustered near to but offset from DSB positions, consistent with joint molecules with incompletely invaded 3' ends. Finally, we provide evidence for PRDM9-dependent chromatin remodeling leading to increased accessibility at recombination sites. Our findings give insight into the mechanisms of DSB processing and repair in meiotic chromatin.

Base Excision Repair in Chromatin and the Requirement for Chromatin Remodelling.

Base excision repair (BER) is a co-ordinated DNA repair pathway that recognises and repairs chemically modified bases and DNA single strand breaks. It is essential for the maintenance of genome integrity and thus in the prevention of the development of human diseases, including premature ageing, neurodegenerative diseases and cancer. Within the cell, DNA is usually packaged with histone proteins to form chromatin which imposes major constraints on the capacity of cells to perform BER. Therefore chromatin remodelling, stimulated through histone post-translational modifications (PTMs) or ATP-dependent chromatin remodelling complexes (ACRs), are required to stimulate access to the DNA damage and therefore enhance the BER process. Despite this, the molecular mechanisms through which this is co-ordinated and the specific enzymes that promote chromatin remodelling required for BER remain elusive. In this review, we summarise the multitude of in vitro studies utilising mononucleosome substrates containing site-specific DNA base damage that demonstrate the requirement for chromatin remodelling to facilitate BER, particularly in occluded regions. We also highlight preliminary evidence to date for the identity of ACRs, their mechanisms and the role of histone PTMs in modulating the cellular capacity for BER.